2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.api.FeatureSettingsControllerI;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.OrderCommand;
37 import jalview.commands.RemoveGapColCommand;
38 import jalview.commands.RemoveGapsCommand;
39 import jalview.commands.SlideSequencesCommand;
40 import jalview.commands.TrimRegionCommand;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AnnotationFile;
51 import jalview.io.AppletFormatAdapter;
52 import jalview.io.DataSourceType;
53 import jalview.io.FeaturesFile;
54 import jalview.io.FileFormat;
55 import jalview.io.TCoffeeScoreFile;
56 import jalview.schemes.Blosum62ColourScheme;
57 import jalview.schemes.BuriedColourScheme;
58 import jalview.schemes.ClustalxColourScheme;
59 import jalview.schemes.ColourSchemeI;
60 import jalview.schemes.HelixColourScheme;
61 import jalview.schemes.HydrophobicColourScheme;
62 import jalview.schemes.NucleotideColourScheme;
63 import jalview.schemes.PIDColourScheme;
64 import jalview.schemes.PurinePyrimidineColourScheme;
65 import jalview.schemes.RNAHelicesColour;
66 import jalview.schemes.StrandColourScheme;
67 import jalview.schemes.TCoffeeColourScheme;
68 import jalview.schemes.TaylorColourScheme;
69 import jalview.schemes.TurnColourScheme;
70 import jalview.schemes.ZappoColourScheme;
71 import jalview.structure.StructureSelectionManager;
72 import jalview.structures.models.AAStructureBindingModel;
73 import jalview.util.MappingUtils;
74 import jalview.util.MessageManager;
75 import jalview.viewmodel.AlignmentViewport;
77 import java.awt.BorderLayout;
78 import java.awt.Canvas;
79 import java.awt.CheckboxMenuItem;
80 import java.awt.Color;
81 import java.awt.FlowLayout;
83 import java.awt.FontMetrics;
84 import java.awt.Frame;
85 import java.awt.Graphics;
86 import java.awt.Label;
88 import java.awt.MenuBar;
89 import java.awt.MenuItem;
90 import java.awt.Panel;
91 import java.awt.event.ActionEvent;
92 import java.awt.event.ActionListener;
93 import java.awt.event.FocusEvent;
94 import java.awt.event.FocusListener;
95 import java.awt.event.ItemEvent;
96 import java.awt.event.ItemListener;
97 import java.awt.event.KeyEvent;
98 import java.awt.event.KeyListener;
99 import java.awt.event.WindowAdapter;
100 import java.awt.event.WindowEvent;
101 import java.io.IOException;
103 import java.net.URLEncoder;
104 import java.util.Arrays;
105 import java.util.Deque;
106 import java.util.HashMap;
107 import java.util.List;
108 import java.util.Map;
109 import java.util.StringTokenizer;
110 import java.util.Vector;
112 import org.jmol.viewer.Viewer;
114 public class AlignFrame extends EmbmenuFrame implements ActionListener,
115 ItemListener, KeyListener, AlignViewControllerGuiI
117 public AlignViewControllerI avc;
119 public AlignmentPanel alignPanel;
121 public AlignViewport viewport;
123 // width and height may be overridden by applet parameters
124 int frameWidth = 700;
126 int frameHeight = 500;
128 String jalviewServletURL;
131 * Flag for showing autocalculated consensus above or below other consensus
134 private boolean showAutoCalculatedAbove;
136 private SequenceAnnotationOrder annotationSortOrder;
139 * Constructor that creates the frame and adds it to the display.
146 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
149 this(al, applet, title, embedded, true);
153 * Constructor that optionally allows the frame to be displayed or only
160 * @param addToDisplay
162 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
163 boolean embedded, boolean addToDisplay)
165 this(al, null, null, applet, title, embedded, addToDisplay);
168 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
169 ColumnSelection columnSelection, JalviewLite applet,
170 String title, boolean embedded)
172 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 ColumnSelection columnSelection, JalviewLite applet,
177 String title, boolean embedded, boolean addToDisplay)
181 jalviewServletURL = applet.getParameter("APPLICATION_URL");
187 } catch (Exception ex)
189 ex.printStackTrace();
191 // need to get window geometry before we calculate alignment layout
197 param = applet.getParameter("windowWidth");
200 int width = Integer.parseInt(param);
203 param = applet.getParameter("windowHeight");
206 int height = Integer.parseInt(param);
207 frameHeight = height;
209 } catch (Exception ex)
213 viewport = new AlignViewport(al, applet);
215 if (hiddenSeqs != null && hiddenSeqs.length > 0)
217 viewport.hideSequence(hiddenSeqs);
219 if (columnSelection != null)
221 viewport.setColumnSelection(columnSelection);
223 viewport.setScaleAboveWrapped(scaleAbove.getState());
225 alignPanel = new AlignmentPanel(this, viewport);
226 avc = new jalview.controller.AlignViewController(this, viewport,
228 viewport.updateConservation(alignPanel);
229 viewport.updateConsensus(alignPanel);
231 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
232 followMouseOverFlag.setState(viewport.isFollowHighlight());
233 showGroupConsensus.setState(viewport.isShowGroupConsensus());
234 showGroupConservation.setState(viewport.isShowGroupConservation());
235 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
236 showSequenceLogo.setState(viewport.isShowSequenceLogo());
237 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
238 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
239 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
240 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
241 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
242 showAlignmentAnnotations.setState(true);
243 showSequenceAnnotations.setState(false);
245 seqLimits.setState(viewport.getShowJVSuffix());
249 String param = applet.getParameter("sortBy");
252 if (param.equalsIgnoreCase("Id"))
254 sortIDMenuItem_actionPerformed();
256 else if (param.equalsIgnoreCase("Pairwise Identity"))
258 sortPairwiseMenuItem_actionPerformed();
260 else if (param.equalsIgnoreCase("Length"))
262 sortLengthMenuItem_actionPerformed();
266 param = applet.getParameter("wrap");
269 if (param.equalsIgnoreCase("true"))
271 wrapMenuItem.setState(true);
272 wrapMenuItem_actionPerformed();
275 param = applet.getParameter("centrecolumnlabels");
278 centreColumnLabelFlag.setState(true);
279 centreColumnLabelFlag_stateChanged();
283 if (viewport.getAlignment().isNucleotide())
285 viewport.updateStrucConsensus(alignPanel);
286 if (viewport.getAlignment().hasRNAStructure())
288 RNAHelixColour.setEnabled(true);
292 RNAHelixColour.setEnabled(false);
297 RNAHelixColour.setEnabled(false);
298 purinePyrimidineColour.setEnabled(false);
299 nucleotideColour.setEnabled(false);
301 // Some JVMS send keyevents to Top frame or lowest panel,
302 // Havent worked out why yet. So add to both this frame and seqCanvas for
304 this.addKeyListener(this);
305 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
306 alignPanel.idPanel.idCanvas.addKeyListener(this);
307 alignPanel.scalePanel.addKeyListener(this);
308 alignPanel.annotationPanel.addKeyListener(this);
309 alignPanel.annotationPanelHolder.addKeyListener(this);
310 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
311 alignPanel.alabels.addKeyListener(this);
313 setAnnotationsVisibility();
317 addToDisplay(embedded);
324 public void addToDisplay(boolean embedded)
326 createAlignFrameWindow(embedded);
328 alignPanel.adjustAnnotationHeight();
329 alignPanel.paintAlignment(true);
332 public AlignViewport getAlignViewport()
337 public SeqCanvas getSeqcanvas()
339 return alignPanel.seqPanel.seqCanvas;
343 * Load a features file onto the alignment
346 * file URL, content, or other resolvable path
348 * is protocol for accessing data referred to by file
351 public boolean parseFeaturesFile(String file, DataSourceType type)
353 return parseFeaturesFile(file, type, true);
357 * Load a features file onto the alignment
360 * file URL, content, or other resolvable path
362 * is protocol for accessing data referred to by file
363 * @param autoenabledisplay
364 * when true, display features flag will be automatically enabled if
365 * features are loaded
366 * @return true if data parsed as a features file
368 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
369 boolean autoenabledisplay)
371 boolean featuresFile = false;
374 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
375 .getFeatureRenderer().getFeatureColours();
376 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
377 "relaxedidmatch", false);
378 featuresFile = new FeaturesFile(file, sourceType).parse(
379 viewport.getAlignment(), colours, true, relaxedIdMatching);
380 } catch (Exception ex)
382 ex.printStackTrace();
387 if (autoenabledisplay)
389 viewport.setShowSequenceFeatures(true);
390 sequenceFeatures.setState(true);
392 if (alignPanel.seqPanel.seqCanvas.fr != null)
394 // update the min/max ranges where necessary
395 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
397 if (viewport.featureSettings != null)
399 viewport.featureSettings.refreshTable();
401 alignPanel.paintAlignment(true);
402 statusBar.setText(MessageManager
403 .getString("label.successfully_added_features_alignment"));
409 public void keyPressed(KeyEvent evt)
411 if (viewport.cursorMode
412 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
413 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
414 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
415 && Character.isDigit(evt.getKeyChar()))
417 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
420 switch (evt.getKeyCode())
422 case 27: // escape key
423 deselectAllSequenceMenuItem_actionPerformed();
425 alignPanel.alabels.cancelDrag();
428 if (evt.isControlDown() || evt.isMetaDown())
430 cut_actionPerformed();
434 if (viewport.cursorMode && !evt.isControlDown())
436 alignPanel.seqPanel.setCursorColumn();
438 if (evt.isControlDown() || evt.isMetaDown())
440 copy_actionPerformed();
444 if (evt.isControlDown())
446 paste(evt.isShiftDown());
450 if (evt.isControlDown() || evt.isMetaDown())
452 selectAllSequenceMenuItem_actionPerformed();
455 case KeyEvent.VK_DOWN:
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.moveCursor(0, 1);
462 moveSelectedSequences(false);
467 if (viewport.cursorMode)
469 alignPanel.seqPanel.moveCursor(0, -1);
473 moveSelectedSequences(true);
477 case KeyEvent.VK_LEFT:
478 if (evt.isAltDown() || !viewport.cursorMode)
480 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
484 alignPanel.seqPanel.moveCursor(-1, 0);
488 case KeyEvent.VK_RIGHT:
489 if (evt.isAltDown() || !viewport.cursorMode)
491 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
495 alignPanel.seqPanel.moveCursor(1, 0);
499 case KeyEvent.VK_SPACE:
500 if (viewport.cursorMode)
502 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
503 || evt.isShiftDown() || evt.isAltDown());
507 case KeyEvent.VK_DELETE:
508 case KeyEvent.VK_BACK_SPACE:
509 if (viewport.cursorMode)
511 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
512 || evt.isShiftDown() || evt.isAltDown());
516 cut_actionPerformed();
517 alignPanel.seqPanel.seqCanvas.repaint();
522 if (viewport.cursorMode)
524 alignPanel.seqPanel.setCursorRow();
528 if (viewport.cursorMode)
530 alignPanel.seqPanel.setCursorPosition();
534 case KeyEvent.VK_ENTER:
535 case KeyEvent.VK_COMMA:
536 if (viewport.cursorMode)
538 alignPanel.seqPanel.setCursorRowAndColumn();
543 if (viewport.cursorMode)
545 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
549 if (viewport.cursorMode)
551 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
556 viewport.cursorMode = !viewport.cursorMode;
557 statusBar.setText(MessageManager.formatMessage(
558 "label.keyboard_editing_mode",
559 new String[] { (viewport.cursorMode ? "on" : "off") }));
560 if (viewport.cursorMode)
562 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
563 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
568 if (evt.isControlDown())
570 findMenuItem_actionPerformed();
576 boolean toggleSeqs = !evt.isControlDown();
577 boolean toggleCols = !evt.isShiftDown();
578 toggleHiddenRegions(toggleSeqs, toggleCols);
582 case KeyEvent.VK_PAGE_UP:
583 if (viewport.getWrapAlignment())
585 alignPanel.scrollUp(true);
589 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
590 - viewport.endSeq + viewport.startSeq);
594 case KeyEvent.VK_PAGE_DOWN:
595 if (viewport.getWrapAlignment())
597 alignPanel.scrollUp(false);
601 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
602 + viewport.endSeq - viewport.startSeq);
607 if (evt.isControlDown())
609 undoMenuItem_actionPerformed();
614 if (evt.isControlDown())
616 redoMenuItem_actionPerformed();
621 if (evt.isControlDown())
628 if (evt.isControlDown())
630 trimAlignment(false);
635 if (evt.isControlDown())
637 if (evt.isShiftDown())
639 this.removeAllGapsMenuItem_actionPerformed();
643 removeGappedColumnMenuItem_actionPerformed();
648 if (evt.isControlDown())
652 invertColSel_actionPerformed();
656 invertSequenceMenuItem_actionPerformed();
662 if (evt.isControlDown())
664 if (evt.isShiftDown())
666 this.unGroup_actionPerformed();
670 this.createGroup_actionPerformed();
676 if (evt.isControlDown())
678 this.deleteGroups_actionPerformed();
683 if (evt.isControlDown())
690 alignPanel.paintAlignment(true);
694 * called by key handler and the hide all/show all menu items
699 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
701 boolean hide = false;
702 SequenceGroup sg = viewport.getSelectionGroup();
703 if (!toggleSeqs && !toggleCols)
705 // Hide everything by the current selection - this is a hack - we do the
706 // invert and then hide
707 // first check that there will be visible columns after the invert.
