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 // TODO: test if importing a features file onto an alignment which already
368 // has features with links overwrites the original links.
370 Hashtable featureLinks = new Hashtable();
371 boolean featuresFile = false;
374 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
375 .getAlignment(), alignPanel.seqPanel.seqCanvas
376 .getFeatureRenderer().getFeatureColours(), featureLinks,
377 true, viewport.applet.getDefaultParameter("relaxedidmatch",
379 } catch (Exception ex)
381 ex.printStackTrace();
386 if (featureLinks.size() > 0)
388 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
390 if (autoenabledisplay)
392 viewport.setShowSequenceFeatures(true);
393 sequenceFeatures.setState(true);
395 if (alignPanel.seqPanel.seqCanvas.fr != null)
397 // update the min/max ranges where necessary
398 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
400 if (viewport.featureSettings != null)
402 viewport.featureSettings.refreshTable();
404 alignPanel.paintAlignment(true);
405 statusBar.setText(MessageManager
406 .getString("label.successfully_added_features_alignment"));
412 public void keyPressed(KeyEvent evt)
414 if (viewport.cursorMode
415 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
416 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
417 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
418 && Character.isDigit(evt.getKeyChar()))
420 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
423 switch (evt.getKeyCode())
425 case 27: // escape key
426 deselectAllSequenceMenuItem_actionPerformed();
428 alignPanel.alabels.cancelDrag();
431 if (evt.isControlDown() || evt.isMetaDown())
433 cut_actionPerformed();
437 if (viewport.cursorMode && !evt.isControlDown())
439 alignPanel.seqPanel.setCursorColumn();
441 if (evt.isControlDown() || evt.isMetaDown())
443 copy_actionPerformed();
447 if (evt.isControlDown())
449 paste(evt.isShiftDown());
453 if (evt.isControlDown() || evt.isMetaDown())
455 selectAllSequenceMenuItem_actionPerformed();
458 case KeyEvent.VK_DOWN:
459 if (viewport.cursorMode)
461 alignPanel.seqPanel.moveCursor(0, 1);
465 moveSelectedSequences(false);
470 if (viewport.cursorMode)
472 alignPanel.seqPanel.moveCursor(0, -1);
476 moveSelectedSequences(true);
480 case KeyEvent.VK_LEFT:
481 if (evt.isAltDown() || !viewport.cursorMode)
483 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
487 alignPanel.seqPanel.moveCursor(-1, 0);
491 case KeyEvent.VK_RIGHT:
492 if (evt.isAltDown() || !viewport.cursorMode)
494 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
498 alignPanel.seqPanel.moveCursor(1, 0);
502 case KeyEvent.VK_SPACE:
503 if (viewport.cursorMode)
505 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
506 || evt.isShiftDown() || evt.isAltDown());
510 case KeyEvent.VK_DELETE:
511 case KeyEvent.VK_BACK_SPACE:
512 if (viewport.cursorMode)
514 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
515 || evt.isShiftDown() || evt.isAltDown());
519 cut_actionPerformed();
520 alignPanel.seqPanel.seqCanvas.repaint();
525 if (viewport.cursorMode)
527 alignPanel.seqPanel.setCursorRow();
531 if (viewport.cursorMode)
533 alignPanel.seqPanel.setCursorPosition();
537 case KeyEvent.VK_ENTER:
538 case KeyEvent.VK_COMMA:
539 if (viewport.cursorMode)
541 alignPanel.seqPanel.setCursorRowAndColumn();
546 if (viewport.cursorMode)
548 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
552 if (viewport.cursorMode)
554 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
559 viewport.cursorMode = !viewport.cursorMode;
560 statusBar.setText(MessageManager.formatMessage(
561 "label.keyboard_editing_mode",
562 new String[] { (viewport.cursorMode ? "on" : "off") }));
563 if (viewport.cursorMode)
565 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
566 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
571 if (evt.isControlDown())
573 findMenuItem_actionPerformed();
579 boolean toggleSeqs = !evt.isControlDown();
580 boolean toggleCols = !evt.isShiftDown();
581 toggleHiddenRegions(toggleSeqs, toggleCols);
585 case KeyEvent.VK_PAGE_UP:
586 if (viewport.getWrapAlignment())
588 alignPanel.scrollUp(true);
592 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
593 - viewport.endSeq + viewport.startSeq);
597 case KeyEvent.VK_PAGE_DOWN:
598 if (viewport.getWrapAlignment())
600 alignPanel.scrollUp(false);
604 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
605 + viewport.endSeq - viewport.startSeq);
610 if (evt.isControlDown())
612 undoMenuItem_actionPerformed();
617 if (evt.isControlDown())
619 redoMenuItem_actionPerformed();
624 if (evt.isControlDown())
631 if (evt.isControlDown())
633 trimAlignment(false);
638 if (evt.isControlDown())
640 if (evt.isShiftDown())
642 this.removeAllGapsMenuItem_actionPerformed();
646 removeGappedColumnMenuItem_actionPerformed();
651 if (evt.isControlDown())
655 invertColSel_actionPerformed();
659 invertSequenceMenuItem_actionPerformed();
665 if (evt.isControlDown())
667 if (evt.isShiftDown())
669 this.unGroup_actionPerformed();
673 this.createGroup_actionPerformed();
679 if (evt.isControlDown())
681 this.deleteGroups_actionPerformed();
686 if (evt.isControlDown())
693 alignPanel.paintAlignment(true);
697 * called by key handler and the hide all/show all menu items
702 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
704 boolean hide = false;
705 SequenceGroup sg = viewport.getSelectionGroup();
706 if (!toggleSeqs && !toggleCols)
708 // Hide everything by the current selection - this is a hack - we do the
709 // invert and then hide
710 // first check that there will be visible columns after the invert.
711 if ((viewport.getColumnSelection() != null
712 && viewport.getColumnSelection().getSelected() != null && viewport
713 .getColumnSelection().getSelected().size() > 0)
714 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
717 // now invert the sequence set, if required - empty selection implies
718 // that no hiding is required.
721 invertSequenceMenuItem_actionPerformed();
722 sg = viewport.getSelectionGroup();
726 viewport.expandColSelection(sg, true);
727 // finally invert the column selection and get the new sequence
728 // selection and indicate it should be hidden.
729 invertColSel_actionPerformed();
736 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
739 viewport.hideAllSelectedSeqs();
741 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
744 viewport.showAllHiddenSeqs();
750 if (viewport.getColumnSelection().getSelected().size() > 0)
752 viewport.hideSelectedColumns();
755 viewport.setSelectionGroup(sg);
760 viewport.showAllHiddenColumns();
762 viewport.sendSelection();
767 public void keyReleased(KeyEvent evt)
772 public void keyTyped(KeyEvent evt)
777 public void itemStateChanged(ItemEvent evt)
779 final Object source = evt.getSource();
780 if (source == displayNonconservedMenuItem)
782 displayNonconservedMenuItem_actionPerformed();
784 else if (source == colourTextMenuItem)
786 colourTextMenuItem_actionPerformed();
788 else if (source == wrapMenuItem)
790 wrapMenuItem_actionPerformed();
792 else if (source == scaleAbove)
794 viewport.setScaleAboveWrapped(scaleAbove.getState());
796 else if (source == scaleLeft)
798 viewport.setScaleLeftWrapped(scaleLeft.getState());
800 else if (source == scaleRight)
802 viewport.setScaleRightWrapped(scaleRight.getState());
804 else if (source == seqLimits)
806 seqLimits_itemStateChanged();
808 else if (source == viewBoxesMenuItem)
810 viewport.setShowBoxes(viewBoxesMenuItem.getState());
812 else if (source == viewTextMenuItem)
814 viewport.setShowText(viewTextMenuItem.getState());
816 else if (source == renderGapsMenuItem)
818 viewport.setRenderGaps(renderGapsMenuItem.getState());
820 else if (source == annotationPanelMenuItem)
822 boolean showAnnotations = annotationPanelMenuItem.getState();
823 showAlignmentAnnotations.setEnabled(showAnnotations);
824 showSequenceAnnotations.setEnabled(showAnnotations);
825 viewport.setShowAnnotation(showAnnotations);
826 alignPanel.setAnnotationVisible(showAnnotations);
828 else if (source == sequenceFeatures)
830 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
831 alignPanel.seqPanel.seqCanvas.repaint();
833 else if (source == showAlignmentAnnotations)
835 setAnnotationsVisibility();
837 else if (source == showSequenceAnnotations)
839 setAnnotationsVisibility();
841 else if (source == sortAnnBySequence)
843 boolean newState = sortAnnBySequence.getState();
844 sortAnnByLabel.setState(false);
845 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
846 : SequenceAnnotationOrder.NONE);
847 setViewportAnnotationOrder();
849 else if (source == sortAnnByLabel)
851 boolean newState = sortAnnByLabel.getState();
852 sortAnnBySequence.setState(false);
853 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
854 : SequenceAnnotationOrder.NONE);
855 setViewportAnnotationOrder();
857 else if (source == showAutoFirst)
859 showAutoLast.setState(!showAutoFirst.getState());
860 setShowAutoCalculatedAbove(showAutoFirst.getState());
861 setViewportAnnotationOrder();
863 else if (source == showAutoLast)
865 showAutoFirst.setState(!showAutoLast.getState());
866 setShowAutoCalculatedAbove(showAutoFirst.getState());
867 setViewportAnnotationOrder();
869 else if (source == conservationMenuItem)
871 conservationMenuItem_actionPerformed();
873 else if (source == abovePIDThreshold)
875 abovePIDThreshold_actionPerformed();
877 else if (source == applyToAllGroups)
879 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
881 else if (source == autoCalculate)
883 viewport.autoCalculateConsensus = autoCalculate.getState();
885 else if (source == sortByTree)
887 viewport.sortByTree = sortByTree.getState();
889 else if (source == this.centreColumnLabelFlag)
891 centreColumnLabelFlag_stateChanged();
893 else if (source == this.followMouseOverFlag)
895 mouseOverFlag_stateChanged();
897 else if (source == showGroupConsensus)
899 showGroupConsensus_actionPerformed();
901 else if (source == showGroupConservation)
903 showGroupConservation_actionPerformed();
905 else if (source == showSequenceLogo)
907 showSequenceLogo_actionPerformed();
909 else if (source == normSequenceLogo)
911 normSequenceLogo_actionPerformed();
913 else if (source == showConsensusHistogram)
915 showConsensusHistogram_actionPerformed();
917 else if (source == applyAutoAnnotationSettings)
919 applyAutoAnnotationSettings_actionPerformed();
921 alignPanel.paintAlignment(true);
925 * Set the visibility state of sequence-related and/or alignment-related
926 * annotations depending on checkbox selections, and repaint.