708 if (viewport.hasSelectedColumns()
709 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
712 // now invert the sequence set, if required - empty selection implies
713 // that no hiding is required.
716 invertSequenceMenuItem_actionPerformed();
717 sg = viewport.getSelectionGroup();
721 viewport.expandColSelection(sg, true);
722 // finally invert the column selection and get the new sequence
723 // selection and indicate it should be hidden.
724 invertColSel_actionPerformed();
731 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
734 viewport.hideAllSelectedSeqs();
736 else if (!(toggleCols && viewport.hasSelectedColumns()))
738 viewport.showAllHiddenSeqs();
744 if (viewport.hasSelectedColumns())
746 viewport.hideSelectedColumns();
749 viewport.setSelectionGroup(sg);
754 viewport.showAllHiddenColumns();
756 viewport.sendSelection();
761 public void keyReleased(KeyEvent evt)
766 public void keyTyped(KeyEvent evt)
771 public void itemStateChanged(ItemEvent evt)
773 final Object source = evt.getSource();
774 if (source == displayNonconservedMenuItem)
776 displayNonconservedMenuItem_actionPerformed();
778 else if (source == colourTextMenuItem)
780 colourTextMenuItem_actionPerformed();
782 else if (source == wrapMenuItem)
784 wrapMenuItem_actionPerformed();
786 else if (source == scaleAbove)
788 viewport.setScaleAboveWrapped(scaleAbove.getState());
790 else if (source == scaleLeft)
792 viewport.setScaleLeftWrapped(scaleLeft.getState());
794 else if (source == scaleRight)
796 viewport.setScaleRightWrapped(scaleRight.getState());
798 else if (source == seqLimits)
800 seqLimits_itemStateChanged();
802 else if (source == viewBoxesMenuItem)
804 viewport.setShowBoxes(viewBoxesMenuItem.getState());
806 else if (source == viewTextMenuItem)
808 viewport.setShowText(viewTextMenuItem.getState());
810 else if (source == renderGapsMenuItem)
812 viewport.setRenderGaps(renderGapsMenuItem.getState());
814 else if (source == annotationPanelMenuItem)
816 boolean showAnnotations = annotationPanelMenuItem.getState();
817 showAlignmentAnnotations.setEnabled(showAnnotations);
818 showSequenceAnnotations.setEnabled(showAnnotations);
819 viewport.setShowAnnotation(showAnnotations);
820 alignPanel.setAnnotationVisible(showAnnotations);
822 else if (source == sequenceFeatures)
824 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
825 alignPanel.seqPanel.seqCanvas.repaint();
827 else if (source == showAlignmentAnnotations)
829 setAnnotationsVisibility();
831 else if (source == showSequenceAnnotations)
833 setAnnotationsVisibility();
835 else if (source == sortAnnBySequence)
837 boolean newState = sortAnnBySequence.getState();
838 sortAnnByLabel.setState(false);
839 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
840 : SequenceAnnotationOrder.NONE);
841 setViewportAnnotationOrder();
843 else if (source == sortAnnByLabel)
845 boolean newState = sortAnnByLabel.getState();
846 sortAnnBySequence.setState(false);
847 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
848 : SequenceAnnotationOrder.NONE);
849 setViewportAnnotationOrder();
851 else if (source == showAutoFirst)
853 showAutoLast.setState(!showAutoFirst.getState());
854 setShowAutoCalculatedAbove(showAutoFirst.getState());
855 setViewportAnnotationOrder();
857 else if (source == showAutoLast)
859 showAutoFirst.setState(!showAutoLast.getState());
860 setShowAutoCalculatedAbove(showAutoFirst.getState());
861 setViewportAnnotationOrder();
863 else if (source == conservationMenuItem)
865 conservationMenuItem_actionPerformed();
867 else if (source == abovePIDThreshold)
869 abovePIDThreshold_actionPerformed();
871 else if (source == applyToAllGroups)
873 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
875 else if (source == autoCalculate)
877 viewport.autoCalculateConsensus = autoCalculate.getState();
879 else if (source == sortByTree)
881 viewport.sortByTree = sortByTree.getState();
883 else if (source == this.centreColumnLabelFlag)
885 centreColumnLabelFlag_stateChanged();
887 else if (source == this.followMouseOverFlag)
889 mouseOverFlag_stateChanged();
891 else if (source == showGroupConsensus)
893 showGroupConsensus_actionPerformed();
895 else if (source == showGroupConservation)
897 showGroupConservation_actionPerformed();
899 else if (source == showSequenceLogo)
901 showSequenceLogo_actionPerformed();
903 else if (source == normSequenceLogo)
905 normSequenceLogo_actionPerformed();
907 else if (source == showConsensusHistogram)
909 showConsensusHistogram_actionPerformed();
911 else if (source == applyAutoAnnotationSettings)
913 applyAutoAnnotationSettings_actionPerformed();
915 alignPanel.paintAlignment(true);
919 * Set the visibility state of sequence-related and/or alignment-related
920 * annotations depending on checkbox selections, and repaint.
924 private void setAnnotationsVisibility()
926 boolean showForAlignment = showAlignmentAnnotations.getState();
927 boolean showForSequences = showSequenceAnnotations.getState();
928 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
930 for (AlignmentAnnotation aa : alignPanel.getAlignment()
931 .getAlignmentAnnotation())
933 boolean visible = (aa.sequenceRef == null ? showForAlignment
935 aa.visible = visible;
938 alignPanel.validateAnnotationDimensions(true);
943 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
945 this.annotationSortOrder = order;
949 * Set flags on the viewport that control annotation ordering
951 private void setViewportAnnotationOrder()
953 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
955 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
958 private void setShowAutoCalculatedAbove(boolean showAbove)
960 this.showAutoCalculatedAbove = showAbove;
963 private void mouseOverFlag_stateChanged()
965 viewport.setFollowHighlight(followMouseOverFlag.getState());
966 // TODO: could kick the scrollTo mechanism to reset view for current
970 private void centreColumnLabelFlag_stateChanged()
972 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
973 this.alignPanel.annotationPanel.repaint();
977 public void actionPerformed(ActionEvent evt)
979 viewport.applet.currentAlignFrame = this;
981 Object source = evt.getSource();
983 if (source == inputText)
985 inputText_actionPerformed();
987 else if (source == loadTree)
989 loadTree_actionPerformed();
991 else if (source == loadApplication)
993 launchFullApplication();
995 else if (source == loadAnnotations)
999 else if (source == outputAnnotations)
1001 outputAnnotations(true);
1003 else if (source == outputFeatures)
1005 outputFeatures(true, "Jalview");
1007 else if (source == closeMenuItem)
1009 closeMenuItem_actionPerformed();
1011 else if (source == copy)
1013 copy_actionPerformed();
1015 else if (source == undoMenuItem)
1017 undoMenuItem_actionPerformed();
1019 else if (source == redoMenuItem)
1021 redoMenuItem_actionPerformed();
1023 else if (source == inputText)
1025 inputText_actionPerformed();
1027 else if (source == closeMenuItem)
1029 closeMenuItem_actionPerformed();
1031 else if (source == undoMenuItem)
1033 undoMenuItem_actionPerformed();
1035 else if (source == redoMenuItem)
1037 redoMenuItem_actionPerformed();
1039 else if (source == copy)
1041 copy_actionPerformed();
1043 else if (source == pasteNew)
1045 pasteNew_actionPerformed();
1047 else if (source == pasteThis)
1049 pasteThis_actionPerformed();
1051 else if (source == cut)
1053 cut_actionPerformed();
1055 else if (source == delete)
1057 delete_actionPerformed();
1059 else if (source == grpsFromSelection)
1061 makeGrpsFromSelection_actionPerformed();
1063 else if (source == deleteGroups)
1065 deleteGroups_actionPerformed();
1067 else if (source == selectAllSequenceMenuItem)
1069 selectAllSequenceMenuItem_actionPerformed();
1071 else if (source == deselectAllSequenceMenuItem)
1073 deselectAllSequenceMenuItem_actionPerformed();
1075 else if (source == invertSequenceMenuItem)
1077 invertSequenceMenuItem_actionPerformed();
1078 // uncomment to slave sequence selections in split frame
1079 // viewport.sendSelection();
1081 else if (source == invertColSel)
1083 viewport.invertColumnSelection();
1084 alignPanel.paintAlignment(true);
1085 viewport.sendSelection();
1087 else if (source == remove2LeftMenuItem)
1089 trimAlignment(true);
1091 else if (source == remove2RightMenuItem)
1093 trimAlignment(false);
1095 else if (source == removeGappedColumnMenuItem)
1097 removeGappedColumnMenuItem_actionPerformed();
1099 else if (source == removeAllGapsMenuItem)
1101 removeAllGapsMenuItem_actionPerformed();
1103 else if (source == findMenuItem)
1105 findMenuItem_actionPerformed();
1107 else if (source == font)
1109 new FontChooser(alignPanel);
1111 else if (source == newView)
1115 else if (source == showColumns)
1117 viewport.showAllHiddenColumns();
1118 alignPanel.paintAlignment(true);
1119 viewport.sendSelection();
1121 else if (source == showSeqs)
1123 viewport.showAllHiddenSeqs();
1124 alignPanel.paintAlignment(true);
1125 // uncomment if we want to slave sequence selections in split frame
1126 // viewport.sendSelection();
1128 else if (source == hideColumns)
1130 viewport.hideSelectedColumns();
1131 alignPanel.paintAlignment(true);
1132 viewport.sendSelection();
1134 else if (source == hideSequences
1135 && viewport.getSelectionGroup() != null)
1137 viewport.hideAllSelectedSeqs();
1138 alignPanel.paintAlignment(true);
1139 // uncomment if we want to slave sequence selections in split frame
1140 // viewport.sendSelection();
1142 else if (source == hideAllButSelection)
1144 toggleHiddenRegions(false, false);
1145 alignPanel.paintAlignment(true);
1146 viewport.sendSelection();
1148 else if (source == hideAllSelection)
1150 SequenceGroup sg = viewport.getSelectionGroup();
1151 viewport.expandColSelection(sg, false);
1152 viewport.hideAllSelectedSeqs();
1153 viewport.hideSelectedColumns();
1154 alignPanel.paintAlignment(true);
1155 viewport.sendSelection();
1157 else if (source == showAllHidden)
1159 viewport.showAllHiddenColumns();
1160 viewport.showAllHiddenSeqs();
1161 alignPanel.paintAlignment(true);
1162 viewport.sendSelection();
1164 else if (source == showGroupConsensus)
1166 showGroupConsensus_actionPerformed();
1168 else if (source == showGroupConservation)
1170 showGroupConservation_actionPerformed();
1172 else if (source == showSequenceLogo)
1174 showSequenceLogo_actionPerformed();
1176 else if (source == normSequenceLogo)
1178 normSequenceLogo_actionPerformed();
1180 else if (source == showConsensusHistogram)
1182 showConsensusHistogram_actionPerformed();
1184 else if (source == applyAutoAnnotationSettings)
1186 applyAutoAnnotationSettings_actionPerformed();
1188 else if (source == featureSettings)
1190 new FeatureSettings(alignPanel);
1192 else if (source == alProperties)
1194 StringBuffer contents = new jalview.io.AlignmentProperties(
1195 viewport.getAlignment()).formatAsString();
1196 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197 cap.setText(contents.toString());
1198 Frame frame = new Frame();
1200 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201 "label.alignment_properties", new String[] { getTitle() }),
1204 else if (source == overviewMenuItem)
1206 overviewMenuItem_actionPerformed();
1208 else if (source == noColourmenuItem)
1212 else if (source == clustalColour)
1214 abovePIDThreshold.setState(false);
1215 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1217 else if (source == zappoColour)
1219 changeColour(new ZappoColourScheme());
1221 else if (source == taylorColour)
1223 changeColour(new TaylorColourScheme());
1225 else if (source == hydrophobicityColour)
1227 changeColour(new HydrophobicColourScheme());
1229 else if (source == helixColour)
1231 changeColour(new HelixColourScheme());
1233 else if (source == strandColour)
1235 changeColour(new StrandColourScheme());
1237 else if (source == turnColour)
1239 changeColour(new TurnColourScheme());
1241 else if (source == buriedColour)
1243 changeColour(new BuriedColourScheme());
1245 else if (source == nucleotideColour)
1247 changeColour(new NucleotideColourScheme());
1249 else if (source == purinePyrimidineColour)
1251 changeColour(new PurinePyrimidineColourScheme());
1253 // else if (source == RNAInteractionColour)
1255 // changeColour(new RNAInteractionColourScheme());
1257 else if (source == RNAHelixColour)
1259 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1260 // new RNAHelicesColourChooser(viewport, alignPanel);
1262 else if (source == modifyPID)
1264 modifyPID_actionPerformed();
1266 else if (source == modifyConservation)
1268 modifyConservation_actionPerformed();
1270 else if (source == userDefinedColour)
1272 new UserDefinedColours(alignPanel, null);
1274 else if (source == PIDColour)
1276 changeColour(new PIDColourScheme());
1278 else if (source == BLOSUM62Colour)
1280 changeColour(new Blosum62ColourScheme());
1282 else if (source == tcoffeeColour)
1284 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1286 else if (source == annotationColour)
1288 new AnnotationColourChooser(viewport, alignPanel);
1290 else if (source == annotationColumnSelection)
1292 new AnnotationColumnChooser(viewport, alignPanel);
1294 else if (source == sortPairwiseMenuItem)
1296 sortPairwiseMenuItem_actionPerformed();
1298 else if (source == sortIDMenuItem)
1300 sortIDMenuItem_actionPerformed();
1302 else if (source == sortLengthMenuItem)
1304 sortLengthMenuItem_actionPerformed();
1306 else if (source == sortGroupMenuItem)
1308 sortGroupMenuItem_actionPerformed();
1310 else if (source == removeRedundancyMenuItem)
1312 removeRedundancyMenuItem_actionPerformed();
1314 else if (source == pairwiseAlignmentMenuItem)
1316 pairwiseAlignmentMenuItem_actionPerformed();
1318 else if (source == PCAMenuItem)
1320 PCAMenuItem_actionPerformed();
1322 else if (source == averageDistanceTreeMenuItem)
1324 averageDistanceTreeMenuItem_actionPerformed();
1326 else if (source == neighbourTreeMenuItem)
1328 neighbourTreeMenuItem_actionPerformed();
1330 else if (source == njTreeBlosumMenuItem)
1332 njTreeBlosumMenuItem_actionPerformed();
1334 else if (source == avDistanceTreeBlosumMenuItem)
1336 avTreeBlosumMenuItem_actionPerformed();
1338 else if (source == documentation)
1340 documentation_actionPerformed();
1342 else if (source == about)
1344 about_actionPerformed();
1349 public void inputText_actionPerformed()
1351 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352 Frame frame = new Frame();
1354 jalview.bin.JalviewLite.addFrame(frame,
1355 MessageManager.getString("label.input_cut_paste"), 500, 500);
1358 protected void outputText_actionPerformed(ActionEvent e)
1360 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361 Frame frame = new Frame();
1363 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364 "label.alignment_output_command",
1365 new Object[] { e.getActionCommand() }), 600, 500);
1367 FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1368 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1369 fileFormat, viewport.getAlignment(),
1370 viewport.getShowJVSuffix()));
1373 public void loadAnnotations()
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376 cap.setText(MessageManager
1377 .getString("label.paste_features_annotations_Tcoffee_here"));
1378 cap.setAnnotationImport();
1379 Frame frame = new Frame();
1381 jalview.bin.JalviewLite.addFrame(frame,
1382 MessageManager.getString("action.paste_annotations"), 400, 300);
1386 public String outputAnnotations(boolean displayTextbox)
1388 String annotation = new AnnotationFile()
1389 .printAnnotationsForView(viewport);
1393 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1394 Frame frame = new Frame();
1396 jalview.bin.JalviewLite.addFrame(frame,
1397 MessageManager.getString("label.annotations"), 600, 500);
1398 cap.setText(annotation);
1404 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1406 if (alignPanel.getFeatureRenderer() != null
1407 && viewport.getFeaturesDisplayed() != null)
1409 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1415 public String outputFeatures(boolean displayTextbox, String format)
1418 FeaturesFile formatter = new FeaturesFile();
1419 if (format.equalsIgnoreCase("Jalview"))
1421 features = formatter.printJalviewFormat(viewport.getAlignment()
1422 .getSequencesArray(), getDisplayedFeatureCols());
1426 features = formatter.printGffFormat(viewport.getAlignment()
1427 .getSequencesArray(), getDisplayedFeatureCols());
1432 boolean frimport = false;
1433 if (features == null || features.equals("No Features Visible"))
1435 features = "# No features visible - paste some and import them here.";
1439 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1442 cap.setAnnotationImport();
1444 Frame frame = new Frame();
1446 jalview.bin.JalviewLite.addFrame(frame,
1447 MessageManager.getString("label.features"), 600, 500);
1448 cap.setText(features);
1452 if (features == null)
1461 void launchFullApplication()
1463 StringBuffer url = new StringBuffer(jalviewServletURL);
1465 // allow servlet parameters to be passed in applet parameter
1466 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1468 url.append(firstSep);
1471 + appendProtocol(viewport.applet.getParameter("file")));
1473 if (viewport.applet.getParameter("features") != null)
1475 url.append("&features=");
1476 url.append(appendProtocol(viewport.applet.getParameter("features")));
1479 if (viewport.applet.getParameter("annotations") != null)
1481 url.append("&annotations=");
1482 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1485 if (viewport.applet.getParameter("jnetfile") != null)
1487 url.append("&annotations=");
1488 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1491 if (viewport.applet.getParameter("defaultColour") != null)
1493 url.append("&colour="
1494 + removeWhiteSpace(viewport.applet
1495 .getParameter("defaultColour")));
1498 if (viewport.applet.getParameter("userDefinedColour") != null)
1500 url.append("&colour="
1501 + removeWhiteSpace(viewport.applet
1502 .getParameter("userDefinedColour")));
1504 if (viewport.applet.getParameter("tree") != null)
1507 + appendProtocol(viewport.applet.getParameter("tree")));
1509 if (viewport.applet.getParameter("treeFile") != null)
1512 + appendProtocol(viewport.applet.getParameter("treeFile")));
1515 showURL(url.toString(), "FULL_APP");
1518 String removeWhiteSpace(String colour)
1520 StringBuffer sb = new StringBuffer();
1521 for (int i = 0; i < colour.length(); i++)
1523 if (Character.isWhitespace(colour.charAt(i)))
1529 sb.append(colour.charAt(i));
1533 return sb.toString();
1536 String appendProtocol(String url)
1541 url = URLEncoder.encode(url);
1544 * When we finally deprecate 1.1 compatibility, we can start to use
1545 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1546 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1547 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1548 * ex.printStackTrace(); }
1550 catch (java.net.MalformedURLException ex)
1552 url = viewport.applet.getCodeBase() + url;
1557 public void closeMenuItem_actionPerformed()
1559 PaintRefresher.RemoveComponent(alignPanel);
1560 if (alignPanel.seqPanel != null
1561 && alignPanel.seqPanel.seqCanvas != null)
1563 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1565 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1567 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1570 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1585 void updateEditMenuBar()
1588 if (viewport.getHistoryList().size() > 0)
1590 undoMenuItem.setEnabled(true);
1591 CommandI command = viewport.getHistoryList().peek();
1592 undoMenuItem.setLabel(MessageManager.formatMessage(
1593 "label.undo_command",
1594 new Object[] { command.getDescription() }));
1598 undoMenuItem.setEnabled(false);
1599 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1602 if (viewport.getRedoList().size() > 0)
1604 redoMenuItem.setEnabled(true);
1606 CommandI command = viewport.getRedoList().peek();
1607 redoMenuItem.setLabel(MessageManager.formatMessage(
1608 "label.redo_command",
1609 new Object[] { command.getDescription() }));
1613 redoMenuItem.setEnabled(false);
1614 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1622 public void addHistoryItem(CommandI command)
1624 if (command.getSize() > 0)
1626 viewport.addToHistoryList(command);
1627 viewport.clearRedoList();
1628 updateEditMenuBar();
1629 viewport.updateHiddenColumns();
1634 * TODO: JAL-1104 DOCUMENT ME!
1639 protected void undoMenuItem_actionPerformed()
1641 if (viewport.getHistoryList().isEmpty())
1646 CommandI command = viewport.getHistoryList().pop();
1647 viewport.addToRedoList(command);
1648 command.undoCommand(null);
1650 AlignmentViewport originalSource = getOriginatingSource(command);
1652 if (originalSource != viewport)
1655 .println("Warning: Viewport object mismatch whilst undoing");
1657 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1658 // viewport.getColumnSelection().getHiddenColumns()
1660 updateEditMenuBar();
1661 originalSource.firePropertyChange("alignment", null, originalSource
1662 .getAlignment().getSequences());
1666 * TODO: JAL-1104 DOCUMENT ME!