930 private void setAnnotationsVisibility()
932 boolean showForAlignment = showAlignmentAnnotations.getState();
933 boolean showForSequences = showSequenceAnnotations.getState();
934 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
936 for (AlignmentAnnotation aa : alignPanel.getAlignment()
937 .getAlignmentAnnotation())
939 boolean visible = (aa.sequenceRef == null ? showForAlignment
941 aa.visible = visible;
944 alignPanel.validateAnnotationDimensions(true);
949 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
951 this.annotationSortOrder = order;
955 * Set flags on the viewport that control annotation ordering
957 private void setViewportAnnotationOrder()
959 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
961 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
964 private void setShowAutoCalculatedAbove(boolean showAbove)
966 this.showAutoCalculatedAbove = showAbove;
969 private void mouseOverFlag_stateChanged()
971 viewport.setFollowHighlight(followMouseOverFlag.getState());
972 // TODO: could kick the scrollTo mechanism to reset view for current
976 private void centreColumnLabelFlag_stateChanged()
978 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
979 this.alignPanel.annotationPanel.repaint();
983 public void actionPerformed(ActionEvent evt)
985 viewport.applet.currentAlignFrame = this;
987 Object source = evt.getSource();
989 if (source == inputText)
991 inputText_actionPerformed();
993 else if (source == loadTree)
995 loadTree_actionPerformed();
997 else if (source == loadApplication)
999 launchFullApplication();
1001 else if (source == loadAnnotations)
1005 else if (source == outputAnnotations)
1007 outputAnnotations(true);
1009 else if (source == outputFeatures)
1011 outputFeatures(true, "Jalview");
1013 else if (source == closeMenuItem)
1015 closeMenuItem_actionPerformed();
1017 else if (source == copy)
1019 copy_actionPerformed();
1021 else if (source == undoMenuItem)
1023 undoMenuItem_actionPerformed();
1025 else if (source == redoMenuItem)
1027 redoMenuItem_actionPerformed();
1029 else if (source == inputText)
1031 inputText_actionPerformed();
1033 else if (source == closeMenuItem)
1035 closeMenuItem_actionPerformed();
1037 else if (source == undoMenuItem)
1039 undoMenuItem_actionPerformed();
1041 else if (source == redoMenuItem)
1043 redoMenuItem_actionPerformed();
1045 else if (source == copy)
1047 copy_actionPerformed();
1049 else if (source == pasteNew)
1051 pasteNew_actionPerformed();
1053 else if (source == pasteThis)
1055 pasteThis_actionPerformed();
1057 else if (source == cut)
1059 cut_actionPerformed();
1061 else if (source == delete)
1063 delete_actionPerformed();
1065 else if (source == grpsFromSelection)
1067 makeGrpsFromSelection_actionPerformed();
1069 else if (source == deleteGroups)
1071 deleteGroups_actionPerformed();
1073 else if (source == selectAllSequenceMenuItem)
1075 selectAllSequenceMenuItem_actionPerformed();
1077 else if (source == deselectAllSequenceMenuItem)
1079 deselectAllSequenceMenuItem_actionPerformed();
1081 else if (source == invertSequenceMenuItem)
1083 invertSequenceMenuItem_actionPerformed();
1084 // uncomment to slave sequence selections in split frame
1085 // viewport.sendSelection();
1087 else if (source == invertColSel)
1089 viewport.invertColumnSelection();
1090 alignPanel.paintAlignment(true);
1091 viewport.sendSelection();
1093 else if (source == remove2LeftMenuItem)
1095 trimAlignment(true);
1097 else if (source == remove2RightMenuItem)
1099 trimAlignment(false);
1101 else if (source == removeGappedColumnMenuItem)
1103 removeGappedColumnMenuItem_actionPerformed();
1105 else if (source == removeAllGapsMenuItem)
1107 removeAllGapsMenuItem_actionPerformed();
1109 else if (source == findMenuItem)
1111 findMenuItem_actionPerformed();
1113 else if (source == font)
1115 new FontChooser(alignPanel);
1117 else if (source == newView)
1121 else if (source == showColumns)
1123 viewport.showAllHiddenColumns();
1124 alignPanel.paintAlignment(true);
1125 viewport.sendSelection();
1127 else if (source == showSeqs)
1129 viewport.showAllHiddenSeqs();
1130 alignPanel.paintAlignment(true);
1131 // uncomment if we want to slave sequence selections in split frame
1132 // viewport.sendSelection();
1134 else if (source == hideColumns)
1136 viewport.hideSelectedColumns();
1137 alignPanel.paintAlignment(true);
1138 viewport.sendSelection();
1140 else if (source == hideSequences
1141 && viewport.getSelectionGroup() != null)
1143 viewport.hideAllSelectedSeqs();
1144 alignPanel.paintAlignment(true);
1145 // uncomment if we want to slave sequence selections in split frame
1146 // viewport.sendSelection();
1148 else if (source == hideAllButSelection)
1150 toggleHiddenRegions(false, false);
1151 alignPanel.paintAlignment(true);
1152 viewport.sendSelection();
1154 else if (source == hideAllSelection)
1156 SequenceGroup sg = viewport.getSelectionGroup();
1157 viewport.expandColSelection(sg, false);
1158 viewport.hideAllSelectedSeqs();
1159 viewport.hideSelectedColumns();
1160 alignPanel.paintAlignment(true);
1161 viewport.sendSelection();
1163 else if (source == showAllHidden)
1165 viewport.showAllHiddenColumns();
1166 viewport.showAllHiddenSeqs();
1167 alignPanel.paintAlignment(true);
1168 viewport.sendSelection();
1170 else if (source == showGroupConsensus)
1172 showGroupConsensus_actionPerformed();
1174 else if (source == showGroupConservation)
1176 showGroupConservation_actionPerformed();
1178 else if (source == showSequenceLogo)
1180 showSequenceLogo_actionPerformed();
1182 else if (source == normSequenceLogo)
1184 normSequenceLogo_actionPerformed();
1186 else if (source == showConsensusHistogram)
1188 showConsensusHistogram_actionPerformed();
1190 else if (source == applyAutoAnnotationSettings)
1192 applyAutoAnnotationSettings_actionPerformed();
1194 else if (source == featureSettings)
1196 new FeatureSettings(alignPanel);
1198 else if (source == alProperties)
1200 StringBuffer contents = new jalview.io.AlignmentProperties(
1201 viewport.getAlignment()).formatAsString();
1202 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1203 cap.setText(contents.toString());
1204 Frame frame = new Frame();
1206 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1207 "label.alignment_properties", new String[] { getTitle() }),
1210 else if (source == overviewMenuItem)
1212 overviewMenuItem_actionPerformed();
1214 else if (source == noColourmenuItem)
1218 else if (source == clustalColour)
1220 abovePIDThreshold.setState(false);
1221 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1223 else if (source == zappoColour)
1225 changeColour(new ZappoColourScheme());
1227 else if (source == taylorColour)
1229 changeColour(new TaylorColourScheme());
1231 else if (source == hydrophobicityColour)
1233 changeColour(new HydrophobicColourScheme());
1235 else if (source == helixColour)
1237 changeColour(new HelixColourScheme());
1239 else if (source == strandColour)
1241 changeColour(new StrandColourScheme());
1243 else if (source == turnColour)
1245 changeColour(new TurnColourScheme());
1247 else if (source == buriedColour)
1249 changeColour(new BuriedColourScheme());
1251 else if (source == nucleotideColour)
1253 changeColour(new NucleotideColourScheme());
1255 else if (source == purinePyrimidineColour)
1257 changeColour(new PurinePyrimidineColourScheme());
1259 // else if (source == RNAInteractionColour)
1261 // changeColour(new RNAInteractionColourScheme());
1263 else if (source == RNAHelixColour)
1265 new RNAHelicesColourChooser(viewport, alignPanel);
1267 else if (source == modifyPID)
1269 modifyPID_actionPerformed();
1271 else if (source == modifyConservation)
1273 modifyConservation_actionPerformed();
1275 else if (source == userDefinedColour)
1277 new UserDefinedColours(alignPanel, null);
1279 else if (source == PIDColour)
1281 changeColour(new PIDColourScheme());
1283 else if (source == BLOSUM62Colour)
1285 changeColour(new Blosum62ColourScheme());
1287 else if (source == tcoffeeColour)
1289 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1291 else if (source == annotationColour)
1293 new AnnotationColourChooser(viewport, alignPanel);
1295 else if (source == annotationColumnSelection)
1297 new AnnotationColumnChooser(viewport, alignPanel);
1299 else if (source == sortPairwiseMenuItem)
1301 sortPairwiseMenuItem_actionPerformed();
1303 else if (source == sortIDMenuItem)
1305 sortIDMenuItem_actionPerformed();
1307 else if (source == sortLengthMenuItem)
1309 sortLengthMenuItem_actionPerformed();
1311 else if (source == sortGroupMenuItem)
1313 sortGroupMenuItem_actionPerformed();
1315 else if (source == removeRedundancyMenuItem)
1317 removeRedundancyMenuItem_actionPerformed();
1319 else if (source == pairwiseAlignmentMenuItem)
1321 pairwiseAlignmentMenuItem_actionPerformed();
1323 else if (source == PCAMenuItem)
1325 PCAMenuItem_actionPerformed();
1327 else if (source == averageDistanceTreeMenuItem)
1329 averageDistanceTreeMenuItem_actionPerformed();
1331 else if (source == neighbourTreeMenuItem)
1333 neighbourTreeMenuItem_actionPerformed();
1335 else if (source == njTreeBlosumMenuItem)
1337 njTreeBlosumMenuItem_actionPerformed();
1339 else if (source == avDistanceTreeBlosumMenuItem)
1341 avTreeBlosumMenuItem_actionPerformed();
1343 else if (source == documentation)
1345 documentation_actionPerformed();
1347 else if (source == about)
1349 about_actionPerformed();
1354 public void inputText_actionPerformed()
1356 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1357 Frame frame = new Frame();
1359 jalview.bin.JalviewLite.addFrame(frame,
1360 MessageManager.getString("label.input_cut_paste"), 500, 500);
1363 protected void outputText_actionPerformed(ActionEvent e)
1365 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1366 Frame frame = new Frame();
1368 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1369 "label.alignment_output_command",
1370 new Object[] { e.getActionCommand() }), 600, 500);
1372 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1373 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1374 e.getActionCommand(), viewport.getAlignment(),
1375 viewport.getShowJVSuffix()));
1378 public void loadAnnotations()
1380 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1381 cap.setText(MessageManager
1382 .getString("label.paste_features_annotations_Tcoffee_here"));
1383 cap.setAnnotationImport();
1384 Frame frame = new Frame();
1386 jalview.bin.JalviewLite.addFrame(frame,
1387 MessageManager.getString("action.paste_annotations"), 400, 300);
1391 public String outputAnnotations(boolean displayTextbox)
1393 String annotation = new AnnotationFile()
1394 .printAnnotationsForView(viewport);
1398 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1399 Frame frame = new Frame();
1401 jalview.bin.JalviewLite.addFrame(frame,
1402 MessageManager.getString("label.annotations"), 600, 500);
1403 cap.setText(annotation);
1409 private Map<String, Object> getDisplayedFeatureCols()
1411 if (alignPanel.getFeatureRenderer() != null
1412 && viewport.getFeaturesDisplayed() != null)
1414 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1420 public String outputFeatures(boolean displayTextbox, String format)
1423 if (format.equalsIgnoreCase("Jalview"))
1425 features = new FeaturesFile().printJalviewFormat(viewport
1426 .getAlignment().getSequencesArray(),
1427 getDisplayedFeatureCols());
1431 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1432 .getSequencesArray(), getDisplayedFeatureCols());
1437 boolean frimport = false;
1438 if (features == null || features.equals("No Features Visible"))
1440 features = "# No features visible - paste some and import them here.";
1444 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1447 cap.setAnnotationImport();
1449 Frame frame = new Frame();
1451 jalview.bin.JalviewLite.addFrame(frame,
1452 MessageManager.getString("label.features"), 600, 500);
1453 cap.setText(features);
1457 if (features == null)
1466 void launchFullApplication()
1468 StringBuffer url = new StringBuffer(jalviewServletURL);
1470 // allow servlet parameters to be passed in applet parameter
1471 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1473 url.append(firstSep);
1476 + appendProtocol(viewport.applet.getParameter("file")));
1478 if (viewport.applet.getParameter("features") != null)
1480 url.append("&features=");
1481 url.append(appendProtocol(viewport.applet.getParameter("features")));
1484 if (viewport.applet.getParameter("annotations") != null)
1486 url.append("&annotations=");
1487 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1490 if (viewport.applet.getParameter("jnetfile") != null)
1492 url.append("&annotations=");
1493 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1496 if (viewport.applet.getParameter("defaultColour") != null)
1498 url.append("&colour="
1499 + removeWhiteSpace(viewport.applet
1500 .getParameter("defaultColour")));
1503 if (viewport.applet.getParameter("userDefinedColour") != null)
1505 url.append("&colour="
1506 + removeWhiteSpace(viewport.applet
1507 .getParameter("userDefinedColour")));
1509 if (viewport.applet.getParameter("tree") != null)
1512 + appendProtocol(viewport.applet.getParameter("tree")));
1514 if (viewport.applet.getParameter("treeFile") != null)
1517 + appendProtocol(viewport.applet.getParameter("treeFile")));
1520 showURL(url.toString(), "FULL_APP");
1523 String removeWhiteSpace(String colour)
1525 StringBuffer sb = new StringBuffer();
1526 for (int i = 0; i < colour.length(); i++)
1528 if (Character.isWhitespace(colour.charAt(i)))
1534 sb.append(colour.charAt(i));
1538 return sb.toString();
1541 String appendProtocol(String url)
1546 url = URLEncoder.encode(url);
1549 * When we finally deprecate 1.1 compatibility, we can start to use
1550 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1551 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1552 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1553 * ex.printStackTrace(); }
1555 catch (java.net.MalformedURLException ex)
1557 url = viewport.applet.getCodeBase() + url;
1562 public void closeMenuItem_actionPerformed()
1564 PaintRefresher.RemoveComponent(alignPanel);
1565 if (alignPanel.seqPanel != null
1566 && alignPanel.seqPanel.seqCanvas != null)
1568 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1570 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1572 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1575 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1590 void updateEditMenuBar()
1593 if (viewport.getHistoryList().size() > 0)
1595 undoMenuItem.setEnabled(true);
1596 CommandI command = viewport.getHistoryList().peek();
1597 undoMenuItem.setLabel(MessageManager.formatMessage(
1598 "label.undo_command",
1599 new Object[] { command.getDescription() }));
1603 undoMenuItem.setEnabled(false);
1604 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1607 if (viewport.getRedoList().size() > 0)
1609 redoMenuItem.setEnabled(true);
1611 CommandI command = viewport.getRedoList().peek();
1612 redoMenuItem.setLabel(MessageManager.formatMessage(
1613 "label.redo_command",
1614 new Object[] { command.getDescription() }));
1618 redoMenuItem.setEnabled(false);
1619 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1627 public void addHistoryItem(CommandI command)
1629 if (command.getSize() > 0)
1631 viewport.addToHistoryList(command);
1632 viewport.clearRedoList();
1633 updateEditMenuBar();
1634 viewport.updateHiddenColumns();
1639 * TODO: JAL-1104 DOCUMENT ME!