1671 protected void redoMenuItem_actionPerformed()
1673 if (viewport.getRedoList().isEmpty())
1678 CommandI command = viewport.getRedoList().pop();
1679 viewport.addToHistoryList(command);
1680 command.doCommand(null);
1682 AlignmentViewport originalSource = getOriginatingSource(command);
1684 if (originalSource != viewport)
1687 .println("Warning: Viewport object mismatch whilst re-doing");
1689 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1690 // viewport.getColumnSelection().getHiddenColumns()
1693 updateEditMenuBar();
1694 originalSource.firePropertyChange("alignment", null, originalSource
1695 .getAlignment().getSequences());
1698 AlignmentViewport getOriginatingSource(CommandI command)
1700 AlignmentViewport originalSource = null;
1701 // For sequence removal and addition, we need to fire
1702 // the property change event FROM the viewport where the
1703 // original alignment was altered
1704 AlignmentI al = null;
1705 if (command instanceof EditCommand)
1707 EditCommand editCommand = (EditCommand) command;
1708 al = editCommand.getAlignment();
1709 Vector comps = (Vector) PaintRefresher.components.get(viewport
1710 .getSequenceSetId());
1711 for (int i = 0; i < comps.size(); i++)
1713 if (comps.elementAt(i) instanceof AlignmentPanel)
1715 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1717 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1724 if (originalSource == null)
1726 // The original view is closed, we must validate
1727 // the current view against the closed view first
1730 PaintRefresher.validateSequences(al, viewport.getAlignment());
1733 originalSource = viewport;
1736 return originalSource;
1740 * Move the currently selected sequences up or down one position in the
1745 public void moveSelectedSequences(boolean up)
1747 SequenceGroup sg = viewport.getSelectionGroup();
1752 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753 up ? null : viewport.getHiddenRepSequences(), up);
1754 alignPanel.paintAlignment(true);
1757 * Also move cDNA/protein complement sequences
1759 AlignViewportI complement = viewport.getCodingComplement();
1760 if (complement != null)
1762 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1763 viewport, complement);
1764 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1765 up ? null : complement.getHiddenRepSequences(), up);
1766 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1770 synchronized void slideSequences(boolean right, int size)
1772 List<SequenceI> sg = new Vector<SequenceI>();
1773 if (viewport.cursorMode)
1775 sg.add(viewport.getAlignment().getSequenceAt(
1776 alignPanel.seqPanel.seqCanvas.cursorY));
1778 else if (viewport.getSelectionGroup() != null
1779 && viewport.getSelectionGroup().getSize() != viewport
1780 .getAlignment().getHeight())
1782 sg = viewport.getSelectionGroup().getSequences(
1783 viewport.getHiddenRepSequences());
1791 Vector<SequenceI> invertGroup = new Vector();
1793 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1795 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1797 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1801 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1803 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1805 for (int i = 0; i < invertGroup.size(); i++)
1807 seqs2[i] = invertGroup.elementAt(i);
1810 SlideSequencesCommand ssc;
1813 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1814 size, viewport.getGapCharacter());
1818 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1819 size, viewport.getGapCharacter());
1822 int groupAdjustment = 0;
1823 if (ssc.getGapsInsertedBegin() && right)
1825 if (viewport.cursorMode)
1827 alignPanel.seqPanel.moveCursor(size, 0);
1831 groupAdjustment = size;
1834 else if (!ssc.getGapsInsertedBegin() && !right)
1836 if (viewport.cursorMode)
1838 alignPanel.seqPanel.moveCursor(-size, 0);
1842 groupAdjustment = -size;
1846 if (groupAdjustment != 0)
1848 viewport.getSelectionGroup().setStartRes(
1849 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1850 viewport.getSelectionGroup().setEndRes(
1851 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1854 boolean appendHistoryItem = false;
1855 Deque<CommandI> historyList = viewport.getHistoryList();
1856 if (historyList != null && historyList.size() > 0
1857 && historyList.peek() instanceof SlideSequencesCommand)
1859 appendHistoryItem = ssc
1860 .appendSlideCommand((SlideSequencesCommand) historyList
1864 if (!appendHistoryItem)
1866 addHistoryItem(ssc);
1872 static StringBuffer copiedSequences;
1874 static Vector copiedHiddenColumns;
1876 protected void copy_actionPerformed()
1878 if (viewport.getSelectionGroup() == null)
1883 SequenceGroup sg = viewport.getSelectionGroup();
1884 copiedSequences = new StringBuffer();
1885 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1886 for (int i = 0; i < sg.getSize(); i++)
1888 SequenceI seq = sg.getSequenceAt(i);
1889 int index = viewport.getAlignment().findIndex(seq);
1890 orderedSeqs.put(index, seq);
1893 int index = 0, startRes, endRes;
1896 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1898 copiedHiddenColumns = new Vector();
1899 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1900 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1902 copiedHiddenColumns.addElement(new int[] {
1903 region[0] - hiddenOffset, region[1] - hiddenOffset });
1908 copiedHiddenColumns = null;
1911 for (int i = 0; i < sg.getSize(); i++)
1913 SequenceI seq = null;
1917 if (orderedSeqs.containsKey(index))
1919 seq = orderedSeqs.get(index);
1930 // Returns residue following index if gap
1931 startRes = seq.findPosition(sg.getStartRes());
1934 // Need to find the residue preceeding index if gap
1937 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1939 ch = seq.getCharAt(j);
1940 if (!jalview.util.Comparison.isGap((ch)))
1948 endRes += seq.getStart() - 1;
1951 copiedSequences.append(seq.getName()
1957 + seq.getSequenceAsString(sg.getStartRes(),
1958 sg.getEndRes() + 1) + "\n");
1963 protected void pasteNew_actionPerformed()
1968 protected void pasteThis_actionPerformed()
1973 void paste(boolean newAlignment)
1978 if (copiedSequences == null)
1983 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1984 Vector seqs = new Vector();
1985 while (st.hasMoreElements())
1987 String name = st.nextToken();
1988 int start = Integer.parseInt(st.nextToken());
1989 int end = Integer.parseInt(st.nextToken());
1990 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1992 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1993 for (int i = 0; i < seqs.size(); i++)
1995 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2000 String newtitle = MessageManager
2001 .getString("label.copied_sequences");
2002 if (getTitle().startsWith(
2003 MessageManager.getString("label.copied_sequences")))
2005 newtitle = getTitle();
2009 newtitle = newtitle.concat(MessageManager.formatMessage(
2010 "label.from_msname", new String[] { getTitle() }));
2012 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2013 viewport.applet, newtitle, false);
2014 if (copiedHiddenColumns != null)
2016 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2018 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2019 af.viewport.hideColumns(region[0], region[1]);
2023 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2028 addSequences(newSeqs);
2031 } catch (Exception ex)
2033 } // could be anything being pasted in here
2037 void addSequences(SequenceI[] seqs)
2039 for (int i = 0; i < seqs.length; i++)
2041 viewport.getAlignment().addSequence(seqs[i]);
2045 addHistoryItem(new EditCommand(
2046 MessageManager.getString("label.add_sequences"), Action.PASTE,
2047 seqs, 0, viewport.getAlignment().getWidth(),
2048 viewport.getAlignment()));
2050 viewport.setEndSeq(viewport.getAlignment().getHeight());
2051 viewport.getAlignment().getWidth();
2052 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2057 protected void cut_actionPerformed()
2059 copy_actionPerformed();
2060 delete_actionPerformed();
2063 protected void delete_actionPerformed()
2066 SequenceGroup sg = viewport.getSelectionGroup();
2072 Vector seqs = new Vector();
2074 for (int i = 0; i < sg.getSize(); i++)
2076 seq = sg.getSequenceAt(i);
2077 seqs.addElement(seq);
2081 * If the cut affects all sequences, warn, remove highlighted columns
2083 if (sg.getSize() == viewport.getAlignment().getHeight())
2085 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2086 .getAlignment().getWidth()) ? true : false;
2087 if (isEntireAlignWidth)
2089 String title = MessageManager.getString("label.delete_all");
2090 Panel infoPanel = new Panel();
2091 infoPanel.setLayout(new FlowLayout());
2093 .add(new Label(MessageManager.getString("warn.delete_all")));
2095 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2096 dialog.setMainPanel(infoPanel);
2097 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2098 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2099 dialog.setVisible(true);
2106 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2107 sg.getEndRes() + 1);
2110 SequenceI[] cut = new SequenceI[seqs.size()];
2111 for (int i = 0; i < seqs.size(); i++)
2113 cut[i] = (SequenceI) seqs.elementAt(i);
2117 * //ADD HISTORY ITEM
2119 addHistoryItem(new EditCommand(
2120 MessageManager.getString("label.cut_sequences"), Action.CUT,
2121 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2122 viewport.getAlignment()));
2124 viewport.setSelectionGroup(null);
2125 viewport.getAlignment().deleteGroup(sg);
2127 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2130 if (viewport.getAlignment().getHeight() < 1)
2132 this.setVisible(false);
2134 viewport.sendSelection();
2138 * group consensus toggled
2141 protected void showGroupConsensus_actionPerformed()
2143 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2144 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2149 * group conservation toggled.
2151 protected void showGroupConservation_actionPerformed()
2153 viewport.setShowGroupConservation(showGroupConservation.getState());
2154 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2161 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2162 * .event.ActionEvent)
2164 protected void showConsensusHistogram_actionPerformed()
2166 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2167 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2175 * .event.ActionEvent)
2177 protected void showSequenceLogo_actionPerformed()
2179 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2180 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183 protected void normSequenceLogo_actionPerformed()
2185 showSequenceLogo.setState(true);
2186 viewport.setShowSequenceLogo(true);
2187 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2188 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2191 protected void applyAutoAnnotationSettings_actionPerformed()
2193 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196 protected void makeGrpsFromSelection_actionPerformed()
2198 if (avc.makeGroupsFromSelection())
2200 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2201 alignPanel.updateAnnotation();
2202 alignPanel.paintAlignment(true);
2206 protected void createGroup_actionPerformed()
2211 protected void unGroup_actionPerformed()
2215 alignPanel.alignmentChanged();
2219 protected void deleteGroups_actionPerformed()
2221 if (avc.deleteGroups())
2223 alignPanel.alignmentChanged();
2227 public void selectAllSequenceMenuItem_actionPerformed()
2229 SequenceGroup sg = new SequenceGroup();
2230 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2232 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2234 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2235 viewport.setSelectionGroup(sg);
2236 // JAL-2034 - should delegate to
2237 // alignPanel to decide if overview needs
2239 alignPanel.paintAlignment(false);
2240 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2241 viewport.sendSelection();
2244 public void deselectAllSequenceMenuItem_actionPerformed()
2246 if (viewport.cursorMode)
2248 alignPanel.seqPanel.keyboardNo1 = null;
2249 alignPanel.seqPanel.keyboardNo2 = null;
2251 viewport.setSelectionGroup(null);
2252 viewport.getColumnSelection().clear();
2253 viewport.setSelectionGroup(null);
2254 alignPanel.idPanel.idCanvas.searchResults = null;
2255 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2256 // JAL-2034 - should delegate to
2257 // alignPanel to decide if overview needs
2259 alignPanel.paintAlignment(false);
2260 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261 viewport.sendSelection();
2264 public void invertSequenceMenuItem_actionPerformed()
2266 SequenceGroup sg = viewport.getSelectionGroup();
2267 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2269 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2272 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273 viewport.sendSelection();
2276 public void invertColSel_actionPerformed()