1644 protected void undoMenuItem_actionPerformed()
1646 if (viewport.getHistoryList().isEmpty())
1651 CommandI command = viewport.getHistoryList().pop();
1652 viewport.addToRedoList(command);
1653 command.undoCommand(null);
1655 AlignmentViewport originalSource = getOriginatingSource(command);
1657 if (originalSource != viewport)
1660 .println("Warning: Viewport object mismatch whilst undoing");
1662 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1663 // viewport.getColumnSelection().getHiddenColumns()
1665 updateEditMenuBar();
1666 originalSource.firePropertyChange("alignment", null, originalSource
1667 .getAlignment().getSequences());
1671 * TODO: JAL-1104 DOCUMENT ME!
1676 protected void redoMenuItem_actionPerformed()
1678 if (viewport.getRedoList().isEmpty())
1683 CommandI command = viewport.getRedoList().pop();
1684 viewport.addToHistoryList(command);
1685 command.doCommand(null);
1687 AlignmentViewport originalSource = getOriginatingSource(command);
1689 if (originalSource != viewport)
1692 .println("Warning: Viewport object mismatch whilst re-doing");
1694 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1695 // viewport.getColumnSelection().getHiddenColumns()
1698 updateEditMenuBar();
1699 originalSource.firePropertyChange("alignment", null, originalSource
1700 .getAlignment().getSequences());
1703 AlignmentViewport getOriginatingSource(CommandI command)
1705 AlignmentViewport originalSource = null;
1706 // For sequence removal and addition, we need to fire
1707 // the property change event FROM the viewport where the
1708 // original alignment was altered
1709 AlignmentI al = null;
1710 if (command instanceof EditCommand)
1712 EditCommand editCommand = (EditCommand) command;
1713 al = editCommand.getAlignment();
1714 Vector comps = (Vector) PaintRefresher.components.get(viewport
1715 .getSequenceSetId());
1716 for (int i = 0; i < comps.size(); i++)
1718 if (comps.elementAt(i) instanceof AlignmentPanel)
1720 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1722 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1729 if (originalSource == null)
1731 // The original view is closed, we must validate
1732 // the current view against the closed view first
1735 PaintRefresher.validateSequences(al, viewport.getAlignment());
1738 originalSource = viewport;
1741 return originalSource;
1745 * Move the currently selected sequences up or down one position in the
1750 public void moveSelectedSequences(boolean up)
1752 SequenceGroup sg = viewport.getSelectionGroup();
1757 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1758 up ? null : viewport.getHiddenRepSequences(), up);
1759 alignPanel.paintAlignment(true);
1762 * Also move cDNA/protein complement sequences
1764 AlignViewportI complement = viewport.getCodingComplement();
1765 if (complement != null)
1767 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1768 viewport, complement);
1769 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1770 up ? null : complement.getHiddenRepSequences(), up);
1771 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1775 synchronized void slideSequences(boolean right, int size)
1777 List<SequenceI> sg = new Vector<SequenceI>();
1778 if (viewport.cursorMode)
1780 sg.add(viewport.getAlignment().getSequenceAt(
1781 alignPanel.seqPanel.seqCanvas.cursorY));
1783 else if (viewport.getSelectionGroup() != null
1784 && viewport.getSelectionGroup().getSize() != viewport
1785 .getAlignment().getHeight())
1787 sg = viewport.getSelectionGroup().getSequences(
1788 viewport.getHiddenRepSequences());
1796 Vector<SequenceI> invertGroup = new Vector();
1798 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1800 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1802 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1806 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1808 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1810 for (int i = 0; i < invertGroup.size(); i++)
1812 seqs2[i] = invertGroup.elementAt(i);
1815 SlideSequencesCommand ssc;
1818 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1819 size, viewport.getGapCharacter());
1823 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1824 size, viewport.getGapCharacter());
1827 int groupAdjustment = 0;
1828 if (ssc.getGapsInsertedBegin() && right)
1830 if (viewport.cursorMode)
1832 alignPanel.seqPanel.moveCursor(size, 0);
1836 groupAdjustment = size;
1839 else if (!ssc.getGapsInsertedBegin() && !right)
1841 if (viewport.cursorMode)
1843 alignPanel.seqPanel.moveCursor(-size, 0);
1847 groupAdjustment = -size;
1851 if (groupAdjustment != 0)
1853 viewport.getSelectionGroup().setStartRes(
1854 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1855 viewport.getSelectionGroup().setEndRes(
1856 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1859 boolean appendHistoryItem = false;
1860 Deque<CommandI> historyList = viewport.getHistoryList();
1861 if (historyList != null && historyList.size() > 0
1862 && historyList.peek() instanceof SlideSequencesCommand)
1864 appendHistoryItem = ssc
1865 .appendSlideCommand((SlideSequencesCommand) historyList
1869 if (!appendHistoryItem)
1871 addHistoryItem(ssc);
1877 static StringBuffer copiedSequences;
1879 static Vector copiedHiddenColumns;
1881 protected void copy_actionPerformed()
1883 if (viewport.getSelectionGroup() == null)
1888 SequenceGroup sg = viewport.getSelectionGroup();
1889 copiedSequences = new StringBuffer();
1890 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1891 for (int i = 0; i < sg.getSize(); i++)
1893 SequenceI seq = sg.getSequenceAt(i);
1894 int index = viewport.getAlignment().findIndex(seq);
1895 orderedSeqs.put(index, seq);
1898 int index = 0, startRes, endRes;
1901 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1903 copiedHiddenColumns = new Vector();
1904 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1905 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1907 copiedHiddenColumns.addElement(new int[] {
1908 region[0] - hiddenOffset, region[1] - hiddenOffset });
1913 copiedHiddenColumns = null;
1916 for (int i = 0; i < sg.getSize(); i++)
1918 SequenceI seq = null;
1922 if (orderedSeqs.containsKey(index))
1924 seq = orderedSeqs.get(index);
1935 // Returns residue following index if gap
1936 startRes = seq.findPosition(sg.getStartRes());
1939 // Need to find the residue preceeding index if gap
1942 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1944 ch = seq.getCharAt(j);
1945 if (!jalview.util.Comparison.isGap((ch)))
1953 endRes += seq.getStart() - 1;
1956 copiedSequences.append(seq.getName()
1962 + seq.getSequenceAsString(sg.getStartRes(),
1963 sg.getEndRes() + 1) + "\n");
1968 protected void pasteNew_actionPerformed()
1973 protected void pasteThis_actionPerformed()
1978 void paste(boolean newAlignment)
1983 if (copiedSequences == null)
1988 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1989 Vector seqs = new Vector();
1990 while (st.hasMoreElements())
1992 String name = st.nextToken();
1993 int start = Integer.parseInt(st.nextToken());
1994 int end = Integer.parseInt(st.nextToken());
1995 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1997 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1998 for (int i = 0; i < seqs.size(); i++)
2000 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2005 String newtitle = MessageManager
2006 .getString("label.copied_sequences");
2007 if (getTitle().startsWith(
2008 MessageManager.getString("label.copied_sequences")))
2010 newtitle = getTitle();
2014 newtitle = newtitle.concat(MessageManager.formatMessage(
2015 "label.from_msname", new String[] { getTitle() }));
2017 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2018 viewport.applet, newtitle, false);
2019 if (copiedHiddenColumns != null)
2021 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2023 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2024 af.viewport.hideColumns(region[0], region[1]);
2028 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2033 addSequences(newSeqs);
2036 } catch (Exception ex)
2038 } // could be anything being pasted in here
2042 void addSequences(SequenceI[] seqs)
2044 for (int i = 0; i < seqs.length; i++)
2046 viewport.getAlignment().addSequence(seqs[i]);
2050 addHistoryItem(new EditCommand(
2051 MessageManager.getString("label.add_sequences"), Action.PASTE,
2052 seqs, 0, viewport.getAlignment().getWidth(),
2053 viewport.getAlignment()));
2055 viewport.setEndSeq(viewport.getAlignment().getHeight());
2056 viewport.getAlignment().getWidth();
2057 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2062 protected void cut_actionPerformed()
2064 copy_actionPerformed();
2065 delete_actionPerformed();
2068 protected void delete_actionPerformed()
2071 SequenceGroup sg = viewport.getSelectionGroup();
2077 Vector seqs = new Vector();
2079 for (int i = 0; i < sg.getSize(); i++)
2081 seq = sg.getSequenceAt(i);
2082 seqs.addElement(seq);
2086 * If the cut affects all sequences, warn, remove highlighted columns
2088 if (sg.getSize() == viewport.getAlignment().getHeight())
2090 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2091 .getAlignment().getWidth()) ? true : false;
2092 if (isEntireAlignWidth)
2094 String title = MessageManager.getString("label.delete_all");
2095 Panel infoPanel = new Panel();
2096 infoPanel.setLayout(new FlowLayout());
2098 .add(new Label(MessageManager.getString("warn.delete_all")));
2100 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2101 dialog.setMainPanel(infoPanel);
2102 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2103 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2104 dialog.setVisible(true);
2111 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2112 sg.getEndRes() + 1);
2115 SequenceI[] cut = new SequenceI[seqs.size()];
2116 for (int i = 0; i < seqs.size(); i++)
2118 cut[i] = (SequenceI) seqs.elementAt(i);
2122 * //ADD HISTORY ITEM
2124 addHistoryItem(new EditCommand(
2125 MessageManager.getString("label.cut_sequences"), Action.CUT,
2126 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2127 viewport.getAlignment()));
2129 viewport.setSelectionGroup(null);
2130 viewport.getAlignment().deleteGroup(sg);
2132 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2135 if (viewport.getAlignment().getHeight() < 1)
2137 this.setVisible(false);
2139 viewport.sendSelection();
2143 * group consensus toggled
2146 protected void showGroupConsensus_actionPerformed()
2148 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2149 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2154 * group conservation toggled.