2278 viewport.invertColumnSelection();
2279 alignPanel.paintAlignment(true);
2280 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281 viewport.sendSelection();
2284 void trimAlignment(boolean trimLeft)
2286 ColumnSelection colSel = viewport.getColumnSelection();
2289 if (!colSel.isEmpty())
2293 column = colSel.getMin();
2297 column = colSel.getMax();
2301 if (viewport.getSelectionGroup() != null)
2303 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2304 viewport.getHiddenRepSequences());
2308 seqs = viewport.getAlignment().getSequencesArray();
2311 TrimRegionCommand trimRegion;
2314 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2315 column, viewport.getAlignment());
2316 viewport.setStartRes(0);
2320 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2321 column, viewport.getAlignment());
2324 statusBar.setText(MessageManager.formatMessage(
2325 "label.removed_columns",
2326 new String[] { Integer.valueOf(trimRegion.getSize())
2328 addHistoryItem(trimRegion);
2330 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2332 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2333 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2335 viewport.getAlignment().deleteGroup(sg);
2339 viewport.firePropertyChange("alignment", null, viewport
2340 .getAlignment().getSequences());
2344 public void removeGappedColumnMenuItem_actionPerformed()
2346 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2349 if (viewport.getSelectionGroup() != null)
2351 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2352 viewport.getHiddenRepSequences());
2353 start = viewport.getSelectionGroup().getStartRes();
2354 end = viewport.getSelectionGroup().getEndRes();
2358 seqs = viewport.getAlignment().getSequencesArray();
2361 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2362 "Remove Gapped Columns", seqs, start, end,
2363 viewport.getAlignment());
2365 addHistoryItem(removeGapCols);
2367 statusBar.setText(MessageManager.formatMessage(
2368 "label.removed_empty_columns",
2369 new String[] { Integer.valueOf(removeGapCols.getSize())
2372 // This is to maintain viewport position on first residue
2373 // of first sequence
2374 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2375 int startRes = seq.findPosition(viewport.startRes);
2376 // ShiftList shifts;
2377 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2378 // edit.alColumnChanges=shifts.getInverse();
2379 // if (viewport.hasHiddenColumns)
2380 // viewport.getColumnSelection().compensateForEdits(shifts);
2381 viewport.setStartRes(seq.findIndex(startRes) - 1);
2382 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2387 public void removeAllGapsMenuItem_actionPerformed()
2389 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2392 if (viewport.getSelectionGroup() != null)
2394 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2395 viewport.getHiddenRepSequences());
2396 start = viewport.getSelectionGroup().getStartRes();
2397 end = viewport.getSelectionGroup().getEndRes();
2401 seqs = viewport.getAlignment().getSequencesArray();
2404 // This is to maintain viewport position on first residue
2405 // of first sequence
2406 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2407 int startRes = seq.findPosition(viewport.startRes);
2409 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2410 viewport.getAlignment()));
2412 viewport.setStartRes(seq.findIndex(startRes) - 1);
2414 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2419 public void findMenuItem_actionPerformed()
2421 new Finder(alignPanel);
2425 * create a new view derived from the current view
2428 * @return frame for the new view
2430 public AlignFrame newView(String viewtitle)
2433 if (viewport.hasHiddenRows())
2435 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2436 .getFullAlignment().getSequencesArray());
2440 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2443 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2445 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2447 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2449 newal.addAnnotation(viewport.getAlignment()
2450 .getAlignmentAnnotation()[i]);
2455 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2457 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2458 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2459 PaintRefresher.Register(newaf.alignPanel,
2460 newaf.alignPanel.av.getSequenceSetId());
2462 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2463 newaf.alignPanel.av.getSequenceSetId());
2464 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2465 newaf.alignPanel.av.getSequenceSetId());
2467 Vector comps = (Vector) PaintRefresher.components.get(viewport
2468 .getSequenceSetId());
2470 for (int i = 0; i < comps.size(); i++)
2472 if (comps.elementAt(i) instanceof AlignmentPanel)
2478 String title = new String(this.getTitle());
2479 if (viewtitle != null)
2481 title = viewtitle + " ( " + title + ")";
2485 if (title.indexOf("(View") > -1)
2487 title = title.substring(0, title.indexOf("(View"));
2489 title += "(View " + viewSize + ")";
2492 newaf.setTitle(title.toString());
2494 newaf.viewport.setHistoryList(viewport.getHistoryList());
2495 newaf.viewport.setRedoList(viewport.getRedoList());
2501 * @return list of feature groups on the view
2503 public String[] getFeatureGroups()
2505 FeatureRenderer fr = null;
2506 if (alignPanel != null
2507 && (fr = alignPanel.getFeatureRenderer()) != null)
2509 List<String> gps = fr.getFeatureGroups();
2510 String[] _gps = gps.toArray(new String[gps.size()]);
2517 * get sequence feature groups that are hidden or shown
2523 public String[] getFeatureGroupsOfState(boolean visible)
2525 FeatureRenderer fr = null;
2526 if (alignPanel != null
2527 && (fr = alignPanel.getFeatureRenderer()) != null)
2529 List<String> gps = fr.getGroups(visible);
2530 String[] _gps = gps.toArray(new String[gps.size()]);
2537 * Change the display state for the given feature groups
2540 * list of group strings
2542 * visible or invisible
2544 public void setFeatureGroupState(String[] groups, boolean state)
2546 FeatureRenderer fr = null;
2547 this.sequenceFeatures.setState(true);
2548 viewport.setShowSequenceFeatures(true);
2549 if (alignPanel != null
2550 && (fr = alignPanel.getFeatureRenderer()) != null)
2553 fr.setGroupVisibility(Arrays.asList(groups), state);
2554 alignPanel.seqPanel.seqCanvas.repaint();
2555 if (alignPanel.overviewPanel != null)
2557 alignPanel.overviewPanel.updateOverviewImage();
2562 public void seqLimits_itemStateChanged()
2564 viewport.setShowJVSuffix(seqLimits.getState());
2565 alignPanel.fontChanged();
2566 alignPanel.paintAlignment(true);
2569 protected void colourTextMenuItem_actionPerformed()
2571 viewport.setColourText(colourTextMenuItem.getState());
2572 alignPanel.paintAlignment(true);
2575 protected void displayNonconservedMenuItem_actionPerformed()
2577 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2578 alignPanel.paintAlignment(true);
2581 protected void wrapMenuItem_actionPerformed()
2583 viewport.setWrapAlignment(wrapMenuItem.getState());
2584 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2585 scaleAbove.setEnabled(wrapMenuItem.getState());
2586 scaleLeft.setEnabled(wrapMenuItem.getState());
2587 scaleRight.setEnabled(wrapMenuItem.getState());
2588 alignPanel.paintAlignment(true);
2591 public void overviewMenuItem_actionPerformed()
2593 if (alignPanel.overviewPanel != null)
2598 Frame frame = new Frame();
2599 OverviewPanel overview = new OverviewPanel(alignPanel);
2600 frame.add(overview);
2601 // +50 must allow for applet frame window
2602 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2603 "label.overview_params", new String[] { this.getTitle() }),
2604 overview.getPreferredSize().width,
2605 overview.getPreferredSize().height + 50);
2608 final AlignmentPanel ap = alignPanel;
2609 frame.addWindowListener(new WindowAdapter()
2612 public void windowClosing(WindowEvent e)
2616 ap.setOverviewPanel(null);
2621 alignPanel.setOverviewPanel(overview);
2626 public void changeColour(ColourSchemeI cs)
2628 // FIXME threshold, conservation, increment belong inside
2629 // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
2632 if (viewport.getAbovePIDThreshold())
2634 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2635 viewport.getViewportColourScheme(), "Background"));
2638 if (viewport.getConservationSelected())
2640 // cs.setConservationApplied(true);
2641 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2642 viewport.getViewportColourScheme(), "Background"));
2646 // cs.setConservationApplied(false);
2649 viewport.setGlobalColourScheme(cs);
2650 viewport.getViewportColourScheme().setConservationApplied(
2651 viewport.getConservationSelected());
2653 alignPanel.paintAlignment(true);
2656 protected void modifyPID_actionPerformed()
2658 if (viewport.getAbovePIDThreshold()
2659 && viewport.getGlobalColourScheme() != null)
2661 SliderPanel.setPIDSliderSource(alignPanel,
2662 viewport.getViewportColourScheme(), "Background");
2663 SliderPanel.showPIDSlider();
2667 protected void modifyConservation_actionPerformed()
2669 if (viewport.getConservationSelected()
2670 && viewport.getGlobalColourScheme() != null)
2672 SliderPanel.setConservationSlider(alignPanel,
2673 viewport.getViewportColourScheme(), "Background");
2674 SliderPanel.showConservationSlider();
2678 protected void conservationMenuItem_actionPerformed()
2680 viewport.setConservationSelected(conservationMenuItem.getState());
2682 viewport.setAbovePIDThreshold(false);
2683 abovePIDThreshold.setState(false);
2685 changeColour(viewport.getGlobalColourScheme());
2687 modifyConservation_actionPerformed();
2690 public void abovePIDThreshold_actionPerformed()
2692 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2694 conservationMenuItem.setState(false);
2695 viewport.setConservationSelected(false);
2697 changeColour(viewport.getGlobalColourScheme());
2699 modifyPID_actionPerformed();
2702 public void sortPairwiseMenuItem_actionPerformed()
2704 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2705 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2706 .getAlignment().getSequenceAt(0), null);
2708 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2709 viewport.getAlignment()));
2710 alignPanel.paintAlignment(true);
2713 public void sortIDMenuItem_actionPerformed()
2715 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2716 AlignmentSorter.sortByID(viewport.getAlignment());
2717 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2718 viewport.getAlignment()));
2719 alignPanel.paintAlignment(true);
2722 public void sortLengthMenuItem_actionPerformed()
2724 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2725 AlignmentSorter.sortByLength(viewport.getAlignment());
2726 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2727 viewport.getAlignment()));
2728 alignPanel.paintAlignment(true);
2731 public void sortGroupMenuItem_actionPerformed()
2733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734 AlignmentSorter.sortByGroup(viewport.getAlignment());
2735 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2736 viewport.getAlignment()));
2737 alignPanel.paintAlignment(true);
2741 public void removeRedundancyMenuItem_actionPerformed()
2743 new RedundancyPanel(alignPanel);
2746 public void pairwiseAlignmentMenuItem_actionPerformed()
2748 if (viewport.getSelectionGroup() != null
2749 && viewport.getSelectionGroup().getSize() > 1)
2751 Frame frame = new Frame();
2752 frame.add(new PairwiseAlignPanel(alignPanel));
2753 jalview.bin.JalviewLite.addFrame(frame,
2754 MessageManager.getString("action.pairwise_alignment"), 600,
2759 public void PCAMenuItem_actionPerformed()
2761 // are the sequences aligned?
2762 if (!viewport.getAlignment().isAligned(false))
2765 int Width = viewport.getAlignment().getWidth();
2767 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2769 current = viewport.getAlignment().getSequenceAt(i);
2771 if (current.getLength() < Width)
2773 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2776 alignPanel.paintAlignment(true);
2779 if ((viewport.getSelectionGroup() != null
2780 && viewport.getSelectionGroup().getSize() < 4 && viewport
2781 .getSelectionGroup().getSize() > 0)
2782 || viewport.getAlignment().getHeight() < 4)
2789 new PCAPanel(viewport);
2790 } catch (java.lang.OutOfMemoryError ex)
2796 public void averageDistanceTreeMenuItem_actionPerformed()
2798 NewTreePanel("AV", "PID", "Average distance tree using PID");
2801 public void neighbourTreeMenuItem_actionPerformed()
2803 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2806 protected void njTreeBlosumMenuItem_actionPerformed()
2808 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2811 protected void avTreeBlosumMenuItem_actionPerformed()
2813 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2816 void NewTreePanel(String type, String pwType, String title)
2818 // are the sequences aligned?