2156 protected void showGroupConservation_actionPerformed()
2158 viewport.setShowGroupConservation(showGroupConservation.getState());
2159 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2166 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2167 * .event.ActionEvent)
2169 protected void showConsensusHistogram_actionPerformed()
2171 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2172 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2179 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2180 * .event.ActionEvent)
2182 protected void showSequenceLogo_actionPerformed()
2184 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2185 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188 protected void normSequenceLogo_actionPerformed()
2190 showSequenceLogo.setState(true);
2191 viewport.setShowSequenceLogo(true);
2192 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2193 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196 protected void applyAutoAnnotationSettings_actionPerformed()
2198 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2201 protected void makeGrpsFromSelection_actionPerformed()
2203 if (avc.makeGroupsFromSelection())
2205 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2206 alignPanel.updateAnnotation();
2207 alignPanel.paintAlignment(true);
2211 protected void createGroup_actionPerformed()
2216 protected void unGroup_actionPerformed()
2220 alignPanel.alignmentChanged();
2224 protected void deleteGroups_actionPerformed()
2226 if (avc.deleteGroups())
2228 alignPanel.alignmentChanged();
2232 public void selectAllSequenceMenuItem_actionPerformed()
2234 SequenceGroup sg = new SequenceGroup();
2235 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2237 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2239 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2240 viewport.setSelectionGroup(sg);
2241 alignPanel.paintAlignment(true);
2242 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2243 viewport.sendSelection();
2246 public void deselectAllSequenceMenuItem_actionPerformed()
2248 if (viewport.cursorMode)
2250 alignPanel.seqPanel.keyboardNo1 = null;
2251 alignPanel.seqPanel.keyboardNo2 = null;
2253 viewport.setSelectionGroup(null);
2254 viewport.getColumnSelection().clear();
2255 viewport.setSelectionGroup(null);
2256 alignPanel.idPanel.idCanvas.searchResults = null;
2257 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2258 alignPanel.paintAlignment(true);
2259 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2260 viewport.sendSelection();
2263 public void invertSequenceMenuItem_actionPerformed()
2265 SequenceGroup sg = viewport.getSelectionGroup();
2266 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2268 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2271 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2272 viewport.sendSelection();
2275 public void invertColSel_actionPerformed()
2277 viewport.invertColumnSelection();
2278 alignPanel.paintAlignment(true);
2279 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2280 viewport.sendSelection();
2283 void trimAlignment(boolean trimLeft)
2285 ColumnSelection colSel = viewport.getColumnSelection();
2288 if (!colSel.isEmpty())
2292 column = colSel.getMin();
2296 column = colSel.getMax();
2300 if (viewport.getSelectionGroup() != null)
2302 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2303 viewport.getHiddenRepSequences());
2307 seqs = viewport.getAlignment().getSequencesArray();
2310 TrimRegionCommand trimRegion;
2313 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2314 column, viewport.getAlignment());
2315 viewport.setStartRes(0);
2319 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2320 column, viewport.getAlignment());
2323 statusBar.setText(MessageManager.formatMessage(
2324 "label.removed_columns",
2325 new String[] { Integer.valueOf(trimRegion.getSize())
2327 addHistoryItem(trimRegion);
2329 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2331 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2332 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2334 viewport.getAlignment().deleteGroup(sg);
2338 viewport.firePropertyChange("alignment", null, viewport
2339 .getAlignment().getSequences());
2343 public void removeGappedColumnMenuItem_actionPerformed()
2345 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2348 if (viewport.getSelectionGroup() != null)
2350 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2351 viewport.getHiddenRepSequences());
2352 start = viewport.getSelectionGroup().getStartRes();
2353 end = viewport.getSelectionGroup().getEndRes();
2357 seqs = viewport.getAlignment().getSequencesArray();
2360 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2361 "Remove Gapped Columns", seqs, start, end,
2362 viewport.getAlignment());
2364 addHistoryItem(removeGapCols);
2366 statusBar.setText(MessageManager.formatMessage(
2367 "label.removed_empty_columns",
2368 new String[] { Integer.valueOf(removeGapCols.getSize())
2371 // This is to maintain viewport position on first residue
2372 // of first sequence
2373 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2374 int startRes = seq.findPosition(viewport.startRes);
2375 // ShiftList shifts;
2376 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2377 // edit.alColumnChanges=shifts.getInverse();
2378 // if (viewport.hasHiddenColumns)
2379 // viewport.getColumnSelection().compensateForEdits(shifts);
2380 viewport.setStartRes(seq.findIndex(startRes) - 1);
2381 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386 public void removeAllGapsMenuItem_actionPerformed()
2388 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2391 if (viewport.getSelectionGroup() != null)
2393 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2394 viewport.getHiddenRepSequences());
2395 start = viewport.getSelectionGroup().getStartRes();
2396 end = viewport.getSelectionGroup().getEndRes();
2400 seqs = viewport.getAlignment().getSequencesArray();
2403 // This is to maintain viewport position on first residue
2404 // of first sequence
2405 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2406 int startRes = seq.findPosition(viewport.startRes);
2408 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2409 viewport.getAlignment()));
2411 viewport.setStartRes(seq.findIndex(startRes) - 1);
2413 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2418 public void findMenuItem_actionPerformed()
2420 new Finder(alignPanel);
2424 * create a new view derived from the current view
2427 * @return frame for the new view
2429 public AlignFrame newView(String viewtitle)
2432 if (viewport.hasHiddenRows())
2434 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2435 .getFullAlignment().getSequencesArray());
2439 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2442 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2444 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2446 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2448 newal.addAnnotation(viewport.getAlignment()
2449 .getAlignmentAnnotation()[i]);
2454 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2456 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2457 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2458 PaintRefresher.Register(newaf.alignPanel,
2459 newaf.alignPanel.av.getSequenceSetId());
2461 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2462 newaf.alignPanel.av.getSequenceSetId());
2463 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2464 newaf.alignPanel.av.getSequenceSetId());
2466 Vector comps = (Vector) PaintRefresher.components.get(viewport
2467 .getSequenceSetId());
2469 for (int i = 0; i < comps.size(); i++)
2471 if (comps.elementAt(i) instanceof AlignmentPanel)
2477 String title = new String(this.getTitle());
2478 if (viewtitle != null)
2480 title = viewtitle + " ( " + title + ")";
2484 if (title.indexOf("(View") > -1)
2486 title = title.substring(0, title.indexOf("(View"));
2488 title += "(View " + viewSize + ")";
2491 newaf.setTitle(title.toString());
2493 newaf.viewport.setHistoryList(viewport.getHistoryList());
2494 newaf.viewport.setRedoList(viewport.getRedoList());
2500 * @return list of feature groups on the view
2502 public String[] getFeatureGroups()
2504 FeatureRenderer fr = null;
2505 if (alignPanel != null
2506 && (fr = alignPanel.getFeatureRenderer()) != null)
2508 List<String> gps = fr.getFeatureGroups();
2509 String[] _gps = gps.toArray(new String[gps.size()]);
2516 * get sequence feature groups that are hidden or shown
2522 public String[] getFeatureGroupsOfState(boolean visible)
2524 FeatureRenderer fr = null;
2525 if (alignPanel != null
2526 && (fr = alignPanel.getFeatureRenderer()) != null)
2528 List<String> gps = fr.getGroups(visible);
2529 String[] _gps = gps.toArray(new String[gps.size()]);
2536 * Change the display state for the given feature groups
2539 * list of group strings
2541 * visible or invisible
2543 public void setFeatureGroupState(String[] groups, boolean state)
2545 FeatureRenderer fr = null;
2546 this.sequenceFeatures.setState(true);
2547 viewport.setShowSequenceFeatures(true);
2548 if (alignPanel != null
2549 && (fr = alignPanel.getFeatureRenderer()) != null)
2552 fr.setGroupVisibility(Arrays.asList(groups), state);
2553 alignPanel.seqPanel.seqCanvas.repaint();
2554 if (alignPanel.overviewPanel != null)
2556 alignPanel.overviewPanel.updateOverviewImage();
2561 public void seqLimits_itemStateChanged()
2563 viewport.setShowJVSuffix(seqLimits.getState());
2564 alignPanel.fontChanged();
2565 alignPanel.paintAlignment(true);
2568 protected void colourTextMenuItem_actionPerformed()
2570 viewport.setColourText(colourTextMenuItem.getState());
2571 alignPanel.paintAlignment(true);
2574 protected void displayNonconservedMenuItem_actionPerformed()
2576 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2577 alignPanel.paintAlignment(true);
2580 protected void wrapMenuItem_actionPerformed()
2582 viewport.setWrapAlignment(wrapMenuItem.getState());
2583 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2584 scaleAbove.setEnabled(wrapMenuItem.getState());
2585 scaleLeft.setEnabled(wrapMenuItem.getState());
2586 scaleRight.setEnabled(wrapMenuItem.getState());
2587 alignPanel.paintAlignment(true);
2590 public void overviewMenuItem_actionPerformed()
2592 if (alignPanel.overviewPanel != null)
2597 Frame frame = new Frame();
2598 OverviewPanel overview = new OverviewPanel(alignPanel);
2599 frame.add(overview);
2600 // +50 must allow for applet frame window
2601 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2602 "label.overview_params", new String[] { this.getTitle() }),
2603 overview.getPreferredSize().width,
2604 overview.getPreferredSize().height + 50);
2607 final AlignmentPanel ap = alignPanel;
2608 frame.addWindowListener(new WindowAdapter()
2611 public void windowClosing(WindowEvent e)
2615 ap.setOverviewPanel(null);
2620 alignPanel.setOverviewPanel(overview);
2625 public void changeColour(ColourSchemeI cs)
2630 if (viewport.getAbovePIDThreshold())
2632 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2636 if (viewport.getConservationSelected())
2638 cs.setConservationApplied(true);
2639 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2644 cs.setConservationApplied(false);
2647 viewport.setGlobalColourScheme(cs);
2649 alignPanel.paintAlignment(true);
2652 protected void modifyPID_actionPerformed()
2654 if (viewport.getAbovePIDThreshold()
2655 && viewport.getGlobalColourScheme() != null)
2657 SliderPanel.setPIDSliderSource(alignPanel,
2658 viewport.getGlobalColourScheme(), "Background");
2659 SliderPanel.showPIDSlider();
2663 protected void modifyConservation_actionPerformed()
2665 if (viewport.getConservationSelected()
2666 && viewport.getGlobalColourScheme() != null)
2668 SliderPanel.setConservationSlider(alignPanel,
2669 viewport.getGlobalColourScheme(), "Background");
2670 SliderPanel.showConservationSlider();
2674 protected void conservationMenuItem_actionPerformed()
2676 viewport.setConservationSelected(conservationMenuItem.getState());
2678 viewport.setAbovePIDThreshold(false);
2679 abovePIDThreshold.setState(false);
2681 changeColour(viewport.getGlobalColourScheme());
2683 modifyConservation_actionPerformed();
2686 public void abovePIDThreshold_actionPerformed()
2688 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2690 conservationMenuItem.setState(false);
2691 viewport.setConservationSelected(false);
2693 changeColour(viewport.getGlobalColourScheme());
2695 modifyPID_actionPerformed();
2698 public void sortPairwiseMenuItem_actionPerformed()
2700 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2701 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2702 .getAlignment().getSequenceAt(0), null);
2704 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2705 viewport.getAlignment()));
2706 alignPanel.paintAlignment(true);
2709 public void sortIDMenuItem_actionPerformed()
2711 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2712 AlignmentSorter.sortByID(viewport.getAlignment());
2713 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2714 viewport.getAlignment()));
2715 alignPanel.paintAlignment(true);
2718 public void sortLengthMenuItem_actionPerformed()
2720 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2721 AlignmentSorter.sortByLength(viewport.getAlignment());
2722 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2723 viewport.getAlignment()));
2724 alignPanel.paintAlignment(true);
2727 public void sortGroupMenuItem_actionPerformed()
2729 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730 AlignmentSorter.sortByGroup(viewport.getAlignment());
2731 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2732 viewport.getAlignment()));
2733 alignPanel.paintAlignment(true);
2737 public void removeRedundancyMenuItem_actionPerformed()
2739 new RedundancyPanel(alignPanel);
2742 public void pairwiseAlignmentMenuItem_actionPerformed()
2744 if (viewport.getSelectionGroup() != null
2745 && viewport.getSelectionGroup().getSize() > 1)
2747 Frame frame = new Frame();
2748 frame.add(new PairwiseAlignPanel(alignPanel));
2749 jalview.bin.JalviewLite.addFrame(frame,
2750 MessageManager.getString("action.pairwise_alignment"), 600,
2755 public void PCAMenuItem_actionPerformed()
2757 // are the sequences aligned?