2819 if (!viewport.getAlignment().isAligned(false))
2822 int Width = viewport.getAlignment().getWidth();
2824 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2826 current = viewport.getAlignment().getSequenceAt(i);
2828 if (current.getLength() < Width)
2830 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2833 alignPanel.paintAlignment(true);
2837 if ((viewport.getSelectionGroup() != null && viewport
2838 .getSelectionGroup().getSize() > 1)
2839 || (viewport.getAlignment().getHeight() > 1))
2841 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2843 addTreeMenuItem(tp, title);
2845 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2849 void loadTree_actionPerformed()
2851 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2852 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2853 cap.setTreeImport();
2854 Frame frame = new Frame();
2856 jalview.bin.JalviewLite.addFrame(frame,
2857 MessageManager.getString("label.paste_newick_file"), 400, 300);
2860 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2862 TreePanel tp = new TreePanel(alignPanel, treeFile,
2863 MessageManager.getString("label.load_tree_from_file"), tree);
2864 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2865 addTreeMenuItem(tp, treeFile);
2869 * sort the alignment using the given treePanel
2872 * tree used to sort view
2874 * string used for undo event name
2876 public void sortByTree(TreePanel treePanel, String title)
2878 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2880 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2881 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2882 // HistoryItem.SORT));
2883 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2884 "label.order_by_params", new String[] { title }), oldOrder,
2885 viewport.getAlignment()));
2886 alignPanel.paintAlignment(true);
2890 * Do any automatic reordering of the alignment and add the necessary bits to
2891 * the menu structure for the new tree
2896 protected void addTreeMenuItem(final TreePanel treePanel,
2899 final MenuItem item = new MenuItem(title);
2900 sortByTreeMenu.add(item);
2901 item.addActionListener(new java.awt.event.ActionListener()
2904 public void actionPerformed(ActionEvent evt)
2906 sortByTree(treePanel, title); // treePanel.getTitle());
2910 treePanel.addWindowListener(new WindowAdapter()
2913 public void windowOpened(WindowEvent e)
2915 if (viewport.sortByTree)
2917 sortByTree(treePanel, title);
2919 super.windowOpened(e);
2923 public void windowClosing(WindowEvent e)
2925 sortByTreeMenu.remove(item);
2930 public boolean sortBy(AlignmentOrder alorder, String undoname)
2932 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2933 if (viewport.applet.debug)
2935 System.err.println("Sorting " + alorder.getOrder().size()
2936 + " in alignment '" + getTitle() + "'");
2938 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2939 if (undoname != null)
2941 addHistoryItem(new OrderCommand(undoname, oldOrder,
2942 viewport.getAlignment()));
2944 alignPanel.paintAlignment(true);
2948 protected void documentation_actionPerformed()
2950 alignPanel.av.applet.openJalviewHelpUrl();
2953 protected void about_actionPerformed()
2956 class AboutPanel extends Canvas
2962 public AboutPanel(String version, String builddate)
2964 this.version = version;
2965 this.builddate = builddate;
2969 public void paint(Graphics g)
2971 g.setColor(Color.white);
2972 g.fillRect(0, 0, getSize().width, getSize().height);
2973 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2974 FontMetrics fm = g.getFontMetrics();
2975 int fh = fm.getHeight();
2977 g.setColor(Color.black);
2978 // TODO: update this text for each release or centrally store it for
2979 // lite and application
2980 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2981 g.drawString(MessageManager.formatMessage(
2982 "label.jalviewLite_release", new String[] { version }), x,
2984 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2985 g.drawString(MessageManager.formatMessage(
2986 "label.jaview_build_date", new String[] { builddate }), x,
2988 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2989 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2991 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2992 x + 50, y += fh + 8);
2994 MessageManager.getString("label.jalview_dev_managers"), x,
2996 g.drawString(MessageManager
2997 .getString("label.jalview_distribution_lists"), x, y += fh);
2998 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3001 MessageManager.getString("label.jalview_cite_1_authors"),
3004 MessageManager.getString("label.jalview_cite_1_title"), x,
3006 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3011 Frame frame = new Frame();
3012 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3014 jalview.bin.JalviewLite.addFrame(frame,
3015 MessageManager.getString("label.jalview"), 580, 220);
3019 public void showURL(String url, String target)
3021 if (viewport.applet == null)
3023 System.out.println("Not running as applet - no browser available.");
3027 viewport.applet.showURL(url, target);
3031 // ////////////////////////////////////////////////////////////////////////////////
3032 // JBuilder Graphics here
3034 MenuBar alignFrameMenuBar = new MenuBar();
3036 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3038 MenuItem loadApplication = new MenuItem(
3039 MessageManager.getString("label.view_full_application"));
3041 MenuItem loadTree = new MenuItem(
3042 MessageManager.getString("label.load_associated_tree"));
3044 MenuItem loadAnnotations = new MenuItem(
3045 MessageManager.getString("label.load_features_annotations"));
3047 MenuItem outputFeatures = new MenuItem(
3048 MessageManager.getString("label.export_features"));
3050 MenuItem outputAnnotations = new MenuItem(
3051 MessageManager.getString("label.export_annotations"));
3053 MenuItem closeMenuItem = new MenuItem(
3054 MessageManager.getString("action.close"));
3056 MenuItem selectAllSequenceMenuItem = new MenuItem(
3057 MessageManager.getString("action.select_all"));
3059 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3060 MessageManager.getString("action.deselect_all"));
3062 MenuItem invertSequenceMenuItem = new MenuItem(
3063 MessageManager.getString("action.invert_selection"));
3065 MenuItem remove2LeftMenuItem = new MenuItem();
3067 MenuItem remove2RightMenuItem = new MenuItem();
3069 MenuItem removeGappedColumnMenuItem = new MenuItem();
3071 MenuItem removeAllGapsMenuItem = new MenuItem();
3073 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3075 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3077 MenuItem sortPairwiseMenuItem = new MenuItem();
3079 MenuItem sortIDMenuItem = new MenuItem();
3081 MenuItem sortLengthMenuItem = new MenuItem();
3083 MenuItem sortGroupMenuItem = new MenuItem();
3085 MenuItem removeRedundancyMenuItem = new MenuItem();
3087 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3089 MenuItem PCAMenuItem = new MenuItem();
3091 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3093 MenuItem neighbourTreeMenuItem = new MenuItem();
3095 BorderLayout borderLayout1 = new BorderLayout();
3097 public Label statusBar = new Label();
3099 MenuItem clustalColour = new MenuItem();
3101 MenuItem zappoColour = new MenuItem();
3103 MenuItem taylorColour = new MenuItem();
3105 MenuItem hydrophobicityColour = new MenuItem();
3107 MenuItem helixColour = new MenuItem();
3109 MenuItem strandColour = new MenuItem();
3111 MenuItem turnColour = new MenuItem();
3113 MenuItem buriedColour = new MenuItem();
3115 MenuItem purinePyrimidineColour = new MenuItem();
3117 // MenuItem RNAInteractionColour = new MenuItem();
3119 MenuItem RNAHelixColour = new MenuItem();
3121 MenuItem userDefinedColour = new MenuItem();
3123 MenuItem PIDColour = new MenuItem();
3125 MenuItem BLOSUM62Colour = new MenuItem();
3127 MenuItem tcoffeeColour = new MenuItem();
3129 MenuItem njTreeBlosumMenuItem = new MenuItem();
3131 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3133 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3135 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3137 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3139 MenuItem alProperties = new MenuItem(
3140 MessageManager.getString("label.alignment_props"));
3142 MenuItem overviewMenuItem = new MenuItem();
3144 MenuItem undoMenuItem = new MenuItem();
3146 MenuItem redoMenuItem = new MenuItem();
3148 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3150 MenuItem noColourmenuItem = new MenuItem();
3152 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3154 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3156 MenuItem findMenuItem = new MenuItem();
3158 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3160 MenuItem nucleotideColour = new MenuItem();
3162 MenuItem deleteGroups = new MenuItem();
3164 MenuItem grpsFromSelection = new MenuItem();
3166 MenuItem createGroup = new MenuItem();
3168 MenuItem unGroup = new MenuItem();
3170 MenuItem delete = new MenuItem();
3172 MenuItem copy = new MenuItem();
3174 MenuItem cut = new MenuItem();
3176 Menu pasteMenu = new Menu();
3178 MenuItem pasteNew = new MenuItem();
3180 MenuItem pasteThis = new MenuItem();
3182 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3184 MenuItem font = new MenuItem();
3186 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3188 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3190 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3192 MenuItem modifyPID = new MenuItem();
3194 MenuItem modifyConservation = new MenuItem();
3196 CheckboxMenuItem autoCalculate = null;
3198 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3199 "Sort Alignment With New Tree", true);
3201 Menu sortByTreeMenu = new Menu();
3203 MenuItem inputText = new MenuItem();
3205 MenuItem documentation = new MenuItem();
3207 MenuItem about = new MenuItem();
3209 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3211 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3213 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3215 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3217 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3219 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3221 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3223 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3225 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3228 * Initialise menus and other items
3232 private void jbInit() throws Exception
3234 setMenuBar(alignFrameMenuBar);
3237 * Configure File menu items and actions
3240 .setLabel(MessageManager.getString("label.input_from_textbox"));
3241 inputText.addActionListener(this);
3242 Menu outputTextboxMenu = new Menu(
3243 MessageManager.getString("label.out_to_textbox"));
3244 for (String ff : FileFormat.getWritableFormats(true))
3246 MenuItem item = new MenuItem(ff);
3248 item.addActionListener(new java.awt.event.ActionListener()
3251 public void actionPerformed(ActionEvent e)
3253 outputText_actionPerformed(e);
3257 outputTextboxMenu.add(item);
3259 closeMenuItem.addActionListener(this);
3260 loadApplication.addActionListener(this);
3261 loadTree.addActionListener(this);
3262 loadAnnotations.addActionListener(this);
3263 outputFeatures.addActionListener(this);
3264 outputAnnotations.addActionListener(this);
3267 * Configure Edit menu items and actions
3269 undoMenuItem.setEnabled(false);
3270 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3271 undoMenuItem.addActionListener(this);
3272 redoMenuItem.setEnabled(false);
3273 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3274 redoMenuItem.addActionListener(this);
3275 copy.setLabel(MessageManager.getString("action.copy"));
3276 copy.addActionListener(this);
3277 cut.setLabel(MessageManager.getString("action.cut"));
3278 cut.addActionListener(this);
3279 delete.setLabel(MessageManager.getString("action.delete"));
3280 delete.addActionListener(this);
3281 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3282 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3283 pasteNew.addActionListener(this);
3284 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3285 pasteThis.addActionListener(this);
3286 remove2LeftMenuItem.setLabel(MessageManager
3287 .getString("action.remove_left"));
3288 remove2LeftMenuItem.addActionListener(this);
3289 remove2RightMenuItem.setLabel(MessageManager
3290 .getString("action.remove_right"));
3291 remove2RightMenuItem.addActionListener(this);
3292 removeGappedColumnMenuItem.setLabel(MessageManager
3293 .getString("action.remove_empty_columns"));
3294 removeGappedColumnMenuItem.addActionListener(this);
3295 removeAllGapsMenuItem.setLabel(MessageManager
3296 .getString("action.remove_all_gaps"));
3297 removeAllGapsMenuItem.addActionListener(this);
3298 removeRedundancyMenuItem.setLabel(MessageManager
3299 .getString("action.remove_redundancy"));
3300 removeRedundancyMenuItem.addActionListener(this);
3303 * Configure Select menu items and actions
3305 findMenuItem.setLabel(MessageManager.getString("action.find"));
3306 findMenuItem.addActionListener(this);
3307 selectAllSequenceMenuItem.addActionListener(this);
3308 deselectAllSequenceMenuItem.addActionListener(this);
3309 invertSequenceMenuItem.setLabel(MessageManager
3310 .getString("action.invert_sequence_selection"));
3311 invertSequenceMenuItem.addActionListener(this);
3312 invertColSel.setLabel(MessageManager
3313 .getString("action.invert_column_selection"));
3314 invertColSel.addActionListener(this);
3315 deleteGroups.setLabel(MessageManager
3316 .getString("action.undefine_groups"));
3317 deleteGroups.addActionListener(this);
3318 grpsFromSelection.setLabel(MessageManager
3319 .getString("action.make_groups_selection"));
3320 grpsFromSelection.addActionListener(this);
3321 createGroup.setLabel(MessageManager.getString("action.create_group"));
3322 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3323 annotationColumnSelection.setLabel(MessageManager
3324 .getString("action.select_by_annotation"));
3325 annotationColumnSelection.addActionListener(this);
3328 * Configure View menu items and actions
3330 newView.setLabel(MessageManager.getString("action.new_view"));
3331 newView.addActionListener(this);
3332 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3333 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3334 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3335 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3337 .setLabel(MessageManager.getString("label.selected_columns"));
3338 hideSequences.setLabel(MessageManager
3339 .getString("label.selected_sequences"));
3340 hideAllButSelection.setLabel(MessageManager
3341 .getString("label.all_but_selected_region"));
3342 hideAllSelection.setLabel(MessageManager
3343 .getString("label.selected_region"));
3344 showAllHidden.setLabel(MessageManager
3345 .getString("label.all_sequences_columns"));
3346 showColumns.addActionListener(this);
3347 showSeqs.addActionListener(this);
3348 hideColumns.addActionListener(this);
3349 hideSequences.addActionListener(this);
3350 hideAllButSelection.addActionListener(this);
3351 hideAllSelection.addActionListener(this);
3352 showAllHidden.addActionListener(this);
3353 featureSettings.setLabel(MessageManager
3354 .getString("action.feature_settings"));
3355 featureSettings.addActionListener(this);
3356 sequenceFeatures.setLabel(MessageManager
3357 .getString("label.show_sequence_features"));
3358 sequenceFeatures.addItemListener(this);
3359 sequenceFeatures.setState(false);
3360 followMouseOverFlag.setLabel(MessageManager
3361 .getString("label.automatic_scrolling"));
3362 followMouseOverFlag.addItemListener(this);
3363 alProperties.addActionListener(this);
3364 overviewMenuItem.setLabel(MessageManager
3365 .getString("label.overview_window"));
3366 overviewMenuItem.addActionListener(this);
3369 * Configure Annotations menu items and actions
3371 annotationPanelMenuItem.setLabel(MessageManager
3372 .getString("label.show_annotations"));
3373 annotationPanelMenuItem.addItemListener(this);
3374 showGroupConsensus.setLabel(MessageManager
3375 .getString("label.group_consensus"));
3376 showGroupConservation.setLabel(MessageManager
3377 .getString("label.group_conservation"));
3378 showConsensusHistogram.setLabel(MessageManager
3379 .getString("label.show_consensus_histogram"));
3380 showSequenceLogo.setLabel(MessageManager
3381 .getString("label.show_consensus_logo"));
3382 normSequenceLogo.setLabel(MessageManager
3383 .getString("label.norm_consensus_logo"));
3384 applyAutoAnnotationSettings.setLabel(MessageManager
3385 .getString("label.apply_all_groups"));
3386 applyAutoAnnotationSettings.setState(true);
3387 Menu autoAnnMenu = new Menu(
3388 MessageManager.getString("label.autocalculated_annotation"));
3389 showGroupConsensus.addItemListener(this);
3390 showGroupConservation.addItemListener(this);
3391 showConsensusHistogram.addItemListener(this);
3392 showSequenceLogo.addItemListener(this);
3393 normSequenceLogo.addItemListener(this);
3394 applyAutoAnnotationSettings.addItemListener(this);
3395 showAlignmentAnnotations = new CheckboxMenuItem(
3396 MessageManager.getString("label.show_all_al_annotations"));
3397 showSequenceAnnotations = new CheckboxMenuItem(
3398 MessageManager.getString("label.show_all_seq_annotations"));
3399 sortAnnBySequence = new CheckboxMenuItem(
3400 MessageManager.getString("label.sort_annotations_by_sequence"));
3401 sortAnnByLabel = new CheckboxMenuItem(
3402 MessageManager.getString("label.sort_annotations_by_label"));
3403 showAutoFirst = new CheckboxMenuItem(
3404 MessageManager.getString("label.show_first"));
3405 showAutoFirst.setState(false); // pending applet parameter
3406 setShowAutoCalculatedAbove(showAutoFirst.getState());
3407 showAutoLast = new CheckboxMenuItem(
3408 MessageManager.getString("label.show_last"));
3409 showAutoLast.setState(!showAutoFirst.getState());
3410 showAlignmentAnnotations.addItemListener(this);
3411 showSequenceAnnotations.addItemListener(this);
3412 sortAnnBySequence.addItemListener(this);
3413 sortAnnByLabel.addItemListener(this);
3414 showAutoFirst.addItemListener(this);
3415 showAutoLast.addItemListener(this);
3418 * Configure Format menu items and actions
3420 font.setLabel(MessageManager.getString("action.font"));
3421 font.addActionListener(this);
3422 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3423 scaleAbove.setState(true);
3424 scaleAbove.setEnabled(false);
3425 scaleAbove.addItemListener(this);
3426 scaleLeft.setEnabled(false);
3427 scaleLeft.setState(true);
3428 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3429 scaleLeft.addItemListener(this);
3430 scaleRight.setEnabled(false);
3431 scaleRight.setState(true);
3432 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3433 scaleRight.addItemListener(this);
3434 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3435 viewBoxesMenuItem.setState(true);
3436 viewBoxesMenuItem.addItemListener(this);
3437 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3438 viewTextMenuItem.setState(true);
3439 viewTextMenuItem.addItemListener(this);
3440 colourTextMenuItem.setLabel(MessageManager
3441 .getString("label.colour_text"));
3442 colourTextMenuItem.addItemListener(this);
3443 displayNonconservedMenuItem.setLabel(MessageManager
3444 .getString("label.show_non_conserved"));
3445 displayNonconservedMenuItem.addItemListener(this);
3446 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3447 wrapMenuItem.addItemListener(this);
3448 renderGapsMenuItem.setLabel(MessageManager
3449 .getString("action.show_gaps"));
3450 renderGapsMenuItem.setState(true);
3451 renderGapsMenuItem.addItemListener(this);
3452 centreColumnLabelFlag.setLabel(MessageManager
3453 .getString("label.centre_column_labels"));
3454 centreColumnLabelFlag.addItemListener(this);
3455 seqLimits.setState(true);
3456 seqLimits.setLabel(MessageManager
3457 .getString("label.show_sequence_limits"));
3458 seqLimits.addItemListener(this);
3461 * Configure Colour menu items and actions
3463 applyToAllGroups.setLabel(MessageManager
3464 .getString("label.apply_colour_to_all_groups"));
3465 applyToAllGroups.setState(true);
3466 applyToAllGroups.addItemListener(this);
3467 clustalColour.setLabel(MessageManager
3468 .getString("label.colourScheme_clustal"));
3469 clustalColour.addActionListener(this);
3470 zappoColour.setLabel(MessageManager
3471 .getString("label.colourScheme_zappo"));
3472 zappoColour.addActionListener(this);
3473 taylorColour.setLabel(MessageManager
3474 .getString("label.colourScheme_taylor"));
3475 taylorColour.addActionListener(this);
3476 hydrophobicityColour.setLabel(MessageManager
3477 .getString("label.colourScheme_hydrophobic"));
3478 hydrophobicityColour.addActionListener(this);
3479 helixColour.setLabel(MessageManager
3480 .getString("label.colourScheme_helix_propensity"));
3481 helixColour.addActionListener(this);
3482 strandColour.setLabel(MessageManager
3483 .getString("label.colourScheme_strand_propensity"));
3484 strandColour.addActionListener(this);
3485 turnColour.setLabel(MessageManager
3486 .getString("label.colourScheme_turn_propensity"));
3487 turnColour.addActionListener(this);
3488 buriedColour.setLabel(MessageManager
3489 .getString("label.colourScheme_buried_index"));
3490 buriedColour.addActionListener(this);
3491 purinePyrimidineColour.setLabel(MessageManager
3492 .getString("label.colourScheme_purine/pyrimidine"));
3493 purinePyrimidineColour.addActionListener(this);
3494 // RNAInteractionColour.setLabel(MessageManager
3495 // .getString("label.rna_interaction"));
3496 // RNAInteractionColour.addActionListener(this);
3497 RNAHelixColour.setLabel(MessageManager
3498 .getString("label.colourScheme_rna_helices"));
3499 RNAHelixColour.addActionListener(this);
3500 userDefinedColour.setLabel(MessageManager
3501 .getString("action.user_defined"));
3502 userDefinedColour.addActionListener(this);
3503 PIDColour.setLabel(MessageManager
3504 .getString("label.colourScheme_%_identity"));
3505 PIDColour.addActionListener(this);
3506 BLOSUM62Colour.setLabel(MessageManager
3507 .getString("label.colourScheme_blosum62"));
3508 BLOSUM62Colour.addActionListener(this);
3509 tcoffeeColour.setLabel(MessageManager
3510 .getString("label.colourScheme_t-coffee_scores"));
3511 // it will be enabled only if a score file is provided
3512 tcoffeeColour.setEnabled(false);
3513 tcoffeeColour.addActionListener(this);
3514 conservationMenuItem.setLabel(MessageManager
3515 .getString("action.by_conservation"));
3516 conservationMenuItem.addItemListener(this);
3517 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3518 noColourmenuItem.addActionListener(this);
3519 abovePIDThreshold.setLabel(MessageManager
3520 .getString("label.above_identity_threshold"));
3521 abovePIDThreshold.addItemListener(this);
3522 nucleotideColour.setLabel(MessageManager
3523 .getString("label.colourScheme_nucleotide"));
3524 nucleotideColour.addActionListener(this);
3525 modifyPID.setLabel(MessageManager
3526 .getString("label.modify_identity_threshold"));
3527 modifyPID.addActionListener(this);
3528 modifyConservation.setLabel(MessageManager
3529 .getString("label.modify_conservation_threshold"));
3530 modifyConservation.addActionListener(this);
3531 annotationColour.setLabel(MessageManager
3532 .getString("action.by_annotation"));
3533 annotationColour.addActionListener(this);
3536 * Configure Calculate menu items and actions
3538 sortPairwiseMenuItem.setLabel(MessageManager
3539 .getString("action.by_pairwise_id"));
3540 sortPairwiseMenuItem.addActionListener(this);
3541 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3542 sortIDMenuItem.addActionListener(this);
3543 sortLengthMenuItem.setLabel(MessageManager
3544 .getString("action.by_length"));
3545 sortLengthMenuItem.addActionListener(this);
3546 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3547 sortGroupMenuItem.addActionListener(this);
3548 pairwiseAlignmentMenuItem.setLabel(MessageManager
3549 .getString("action.pairwise_alignment"));
3550 pairwiseAlignmentMenuItem.addActionListener(this);
3551 PCAMenuItem.setLabel(MessageManager
3552 .getString("label.principal_component_analysis"));
3553 PCAMenuItem.addActionListener(this);
3554 autoCalculate = new CheckboxMenuItem(
3555 MessageManager.getString("label.autocalculate_consensus"), true);
3556 averageDistanceTreeMenuItem.setLabel(MessageManager
3557 .getString("label.average_distance_identity"));
3558 averageDistanceTreeMenuItem.addActionListener(this);
3559 neighbourTreeMenuItem.setLabel(MessageManager
3560 .getString("label.neighbour_joining_identity"));
3561 neighbourTreeMenuItem.addActionListener(this);
3562 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3563 .getString("label.average_distance_blosum62"));
3564 avDistanceTreeBlosumMenuItem.addActionListener(this);
3565 njTreeBlosumMenuItem.setLabel(MessageManager
3566 .getString("label.neighbour_blosum62"));
3567 njTreeBlosumMenuItem.addActionListener(this);
3568 sortByTreeMenu.setLabel(MessageManager
3569 .getString("action.by_tree_order"));
3570 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3571 Menu calculateTreeMenu = new Menu(
3572 MessageManager.getString("action.calculate_tree"));
3573 autoCalculate.addItemListener(this);
3574 sortByTree.addItemListener(this);
3577 * Configure Help menu items and actions
3579 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3580 documentation.setLabel(MessageManager.getString("label.documentation"));
3581 documentation.addActionListener(this);
3582 about.setLabel(MessageManager.getString("label.about"));
3583 about.addActionListener(this);
3586 * Add top level menus to frame
3588 alignFrameMenuBar.add(fileMenu);
3589 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3590 alignFrameMenuBar.add(editMenu);
3591 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3592 alignFrameMenuBar.add(selectMenu);
3593 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3594 alignFrameMenuBar.add(viewMenu);