2758 if (!viewport.getAlignment().isAligned(false))
2761 int Width = viewport.getAlignment().getWidth();
2763 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2765 current = viewport.getAlignment().getSequenceAt(i);
2767 if (current.getLength() < Width)
2769 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2772 alignPanel.paintAlignment(true);
2775 if ((viewport.getSelectionGroup() != null
2776 && viewport.getSelectionGroup().getSize() < 4 && viewport
2777 .getSelectionGroup().getSize() > 0)
2778 || viewport.getAlignment().getHeight() < 4)
2785 new PCAPanel(viewport);
2786 } catch (java.lang.OutOfMemoryError ex)
2792 public void averageDistanceTreeMenuItem_actionPerformed()
2794 NewTreePanel("AV", "PID", "Average distance tree using PID");
2797 public void neighbourTreeMenuItem_actionPerformed()
2799 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2802 protected void njTreeBlosumMenuItem_actionPerformed()
2804 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2807 protected void avTreeBlosumMenuItem_actionPerformed()
2809 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2812 void NewTreePanel(String type, String pwType, String title)
2814 // are the sequences aligned?
2815 if (!viewport.getAlignment().isAligned(false))
2818 int Width = viewport.getAlignment().getWidth();
2820 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2822 current = viewport.getAlignment().getSequenceAt(i);
2824 if (current.getLength() < Width)
2826 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2829 alignPanel.paintAlignment(true);
2833 if ((viewport.getSelectionGroup() != null && viewport
2834 .getSelectionGroup().getSize() > 1)
2835 || (viewport.getAlignment().getHeight() > 1))
2837 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2839 addTreeMenuItem(tp, title);
2841 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2845 void loadTree_actionPerformed()
2847 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2848 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2849 cap.setTreeImport();
2850 Frame frame = new Frame();
2852 jalview.bin.JalviewLite.addFrame(frame,
2853 MessageManager.getString("label.paste_newick_file"), 400, 300);
2856 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2858 TreePanel tp = new TreePanel(alignPanel, treeFile,
2859 MessageManager.getString("label.load_tree_from_file"), tree);
2860 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2861 addTreeMenuItem(tp, treeFile);
2865 * sort the alignment using the given treePanel
2868 * tree used to sort view
2870 * string used for undo event name
2872 public void sortByTree(TreePanel treePanel, String title)
2874 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2876 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2877 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2878 // HistoryItem.SORT));
2879 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2880 "label.order_by_params", new String[] { title }), oldOrder,
2881 viewport.getAlignment()));
2882 alignPanel.paintAlignment(true);
2886 * Do any automatic reordering of the alignment and add the necessary bits to
2887 * the menu structure for the new tree
2892 protected void addTreeMenuItem(final TreePanel treePanel,
2895 final MenuItem item = new MenuItem(title);
2896 sortByTreeMenu.add(item);
2897 item.addActionListener(new java.awt.event.ActionListener()
2900 public void actionPerformed(ActionEvent evt)
2902 sortByTree(treePanel, title); // treePanel.getTitle());
2906 treePanel.addWindowListener(new WindowAdapter()
2909 public void windowOpened(WindowEvent e)
2911 if (viewport.sortByTree)
2913 sortByTree(treePanel, title);
2915 super.windowOpened(e);
2919 public void windowClosing(WindowEvent e)
2921 sortByTreeMenu.remove(item);
2926 public boolean sortBy(AlignmentOrder alorder, String undoname)
2928 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2929 if (viewport.applet.debug)
2931 System.err.println("Sorting " + alorder.getOrder().size()
2932 + " in alignment '" + getTitle() + "'");
2934 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2935 if (undoname != null)
2937 addHistoryItem(new OrderCommand(undoname, oldOrder,
2938 viewport.getAlignment()));
2940 alignPanel.paintAlignment(true);
2944 protected void documentation_actionPerformed()
2946 alignPanel.av.applet.openJalviewHelpUrl();
2949 protected void about_actionPerformed()
2952 class AboutPanel extends Canvas
2958 public AboutPanel(String version, String builddate)
2960 this.version = version;
2961 this.builddate = builddate;
2965 public void paint(Graphics g)
2967 g.setColor(Color.white);
2968 g.fillRect(0, 0, getSize().width, getSize().height);
2969 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2970 FontMetrics fm = g.getFontMetrics();
2971 int fh = fm.getHeight();
2973 g.setColor(Color.black);
2974 // TODO: update this text for each release or centrally store it for
2975 // lite and application
2976 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2977 g.drawString(MessageManager.formatMessage(
2978 "label.jalviewLite_release", new String[] { version }), x,
2980 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2981 g.drawString(MessageManager.formatMessage(
2982 "label.jaview_build_date", new String[] { builddate }), x,
2984 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2985 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2987 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2988 x + 50, y += fh + 8);
2990 MessageManager.getString("label.jalview_dev_managers"), x,
2992 g.drawString(MessageManager
2993 .getString("label.jalview_distribution_lists"), x, y += fh);
2994 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2997 MessageManager.getString("label.jalview_cite_1_authors"),
3000 MessageManager.getString("label.jalview_cite_1_title"), x,
3002 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3007 Frame frame = new Frame();
3008 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3010 jalview.bin.JalviewLite.addFrame(frame,
3011 MessageManager.getString("label.jalview"), 580, 220);
3015 public void showURL(String url, String target)
3017 if (viewport.applet == null)
3019 System.out.println("Not running as applet - no browser available.");
3023 viewport.applet.showURL(url, target);
3027 // ////////////////////////////////////////////////////////////////////////////////
3028 // JBuilder Graphics here
3030 MenuBar alignFrameMenuBar = new MenuBar();
3032 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3034 MenuItem loadApplication = new MenuItem(
3035 MessageManager.getString("label.view_full_application"));
3037 MenuItem loadTree = new MenuItem(
3038 MessageManager.getString("label.load_associated_tree"));
3040 MenuItem loadAnnotations = new MenuItem(
3041 MessageManager.getString("label.load_features_annotations"));
3043 MenuItem outputFeatures = new MenuItem(
3044 MessageManager.getString("label.export_features"));
3046 MenuItem outputAnnotations = new MenuItem(
3047 MessageManager.getString("label.export_annotations"));
3049 MenuItem closeMenuItem = new MenuItem(
3050 MessageManager.getString("action.close"));
3052 MenuItem selectAllSequenceMenuItem = new MenuItem(
3053 MessageManager.getString("action.select_all"));
3055 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3056 MessageManager.getString("action.deselect_all"));
3058 MenuItem invertSequenceMenuItem = new MenuItem(
3059 MessageManager.getString("action.invert_selection"));
3061 MenuItem remove2LeftMenuItem = new MenuItem();
3063 MenuItem remove2RightMenuItem = new MenuItem();
3065 MenuItem removeGappedColumnMenuItem = new MenuItem();
3067 MenuItem removeAllGapsMenuItem = new MenuItem();
3069 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3071 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3073 MenuItem sortPairwiseMenuItem = new MenuItem();
3075 MenuItem sortIDMenuItem = new MenuItem();
3077 MenuItem sortLengthMenuItem = new MenuItem();
3079 MenuItem sortGroupMenuItem = new MenuItem();
3081 MenuItem removeRedundancyMenuItem = new MenuItem();
3083 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3085 MenuItem PCAMenuItem = new MenuItem();
3087 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3089 MenuItem neighbourTreeMenuItem = new MenuItem();
3091 BorderLayout borderLayout1 = new BorderLayout();
3093 public Label statusBar = new Label();
3095 MenuItem clustalColour = new MenuItem();
3097 MenuItem zappoColour = new MenuItem();
3099 MenuItem taylorColour = new MenuItem();
3101 MenuItem hydrophobicityColour = new MenuItem();
3103 MenuItem helixColour = new MenuItem();
3105 MenuItem strandColour = new MenuItem();
3107 MenuItem turnColour = new MenuItem();
3109 MenuItem buriedColour = new MenuItem();
3111 MenuItem purinePyrimidineColour = new MenuItem();
3113 // MenuItem RNAInteractionColour = new MenuItem();
3115 MenuItem RNAHelixColour = new MenuItem();
3117 MenuItem userDefinedColour = new MenuItem();
3119 MenuItem PIDColour = new MenuItem();
3121 MenuItem BLOSUM62Colour = new MenuItem();
3123 MenuItem tcoffeeColour = new MenuItem();
3125 MenuItem njTreeBlosumMenuItem = new MenuItem();
3127 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3129 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3131 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3133 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3135 MenuItem alProperties = new MenuItem(
3136 MessageManager.getString("label.alignment_props"));
3138 MenuItem overviewMenuItem = new MenuItem();
3140 MenuItem undoMenuItem = new MenuItem();
3142 MenuItem redoMenuItem = new MenuItem();
3144 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3146 MenuItem noColourmenuItem = new MenuItem();
3148 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3150 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3152 MenuItem findMenuItem = new MenuItem();
3154 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3156 MenuItem nucleotideColour = new MenuItem();
3158 MenuItem deleteGroups = new MenuItem();
3160 MenuItem grpsFromSelection = new MenuItem();
3162 MenuItem createGroup = new MenuItem();
3164 MenuItem unGroup = new MenuItem();
3166 MenuItem delete = new MenuItem();
3168 MenuItem copy = new MenuItem();
3170 MenuItem cut = new MenuItem();
3172 Menu pasteMenu = new Menu();
3174 MenuItem pasteNew = new MenuItem();
3176 MenuItem pasteThis = new MenuItem();
3178 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3180 MenuItem font = new MenuItem();
3182 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3184 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3186 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3188 MenuItem modifyPID = new MenuItem();
3190 MenuItem modifyConservation = new MenuItem();
3192 CheckboxMenuItem autoCalculate = null;
3194 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3195 "Sort Alignment With New Tree", true);
3197 Menu sortByTreeMenu = new Menu();
3199 MenuItem inputText = new MenuItem();
3201 MenuItem documentation = new MenuItem();
3203 MenuItem about = new MenuItem();
3205 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3207 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3209 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3211 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3213 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3215 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3217 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3219 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3221 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3224 * Initialise menus and other items
3228 private void jbInit() throws Exception
3230 setMenuBar(alignFrameMenuBar);
3233 * Configure File menu items and actions
3236 .setLabel(MessageManager.getString("label.input_from_textbox"));
3237 inputText.addActionListener(this);
3238 Menu outputTextboxMenu = new Menu(
3239 MessageManager.getString("label.out_to_textbox"));
3240 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3243 MenuItem item = new MenuItem(
3244 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3246 item.addActionListener(new java.awt.event.ActionListener()
3249 public void actionPerformed(ActionEvent e)
3251 outputText_actionPerformed(e);
3255 outputTextboxMenu.add(item);
3257 closeMenuItem.addActionListener(this);
3258 loadApplication.addActionListener(this);
3259 loadTree.addActionListener(this);
3260 loadAnnotations.addActionListener(this);
3261 outputFeatures.addActionListener(this);
3262 outputAnnotations.addActionListener(this);
3265 * Configure Edit menu items and actions
3267 undoMenuItem.setEnabled(false);
3268 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3269 undoMenuItem.addActionListener(this);
3270 redoMenuItem.setEnabled(false);
3271 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3272 redoMenuItem.addActionListener(this);
3273 copy.setLabel(MessageManager.getString("action.copy"));
3274 copy.addActionListener(this);
3275 cut.setLabel(MessageManager.getString("action.cut"));
3276 cut.addActionListener(this);
3277 delete.setLabel(MessageManager.getString("action.delete"));
3278 delete.addActionListener(this);
3279 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3280 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3281 pasteNew.addActionListener(this);
3282 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3283 pasteThis.addActionListener(this);
3284 remove2LeftMenuItem.setLabel(MessageManager
3285 .getString("action.remove_left"));
3286 remove2LeftMenuItem.addActionListener(this);
3287 remove2RightMenuItem.setLabel(MessageManager
3288 .getString("action.remove_right"));
3289 remove2RightMenuItem.addActionListener(this);
3290 removeGappedColumnMenuItem.setLabel(MessageManager
3291 .getString("action.remove_empty_columns"));
3292 removeGappedColumnMenuItem.addActionListener(this);
3293 removeAllGapsMenuItem.setLabel(MessageManager
3294 .getString("action.remove_all_gaps"));
3295 removeAllGapsMenuItem.addActionListener(this);
3296 removeRedundancyMenuItem.setLabel(MessageManager
3297 .getString("action.remove_redundancy"));
3298 removeRedundancyMenuItem.addActionListener(this);
3301 * Configure Select menu items and actions
3303 findMenuItem.setLabel(MessageManager.getString("action.find"));
3304 findMenuItem.addActionListener(this);
3305 selectAllSequenceMenuItem.addActionListener(this);
3306 deselectAllSequenceMenuItem.addActionListener(this);
3307 invertSequenceMenuItem.setLabel(MessageManager
3308 .getString("action.invert_sequence_selection"));
3309 invertSequenceMenuItem.addActionListener(this);
3310 invertColSel.setLabel(MessageManager
3311 .getString("action.invert_column_selection"));
3312 invertColSel.addActionListener(this);
3313 deleteGroups.setLabel(MessageManager
3314 .getString("action.undefine_groups"));
3315 deleteGroups.addActionListener(this);
3316 grpsFromSelection.setLabel(MessageManager
3317 .getString("action.make_groups_selection"));
3318 grpsFromSelection.addActionListener(this);
3319 createGroup.setLabel(MessageManager.getString("action.create_group"));
3320 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3321 annotationColumnSelection.setLabel(MessageManager
3322 .getString("action.select_by_annotation"));
3323 annotationColumnSelection.addActionListener(this);
3326 * Configure View menu items and actions
3328 newView.setLabel(MessageManager.getString("action.new_view"));
3329 newView.addActionListener(this);
3330 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3331 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3332 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3333 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3335 .setLabel(MessageManager.getString("label.selected_columns"));
3336 hideSequences.setLabel(MessageManager
3337 .getString("label.selected_sequences"));
3338 hideAllButSelection.setLabel(MessageManager
3339 .getString("label.all_but_selected_region"));
3340 hideAllSelection.setLabel(MessageManager
3341 .getString("label.selected_region"));
3342 showAllHidden.setLabel(MessageManager
3343 .getString("label.all_sequences_columns"));
3344 showColumns.addActionListener(this);
3345 showSeqs.addActionListener(this);
3346 hideColumns.addActionListener(this);
3347 hideSequences.addActionListener(this);
3348 hideAllButSelection.addActionListener(this);
3349 hideAllSelection.addActionListener(this);
3350 showAllHidden.addActionListener(this);
3351 featureSettings.setLabel(MessageManager
3352 .getString("action.feature_settings"));
3353 featureSettings.addActionListener(this);
3354 sequenceFeatures.setLabel(MessageManager
3355 .getString("label.show_sequence_features"));
3356 sequenceFeatures.addItemListener(this);
3357 sequenceFeatures.setState(false);
3358 followMouseOverFlag.setLabel(MessageManager
3359 .getString("label.automatic_scrolling"));
3360 followMouseOverFlag.addItemListener(this);
3361 alProperties.addActionListener(this);
3362 overviewMenuItem.setLabel(MessageManager
3363 .getString("label.overview_window"));
3364 overviewMenuItem.addActionListener(this);
3367 * Configure Annotations menu items and actions
3369 annotationPanelMenuItem.setLabel(MessageManager
3370 .getString("label.show_annotations"));
3371 annotationPanelMenuItem.addItemListener(this);
3372 showGroupConsensus.setLabel(MessageManager
3373 .getString("label.group_consensus"));
3374 showGroupConservation.setLabel(MessageManager
3375 .getString("label.group_conservation"));
3376 showConsensusHistogram.setLabel(MessageManager
3377 .getString("label.show_consensus_histogram"));
3378 showSequenceLogo.setLabel(MessageManager
3379 .getString("label.show_consensus_logo"));
3380 normSequenceLogo.setLabel(MessageManager
3381 .getString("label.norm_consensus_logo"));
3382 applyAutoAnnotationSettings.setLabel(MessageManager
3383 .getString("label.apply_all_groups"));
3384 applyAutoAnnotationSettings.setState(true);
3385 Menu autoAnnMenu = new Menu(
3386 MessageManager.getString("label.autocalculated_annotation"));
3387 showGroupConsensus.addItemListener(this);
3388 showGroupConservation.addItemListener(this);
3389 showConsensusHistogram.addItemListener(this);
3390 showSequenceLogo.addItemListener(this);
3391 normSequenceLogo.addItemListener(this);
3392 applyAutoAnnotationSettings.addItemListener(this);
3393 showAlignmentAnnotations = new CheckboxMenuItem(
3394 MessageManager.getString("label.show_all_al_annotations"));
3395 showSequenceAnnotations = new CheckboxMenuItem(
3396 MessageManager.getString("label.show_all_seq_annotations"));
3397 sortAnnBySequence = new CheckboxMenuItem(
3398 MessageManager.getString("label.sort_annotations_by_sequence"));
3399 sortAnnByLabel = new CheckboxMenuItem(
3400 MessageManager.getString("label.sort_annotations_by_label"));
3401 showAutoFirst = new CheckboxMenuItem(
3402 MessageManager.getString("label.show_first"));
3403 showAutoFirst.setState(false); // pending applet parameter
3404 setShowAutoCalculatedAbove(showAutoFirst.getState());
3405 showAutoLast = new CheckboxMenuItem(
3406 MessageManager.getString("label.show_last"));
3407 showAutoLast.setState(!showAutoFirst.getState());
3408 showAlignmentAnnotations.addItemListener(this);
3409 showSequenceAnnotations.addItemListener(this);
3410 sortAnnBySequence.addItemListener(this);
3411 sortAnnByLabel.addItemListener(this);
3412 showAutoFirst.addItemListener(this);
3413 showAutoLast.addItemListener(this);
3416 * Configure Format menu items and actions
3418 font.setLabel(MessageManager.getString("action.font"));
3419 font.addActionListener(this);
3420 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3421 scaleAbove.setState(true);
3422 scaleAbove.setEnabled(false);
3423 scaleAbove.addItemListener(this);
3424 scaleLeft.setEnabled(false);
3425 scaleLeft.setState(true);
3426 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3427 scaleLeft.addItemListener(this);
3428 scaleRight.setEnabled(false);
3429 scaleRight.setState(true);
3430 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3431 scaleRight.addItemListener(this);
3432 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3433 viewBoxesMenuItem.setState(true);
3434 viewBoxesMenuItem.addItemListener(this);
3435 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3436 viewTextMenuItem.setState(true);
3437 viewTextMenuItem.addItemListener(this);
3438 colourTextMenuItem.setLabel(MessageManager
3439 .getString("label.colour_text"));
3440 colourTextMenuItem.addItemListener(this);
3441 displayNonconservedMenuItem.setLabel(MessageManager
3442 .getString("label.show_non_conversed"));
3443 displayNonconservedMenuItem.addItemListener(this);
3444 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3445 wrapMenuItem.addItemListener(this);
3446 renderGapsMenuItem.setLabel(MessageManager
3447 .getString("action.show_gaps"));
3448 renderGapsMenuItem.setState(true);
3449 renderGapsMenuItem.addItemListener(this);
3450 centreColumnLabelFlag.setLabel(MessageManager
3451 .getString("label.centre_column_labels"));
3452 centreColumnLabelFlag.addItemListener(this);
3453 seqLimits.setState(true);
3454 seqLimits.setLabel(MessageManager
3455 .getString("label.show_sequence_limits"));
3456 seqLimits.addItemListener(this);
3459 * Configure Colour menu items and actions
3461 applyToAllGroups.setLabel(MessageManager
3462 .getString("label.apply_colour_to_all_groups"));
3463 applyToAllGroups.setState(true);
3464 applyToAllGroups.addItemListener(this);
3465 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3466 clustalColour.addActionListener(this);
3467 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3468 zappoColour.addActionListener(this);
3469 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3470 taylorColour.addActionListener(this);
3471 hydrophobicityColour.setLabel(MessageManager
3472 .getString("label.hydrophobicity"));
3473 hydrophobicityColour.addActionListener(this);
3475 .setLabel(MessageManager.getString("label.helix_propensity"));
3476 helixColour.addActionListener(this);
3477 strandColour.setLabel(MessageManager
3478 .getString("label.strand_propensity"));
3479 strandColour.addActionListener(this);
3480 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3481 turnColour.addActionListener(this);
3482 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3483 buriedColour.addActionListener(this);
3484 purinePyrimidineColour.setLabel(MessageManager
3485 .getString("label.purine_pyrimidine"));
3486 purinePyrimidineColour.addActionListener(this);
3487 // RNAInteractionColour.setLabel(MessageManager
3488 // .getString("label.rna_interaction"));
3489 // RNAInteractionColour.addActionListener(this);
3490 RNAHelixColour.setLabel(MessageManager
3491 .getString("action.by_rna_helixes"));
3492 RNAHelixColour.addActionListener(this);
3493 userDefinedColour.setLabel(MessageManager
3494 .getString("action.user_defined"));
3495 userDefinedColour.addActionListener(this);
3496 PIDColour.setLabel(MessageManager
3497 .getString("label.percentage_identity"));
3498 PIDColour.addActionListener(this);
3499 BLOSUM62Colour.setLabel(MessageManager
3500 .getString("label.blosum62_score"));
3501 BLOSUM62Colour.addActionListener(this);
3503 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3504 // it will be enabled only if a score file is provided
3505 tcoffeeColour.setEnabled(false);
3506 tcoffeeColour.addActionListener(this);
3507 conservationMenuItem.setLabel(MessageManager
3508 .getString("action.by_conservation"));
3509 conservationMenuItem.addItemListener(this);
3510 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3511 noColourmenuItem.addActionListener(this);
3512 abovePIDThreshold.setLabel(MessageManager
3513 .getString("label.above_identity_threshold"));
3514 abovePIDThreshold.addItemListener(this);
3515 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3516 nucleotideColour.addActionListener(this);
3517 modifyPID.setLabel(MessageManager
3518 .getString("label.modify_identity_thereshold"));
3519 modifyPID.addActionListener(this);
3520 modifyConservation.setLabel(MessageManager
3521 .getString("label.modify_conservation_thereshold"));
3522 modifyConservation.addActionListener(this);
3523 annotationColour.setLabel(MessageManager
3524 .getString("action.by_annotation"));
3525 annotationColour.addActionListener(this);
3528 * Configure Calculate menu items and actions
3530 sortPairwiseMenuItem.setLabel(MessageManager
3531 .getString("action.by_pairwise_id"));
3532 sortPairwiseMenuItem.addActionListener(this);
3533 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3534 sortIDMenuItem.addActionListener(this);
3535 sortLengthMenuItem.setLabel(MessageManager
3536 .getString("action.by_length"));
3537 sortLengthMenuItem.addActionListener(this);
3538 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3539 sortGroupMenuItem.addActionListener(this);
3540 pairwiseAlignmentMenuItem.setLabel(MessageManager
3541 .getString("action.pairwise_alignment"));
3542 pairwiseAlignmentMenuItem.addActionListener(this);
3543 PCAMenuItem.setLabel(MessageManager
3544 .getString("label.principal_component_analysis"));
3545 PCAMenuItem.addActionListener(this);
3546 autoCalculate = new CheckboxMenuItem(
3547 MessageManager.getString("label.autocalculate_consensus"), true);
3548 averageDistanceTreeMenuItem.setLabel(MessageManager
3549 .getString("label.average_distance_identity"));
3550 averageDistanceTreeMenuItem.addActionListener(this);
3551 neighbourTreeMenuItem.setLabel(MessageManager
3552 .getString("label.neighbour_joining_identity"));
3553 neighbourTreeMenuItem.addActionListener(this);
3554 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3555 .getString("label.average_distance_bloslum62"));
3556 avDistanceTreeBlosumMenuItem.addActionListener(this);
3557 njTreeBlosumMenuItem.setLabel(MessageManager
3558 .getString("label.neighbour_blosum62"));
3559 njTreeBlosumMenuItem.addActionListener(this);
3560 sortByTreeMenu.setLabel(MessageManager
3561 .getString("action.by_tree_order"));
3562 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3563 Menu calculateTreeMenu = new Menu(
3564 MessageManager.getString("action.calculate_tree"));
3565 autoCalculate.addItemListener(this);
3566 sortByTree.addItemListener(this);
3569 * Configure Help menu items and actions
3571 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3572 documentation.setLabel(MessageManager.getString("label.documentation"));
3573 documentation.addActionListener(this);
3574 about.setLabel(MessageManager.getString("label.about"));
3575 about.addActionListener(this);
3578 * Add top level menus to frame
3580 alignFrameMenuBar.add(fileMenu);
3581 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3582 alignFrameMenuBar.add(editMenu);
3583 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3584 alignFrameMenuBar.add(selectMenu);
3585 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3586 alignFrameMenuBar.add(viewMenu);
3587 Menu annotationsMenu = new Menu(
3588 MessageManager.getString("action.annotations"));
3589 alignFrameMenuBar.add(annotationsMenu);
3590 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3591 alignFrameMenuBar.add(formatMenu);
3592 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3593 alignFrameMenuBar.add(colourMenu);
3594 Menu calculateMenu = new Menu(
3595 MessageManager.getString("action.calculate"));
3596 alignFrameMenuBar.add(calculateMenu);
3597 alignFrameMenuBar.add(helpMenu);
3602 fileMenu.add(inputText);
3603 fileMenu.add(loadTree);
3604 fileMenu.add(loadAnnotations);
3605 fileMenu.addSeparator();
3606 fileMenu.add(outputTextboxMenu);
3607 fileMenu.add(outputFeatures);
3608 fileMenu.add(outputAnnotations);
3609 if (jalviewServletURL != null)
3611 fileMenu.add(loadApplication);
3613 fileMenu.addSeparator();
3614 fileMenu.add(closeMenuItem);
3619 editMenu.add(undoMenuItem);
3620 editMenu.add(redoMenuItem);
3623 pasteMenu.add(pasteNew);
3624 pasteMenu.add(pasteThis);
3625 editMenu.add(pasteMenu);
3626 editMenu.add(delete);
3627 editMenu.addSeparator();
3628 editMenu.add(remove2LeftMenuItem);
3629 editMenu.add(remove2RightMenuItem);
3630 editMenu.add(removeGappedColumnMenuItem);
3631 editMenu.add(removeAllGapsMenuItem);
3632 editMenu.add(removeRedundancyMenuItem);
3637 selectMenu.add(findMenuItem);
3638 selectMenu.addSeparator();
3639 selectMenu.add(selectAllSequenceMenuItem);
3640 selectMenu.add(deselectAllSequenceMenuItem);
3641 selectMenu.add(invertSequenceMenuItem);
3642 selectMenu.add(invertColSel);
3643 selectMenu.add(createGroup);
3644 selectMenu.add(unGroup);
3645 selectMenu.add(grpsFromSelection);
3646 selectMenu.add(deleteGroups);
3647 selectMenu.add(annotationColumnSelection);
3652 viewMenu.add(newView);
3653 viewMenu.addSeparator();
3654 showMenu.add(showColumns);
3655 showMenu.add(showSeqs);
3656 showMenu.add(showAllHidden);
3657 viewMenu.add(showMenu);
3658 hideMenu.add(hideColumns);
3659 hideMenu.add(hideSequences);
3660 hideMenu.add(hideAllSelection);
3661 hideMenu.add(hideAllButSelection);
3662 viewMenu.add(hideMenu);
3663 viewMenu.addSeparator();
3664 viewMenu.add(followMouseOverFlag);
3665 viewMenu.addSeparator();
3666 viewMenu.add(sequenceFeatures);
3667 viewMenu.add(featureSettings);
3668 viewMenu.addSeparator();
3669 viewMenu.add(alProperties);
3670 viewMenu.addSeparator();
3671 viewMenu.add(overviewMenuItem);
3676 annotationsMenu.add(annotationPanelMenuItem);
3677 annotationsMenu.addSeparator();
3678 annotationsMenu.add(showAlignmentAnnotations);
3679 annotationsMenu.add(showSequenceAnnotations);
3680 annotationsMenu.add(sortAnnBySequence);
3681 annotationsMenu.add(sortAnnByLabel);
3682 annotationsMenu.addSeparator();
3683 autoAnnMenu.add(showAutoFirst);
3684 autoAnnMenu.add(showAutoLast);
3685 autoAnnMenu.addSeparator();
3686 autoAnnMenu.add(applyAutoAnnotationSettings);
3687 autoAnnMenu.add(showConsensusHistogram);
3688 autoAnnMenu.add(showSequenceLogo);
3689 autoAnnMenu.add(normSequenceLogo);
3690 autoAnnMenu.addSeparator();
3691 autoAnnMenu.add(showGroupConservation);
3692 autoAnnMenu.add(showGroupConsensus);
3693 annotationsMenu.add(autoAnnMenu);
3698 formatMenu.add(font);
3699 formatMenu.add(seqLimits);
3700 formatMenu.add(wrapMenuItem);
3701 formatMenu.add(scaleAbove);
3702 formatMenu.add(scaleLeft);
3703 formatMenu.add(scaleRight);
3704 formatMenu.add(viewBoxesMenuItem);
3705 formatMenu.add(viewTextMenuItem);
3706 formatMenu.add(colourTextMenuItem);
3707 formatMenu.add(displayNonconservedMenuItem);
3708 formatMenu.add(renderGapsMenuItem);
3709 formatMenu.add(centreColumnLabelFlag);
3714 colourMenu.add(applyToAllGroups);
3715 colourMenu.addSeparator();
3716 colourMenu.add(noColourmenuItem);
3717 colourMenu.add(clustalColour);
3718 colourMenu.add(BLOSUM62Colour);
3719 colourMenu.add(PIDColour);
3720 colourMenu.add(zappoColour);
3721 colourMenu.add(taylorColour);
3722 colourMenu.add(hydrophobicityColour);
3723 colourMenu.add(helixColour);
3724 colourMenu.add(strandColour);
3725 colourMenu.add(turnColour);
3726 colourMenu.add(buriedColour);
3727 colourMenu.add(nucleotideColour);
3728 colourMenu.add(purinePyrimidineColour);
3729 // colourMenu.add(RNAInteractionColour);
3730 colourMenu.add(tcoffeeColour);
3731 colourMenu.add(userDefinedColour);
3732 colourMenu.addSeparator();
3733 colourMenu.add(conservationMenuItem);
3734 colourMenu.add(modifyConservation);
3735 colourMenu.add(abovePIDThreshold);
3736 colourMenu.add(modifyPID);
3737 colourMenu.add(annotationColour);
3738 colourMenu.add(RNAHelixColour);
3743 sortMenu.add(sortIDMenuItem);
3744 sortMenu.add(sortLengthMenuItem);
3745 sortMenu.add(sortByTreeMenu);
3746 sortMenu.add(sortGroupMenuItem);
3747 sortMenu.add(sortPairwiseMenuItem);
3748 calculateMenu.add(sortMenu);
3749 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3750 calculateTreeMenu.add(neighbourTreeMenuItem);
3751 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3752 calculateTreeMenu.add(njTreeBlosumMenuItem);
3753 calculateMenu.add(calculateTreeMenu);
3754 calculateMenu.addSeparator();
3755 calculateMenu.add(pairwiseAlignmentMenuItem);
3756 calculateMenu.add(PCAMenuItem);
3757 calculateMenu.add(autoCalculate);
3758 calculateMenu.add(sortByTree);
3763 helpMenu.add(documentation);
3764 helpMenu.add(about);
3769 statusBar.setBackground(Color.white);
3770 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3771 statusBar.setText(MessageManager.getString("label.status_bar"));
3772 this.add(statusBar, BorderLayout.SOUTH);
3776 public void setStatus(String string)
3778 statusBar.setText(string);
3781 MenuItem featureSettings = new MenuItem();
3783 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3785 MenuItem annotationColour = new MenuItem();
3787 MenuItem annotationColumnSelection = new MenuItem();
3789 MenuItem invertColSel = new MenuItem();
3791 MenuItem showColumns = new MenuItem();
3793 MenuItem showSeqs = new MenuItem();
3795 MenuItem hideColumns = new MenuItem();
3797 MenuItem hideSequences = new MenuItem();
3799 MenuItem hideAllButSelection = new MenuItem();
3801 MenuItem hideAllSelection = new MenuItem();
3803 MenuItem showAllHidden = new MenuItem();
3805 MenuItem newView = new MenuItem();
3807 private CheckboxMenuItem showAlignmentAnnotations;
3809 private CheckboxMenuItem showSequenceAnnotations;
3811 private CheckboxMenuItem sortAnnBySequence;
3813 private CheckboxMenuItem sortAnnByLabel;
3815 private CheckboxMenuItem showAutoFirst;
3817 private CheckboxMenuItem showAutoLast;
3819 private SplitFrame splitFrame;
3822 * Attach the alignFrame panels after embedding menus, if necessary. This used
3823 * to be called setEmbedded, but is now creates the dropdown menus in a
3824 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3826 * @param reallyEmbedded
3827 * true to attach the view to the applet area on the page rather than
3830 public void createAlignFrameWindow(boolean reallyEmbedded)
3834 embedAlignFrameInApplet(viewport.applet);
3839 // test and embed menu bar if necessary.
3841 if (embedMenuIfNeeded(alignPanel))
3844 * adjust for status bar height too. ? pointless as overridden by layout
3847 alignPanel.setSize(getSize().width,
3848 getSize().height - statusBar.getHeight());
3850 add(statusBar, BorderLayout.SOUTH);
3851 add(alignPanel, BorderLayout.CENTER);
3852 // and register with the applet so it can pass external API calls to us
3853 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3859 * Add the components of this AlignFrame to the applet container.
3863 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3866 // Explicitly build the embedded menu panel for the on-page applet
3868 // view cannot be closed if its actually on the page
3869 fileMenu.remove(closeMenuItem);
3870 fileMenu.remove(3); // Remove Separator
3871 // construct embedded menu, using default font
3872 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3873 // and actually add the components to the applet area
3874 theApplet.setLayout(new BorderLayout());
3875 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3876 theApplet.add(statusBar, BorderLayout.SOUTH);
3877 // TODO should size be left to the layout manager?
3878 alignPanel.setSize(theApplet.getSize().width,
3879 theApplet.getSize().height - embeddedMenu.getHeight()
3880 - statusBar.getHeight());
3881 theApplet.add(alignPanel, BorderLayout.CENTER);
3882 final AlignFrame me = this;
3883 theApplet.addFocusListener(new FocusListener()
3887 public void focusLost(FocusEvent e)
3889 if (theApplet.currentAlignFrame == me)
3891 theApplet.currentAlignFrame = null;
3896 public void focusGained(FocusEvent e)
3898 theApplet.currentAlignFrame = me;
3901 theApplet.validate();
3905 * create a new binding between structures in an existing jmol viewer instance
3906 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3907 * this does not open a new Jmol window, or modify the display of the
3908 * structures in the original jmol window. Note This method doesn't work
3909 * without an additional javascript library to exchange messages between the
3910 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3913 * JmolViewer instance
3914 * @param sequenceIds
3915 * - sequence Ids to search for associations
3917 public SequenceStructureBinding addStructureViewInstance(
3918 Object jmolviewer, String[] sequenceIds)
3920 Viewer viewer = null;
3923 viewer = (Viewer) jmolviewer;
3924 } catch (ClassCastException ex)
3926 System.err.println("Unsupported viewer object :"
3927 + jmolviewer.getClass());
3931 System.err.println("Can't use this object as a structure viewer:"
3932 + jmolviewer.getClass());
3935 SequenceI[] seqs = null;
3936 if (sequenceIds == null || sequenceIds.length == 0)
3938 seqs = viewport.getAlignment().getSequencesArray();
3942 Vector sqi = new Vector();
3943 AlignmentI al = viewport.getAlignment();
3944 for (int sid = 0; sid < sequenceIds.length; sid++)
3946 SequenceI sq = al.findName(sequenceIds[sid]);
3954 seqs = new SequenceI[sqi.size()];
3955 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3957 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3965 AAStructureBindingModel jmv = null;
3966 // TODO: search for a jmv that involves viewer
3968 { // create a new viewer/jalview binding.
3969 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3976 * bind a pdb file to a sequence in the current view
3979 * - sequenceId within the dataset.
3980 * @param pdbEntryString
3981 * - the short name for the PDB file
3983 * - pdb file - either a URL or a valid PDB file.
3984 * @return true if binding was as success TODO: consider making an exception
3985 * structure for indicating when PDB parsing or sequenceId location
3988 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3991 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3992 boolean needtoadd = false;
3993 if (toaddpdb != null)
3995 Vector pdbe = toaddpdb.getAllPDBEntries();
3996 PDBEntry pdbentry = null;
3997 if (pdbe != null && pdbe.size() > 0)
3999 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4001 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4002 if (!pdbentry.getId().equals(pdbEntryString)
4003 && !pdbentry.getFile().equals(pdbFile))
4013 if (pdbentry == null)
4015 pdbentry = new PDBEntry();
4016 pdbentry.setId(pdbEntryString);
4017 pdbentry.setFile(pdbFile);
4018 needtoadd = true; // add this new entry to sequence.
4020 // resolve data source
4021 // TODO: this code should be a refactored to an io package
4022 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4023 if (protocol == null)
4029 // make a note of the access mode and add
4030 if (pdbentry.getProperty() == null)
4032 pdbentry.setProperty(new Hashtable());
4034 pdbentry.getProperty().put("protocol", protocol);
4035 toaddpdb.addPDBId(pdbentry);
4036 alignPanel.getStructureSelectionManager()
4037 .registerPDBEntry(pdbentry);
4043 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4047 Vector sequences = new Vector();
4048 for (int i = 0; i < seqs.length; i++)
4050 if (seqs[i] != null)
4052 sequences.addElement(new Object[] { seqs[i],
4053 (chains != null) ? chains[i] : null });
4056 seqs = new SequenceI[sequences.size()];
4057 chains = new String[sequences.size()];
4058 for (int i = 0, isize = sequences.size(); i < isize; i++)
4060 Object[] oj = (Object[]) sequences.elementAt(i);
4062 seqs[i] = (SequenceI) oj[0];
4063 chains[i] = (String) oj[1];
4066 return new Object[] { seqs, chains };
4070 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4071 SequenceI[] seqs, String[] chains, String protocol)
4073 // Scrub any null sequences from the array
4074 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4075 seqs = (SequenceI[]) sqch[0];
4076 chains = (String[]) sqch[1];
4077 if (seqs == null || seqs.length == 0)
4080 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4082 if (protocol == null || protocol.trim().length() == 0
4083 || protocol.equals("null"))
4085 protocol = (String) pdb.getProperty().get("protocol");
4086 if (protocol == null)
4088 System.err.println("Couldn't work out protocol to open structure: "
4093 if (applet.useXtrnalSviewer)
4095 // register the association(s) and quit, don't create any windows.
4096 if (StructureSelectionManager.getStructureSelectionManager(applet)
4097 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4099 System.err.println("Failed to map " + pdb.getFile() + " ("
4100 + protocol + ") to any sequences");
4104 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4106 // can only do alignments with Jmol
4107 // find the last jmol window assigned to this alignment
4108 jalview.appletgui.AppletJmol ajm = null, tajm;
4109 Vector jmols = applet
4110 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4111 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4113 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4114 if (tajm.ap.alignFrame == this)
4123 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4124 // try and add the pdb structure
4129 // otherwise, create a new window
4130 if (applet.jmolAvailable)
4132 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4134 applet.lastFrameX += 40;
4135 applet.lastFrameY += 40;
4139 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4144 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4145 SequenceI[][] seqs, String[][] chains, String[] protocols)
4147 // TODO Auto-generated method stub
4148 System.err.println("Aligned Structure View: Not yet implemented.");
4152 * modify the current selection, providing the user has not made a selection
4156 * - sequences from this alignment
4158 * - columns to be selected on the alignment
4160 public void select(SequenceGroup sel, ColumnSelection csel)
4162 alignPanel.seqPanel.selection(sel, csel, null);
4165 public void scrollTo(int row, int column)
4167 alignPanel.seqPanel.scrollTo(row, column);
4170 public void scrollToRow(int row)
4172 alignPanel.seqPanel.scrollToRow(row);
4175 public void scrollToColumn(int column)
4177 alignPanel.seqPanel.scrollToColumn(column);
4181 * @return the alignments unique ID.
4183 public String getSequenceSetId()
4185 return viewport.getSequenceSetId();
4189 * Load the (T-Coffee) score file from the specified url
4192 * File/URL/T-COFFEE score file contents
4193 * @throws IOException
4194 * @return true if alignment was annotated with data from source
4196 public boolean loadScoreFile(String source) throws IOException
4199 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4200 AppletFormatAdapter.checkProtocol(source));
4201 if (!file.isValid())
4203 // TODO: raise dialog for gui
4204 System.err.println("Problems parsing T-Coffee scores: "
4205 + file.getWarningMessage());
4206 System.err.println("Origin was:\n" + source);
4211 * check that the score matrix matches the alignment dimensions
4214 if ((aln = viewport.getAlignment()) != null
4215 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4218 // TODO: raise a dialog box here rather than bomb out.
4220 .println("The scores matrix does not match the alignment dimensions");
4224 // TODO add parameter to indicate if matching should be done
4225 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4227 alignPanel.fontChanged();
4228 tcoffeeColour.setEnabled(true);
4229 // switch to this color
4230 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4235 System.err.println("Problems resolving T-Coffee scores:");
4236 if (file.getWarningMessage() != null)
4238 System.err.println(file.getWarningMessage());
4244 public SplitFrame getSplitFrame()
4246 return this.splitFrame;
4249 public void setSplitFrame(SplitFrame sf)
4251 this.splitFrame = sf;
4254 // may not need this
4256 public void setShowSeqFeatures(boolean b)
4258 // showSeqFeatures.setSelected(b);
4259 viewport.setShowSequenceFeatures(b);
4264 public void setMenusForViewport()
4266 // setMenusFromViewport(viewport);
4271 public void refreshFeatureUI(boolean enableIfNecessary)
4273 if (enableIfNecessary)
4275 sequenceFeatures.setState(true);
4276 alignPanel.av.setShowSequenceFeatures(true);
4281 public FeatureSettingsControllerI getFeatureSettingsUI()
4283 return alignPanel.av.featureSettings;