3595 Menu annotationsMenu = new Menu(
3596 MessageManager.getString("action.annotations"));
3597 alignFrameMenuBar.add(annotationsMenu);
3598 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3599 alignFrameMenuBar.add(formatMenu);
3600 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3601 alignFrameMenuBar.add(colourMenu);
3602 Menu calculateMenu = new Menu(
3603 MessageManager.getString("action.calculate"));
3604 alignFrameMenuBar.add(calculateMenu);
3605 alignFrameMenuBar.add(helpMenu);
3610 fileMenu.add(inputText);
3611 fileMenu.add(loadTree);
3612 fileMenu.add(loadAnnotations);
3613 fileMenu.addSeparator();
3614 fileMenu.add(outputTextboxMenu);
3615 fileMenu.add(outputFeatures);
3616 fileMenu.add(outputAnnotations);
3617 if (jalviewServletURL != null)
3619 fileMenu.add(loadApplication);
3621 fileMenu.addSeparator();
3622 fileMenu.add(closeMenuItem);
3627 editMenu.add(undoMenuItem);
3628 editMenu.add(redoMenuItem);
3631 pasteMenu.add(pasteNew);
3632 pasteMenu.add(pasteThis);
3633 editMenu.add(pasteMenu);
3634 editMenu.add(delete);
3635 editMenu.addSeparator();
3636 editMenu.add(remove2LeftMenuItem);
3637 editMenu.add(remove2RightMenuItem);
3638 editMenu.add(removeGappedColumnMenuItem);
3639 editMenu.add(removeAllGapsMenuItem);
3640 editMenu.add(removeRedundancyMenuItem);
3645 selectMenu.add(findMenuItem);
3646 selectMenu.addSeparator();
3647 selectMenu.add(selectAllSequenceMenuItem);
3648 selectMenu.add(deselectAllSequenceMenuItem);
3649 selectMenu.add(invertSequenceMenuItem);
3650 selectMenu.add(invertColSel);
3651 selectMenu.add(createGroup);
3652 selectMenu.add(unGroup);
3653 selectMenu.add(grpsFromSelection);
3654 selectMenu.add(deleteGroups);
3655 selectMenu.add(annotationColumnSelection);
3660 viewMenu.add(newView);
3661 viewMenu.addSeparator();
3662 showMenu.add(showColumns);
3663 showMenu.add(showSeqs);
3664 showMenu.add(showAllHidden);
3665 viewMenu.add(showMenu);
3666 hideMenu.add(hideColumns);
3667 hideMenu.add(hideSequences);
3668 hideMenu.add(hideAllSelection);
3669 hideMenu.add(hideAllButSelection);
3670 viewMenu.add(hideMenu);
3671 viewMenu.addSeparator();
3672 viewMenu.add(followMouseOverFlag);
3673 viewMenu.addSeparator();
3674 viewMenu.add(sequenceFeatures);
3675 viewMenu.add(featureSettings);
3676 viewMenu.addSeparator();
3677 viewMenu.add(alProperties);
3678 viewMenu.addSeparator();
3679 viewMenu.add(overviewMenuItem);
3684 annotationsMenu.add(annotationPanelMenuItem);
3685 annotationsMenu.addSeparator();
3686 annotationsMenu.add(showAlignmentAnnotations);
3687 annotationsMenu.add(showSequenceAnnotations);
3688 annotationsMenu.add(sortAnnBySequence);
3689 annotationsMenu.add(sortAnnByLabel);
3690 annotationsMenu.addSeparator();
3691 autoAnnMenu.add(showAutoFirst);
3692 autoAnnMenu.add(showAutoLast);
3693 autoAnnMenu.addSeparator();
3694 autoAnnMenu.add(applyAutoAnnotationSettings);
3695 autoAnnMenu.add(showConsensusHistogram);
3696 autoAnnMenu.add(showSequenceLogo);
3697 autoAnnMenu.add(normSequenceLogo);
3698 autoAnnMenu.addSeparator();
3699 autoAnnMenu.add(showGroupConservation);
3700 autoAnnMenu.add(showGroupConsensus);
3701 annotationsMenu.add(autoAnnMenu);
3706 formatMenu.add(font);
3707 formatMenu.add(seqLimits);
3708 formatMenu.add(wrapMenuItem);
3709 formatMenu.add(scaleAbove);
3710 formatMenu.add(scaleLeft);
3711 formatMenu.add(scaleRight);
3712 formatMenu.add(viewBoxesMenuItem);
3713 formatMenu.add(viewTextMenuItem);
3714 formatMenu.add(colourTextMenuItem);
3715 formatMenu.add(displayNonconservedMenuItem);
3716 formatMenu.add(renderGapsMenuItem);
3717 formatMenu.add(centreColumnLabelFlag);
3722 colourMenu.add(applyToAllGroups);
3723 colourMenu.addSeparator();
3724 colourMenu.add(noColourmenuItem);
3725 colourMenu.add(clustalColour);
3726 colourMenu.add(BLOSUM62Colour);
3727 colourMenu.add(PIDColour);
3728 colourMenu.add(zappoColour);
3729 colourMenu.add(taylorColour);
3730 colourMenu.add(hydrophobicityColour);
3731 colourMenu.add(helixColour);
3732 colourMenu.add(strandColour);
3733 colourMenu.add(turnColour);
3734 colourMenu.add(buriedColour);
3735 colourMenu.add(nucleotideColour);
3736 colourMenu.add(purinePyrimidineColour);
3737 // colourMenu.add(RNAInteractionColour);
3738 colourMenu.add(tcoffeeColour);
3739 colourMenu.add(userDefinedColour);
3740 colourMenu.addSeparator();
3741 colourMenu.add(conservationMenuItem);
3742 colourMenu.add(modifyConservation);
3743 colourMenu.add(abovePIDThreshold);
3744 colourMenu.add(modifyPID);
3745 colourMenu.add(annotationColour);
3746 colourMenu.add(RNAHelixColour);
3751 sortMenu.add(sortIDMenuItem);
3752 sortMenu.add(sortLengthMenuItem);
3753 sortMenu.add(sortByTreeMenu);
3754 sortMenu.add(sortGroupMenuItem);
3755 sortMenu.add(sortPairwiseMenuItem);
3756 calculateMenu.add(sortMenu);
3757 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3758 calculateTreeMenu.add(neighbourTreeMenuItem);
3759 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3760 calculateTreeMenu.add(njTreeBlosumMenuItem);
3761 calculateMenu.add(calculateTreeMenu);
3762 calculateMenu.addSeparator();
3763 calculateMenu.add(pairwiseAlignmentMenuItem);
3764 calculateMenu.add(PCAMenuItem);
3765 calculateMenu.add(autoCalculate);
3766 calculateMenu.add(sortByTree);
3771 helpMenu.add(documentation);
3772 helpMenu.add(about);
3777 statusBar.setBackground(Color.white);
3778 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3779 statusBar.setText(MessageManager.getString("label.status_bar"));
3780 this.add(statusBar, BorderLayout.SOUTH);
3784 public void setStatus(String string)
3786 statusBar.setText(string);
3789 MenuItem featureSettings = new MenuItem();
3791 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3793 MenuItem annotationColour = new MenuItem();
3795 MenuItem annotationColumnSelection = new MenuItem();
3797 MenuItem invertColSel = new MenuItem();
3799 MenuItem showColumns = new MenuItem();
3801 MenuItem showSeqs = new MenuItem();
3803 MenuItem hideColumns = new MenuItem();
3805 MenuItem hideSequences = new MenuItem();
3807 MenuItem hideAllButSelection = new MenuItem();
3809 MenuItem hideAllSelection = new MenuItem();
3811 MenuItem showAllHidden = new MenuItem();
3813 MenuItem newView = new MenuItem();
3815 private CheckboxMenuItem showAlignmentAnnotations;
3817 private CheckboxMenuItem showSequenceAnnotations;
3819 private CheckboxMenuItem sortAnnBySequence;
3821 private CheckboxMenuItem sortAnnByLabel;
3823 private CheckboxMenuItem showAutoFirst;
3825 private CheckboxMenuItem showAutoLast;
3827 private SplitFrame splitFrame;
3830 * Attach the alignFrame panels after embedding menus, if necessary. This used
3831 * to be called setEmbedded, but is now creates the dropdown menus in a
3832 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3834 * @param reallyEmbedded
3835 * true to attach the view to the applet area on the page rather than
3838 public void createAlignFrameWindow(boolean reallyEmbedded)
3842 embedAlignFrameInApplet(viewport.applet);
3847 // test and embed menu bar if necessary.
3849 if (embedMenuIfNeeded(alignPanel))
3852 * adjust for status bar height too. ? pointless as overridden by layout
3855 alignPanel.setSize(getSize().width,
3856 getSize().height - statusBar.getHeight());
3858 add(statusBar, BorderLayout.SOUTH);
3859 add(alignPanel, BorderLayout.CENTER);
3860 // and register with the applet so it can pass external API calls to us
3861 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3867 * Add the components of this AlignFrame to the applet container.
3871 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3874 // Explicitly build the embedded menu panel for the on-page applet
3876 // view cannot be closed if its actually on the page
3877 fileMenu.remove(closeMenuItem);
3878 fileMenu.remove(3); // Remove Separator
3879 // construct embedded menu, using default font
3880 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3881 // and actually add the components to the applet area
3882 theApplet.setLayout(new BorderLayout());
3883 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3884 theApplet.add(statusBar, BorderLayout.SOUTH);
3885 // TODO should size be left to the layout manager?
3886 alignPanel.setSize(theApplet.getSize().width,
3887 theApplet.getSize().height - embeddedMenu.getHeight()
3888 - statusBar.getHeight());
3889 theApplet.add(alignPanel, BorderLayout.CENTER);
3890 final AlignFrame me = this;
3891 theApplet.addFocusListener(new FocusListener()
3895 public void focusLost(FocusEvent e)
3897 if (theApplet.currentAlignFrame == me)
3899 theApplet.currentAlignFrame = null;
3904 public void focusGained(FocusEvent e)
3906 theApplet.currentAlignFrame = me;
3909 theApplet.validate();
3913 * create a new binding between structures in an existing jmol viewer instance
3914 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3915 * this does not open a new Jmol window, or modify the display of the
3916 * structures in the original jmol window. Note This method doesn't work
3917 * without an additional javascript library to exchange messages between the
3918 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3921 * JmolViewer instance
3922 * @param sequenceIds
3923 * - sequence Ids to search for associations
3925 public SequenceStructureBinding addStructureViewInstance(
3926 Object jmolviewer, String[] sequenceIds)
3928 Viewer viewer = null;
3931 viewer = (Viewer) jmolviewer;
3932 } catch (ClassCastException ex)
3934 System.err.println("Unsupported viewer object :"
3935 + jmolviewer.getClass());
3939 System.err.println("Can't use this object as a structure viewer:"
3940 + jmolviewer.getClass());
3943 SequenceI[] seqs = null;
3944 if (sequenceIds == null || sequenceIds.length == 0)
3946 seqs = viewport.getAlignment().getSequencesArray();
3950 Vector sqi = new Vector();
3951 AlignmentI al = viewport.getAlignment();
3952 for (int sid = 0; sid < sequenceIds.length; sid++)
3954 SequenceI sq = al.findName(sequenceIds[sid]);
3962 seqs = new SequenceI[sqi.size()];
3963 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3965 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3973 AAStructureBindingModel jmv = null;
3974 // TODO: search for a jmv that involves viewer
3976 { // create a new viewer/jalview binding.
3977 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3984 * bind a pdb file to a sequence in the current view
3987 * - sequenceId within the dataset.
3988 * @param pdbEntryString
3989 * - the short name for the PDB file
3991 * - pdb file - either a URL or a valid PDB file.
3992 * @return true if binding was as success TODO: consider making an exception
3993 * structure for indicating when PDB parsing or sequenceId location
3996 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3999 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4000 boolean needtoadd = false;
4001 if (toaddpdb != null)
4003 Vector pdbe = toaddpdb.getAllPDBEntries();
4004 PDBEntry pdbentry = null;
4005 if (pdbe != null && pdbe.size() > 0)
4007 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4009 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4010 if (!pdbentry.getId().equals(pdbEntryString)
4011 && !pdbentry.getFile().equals(pdbFile))
4021 if (pdbentry == null)
4023 pdbentry = new PDBEntry();
4024 pdbentry.setId(pdbEntryString);
4025 pdbentry.setFile(pdbFile);
4026 needtoadd = true; // add this new entry to sequence.
4028 // resolve data source
4029 // TODO: this code should be a refactored to an io package
4030 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4031 pdbFile, FileFormat.PDB);
4032 if (protocol == null)
4038 pdbentry.setProperty("protocol", protocol);
4039 toaddpdb.addPDBId(pdbentry);
4040 alignPanel.getStructureSelectionManager()
4041 .registerPDBEntry(pdbentry);
4047 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4051 Vector sequences = new Vector();
4052 for (int i = 0; i < seqs.length; i++)
4054 if (seqs[i] != null)
4056 sequences.addElement(new Object[] { seqs[i],
4057 (chains != null) ? chains[i] : null });
4060 seqs = new SequenceI[sequences.size()];
4061 chains = new String[sequences.size()];
4062 for (int i = 0, isize = sequences.size(); i < isize; i++)
4064 Object[] oj = (Object[]) sequences.elementAt(i);
4066 seqs[i] = (SequenceI) oj[0];
4067 chains[i] = (String) oj[1];
4070 return new Object[] { seqs, chains };
4074 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4075 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4077 // Scrub any null sequences from the array
4078 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4079 seqs = (SequenceI[]) sqch[0];
4080 chains = (String[]) sqch[1];
4081 if (seqs == null || seqs.length == 0)
4084 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4086 if (protocol == null)
4088 String sourceType = (String) pdb.getProperty("protocol");
4091 protocol = DataSourceType.valueOf(sourceType);
4092 } catch (IllegalArgumentException e)
4096 if (protocol == null)
4098 System.err.println("Couldn't work out protocol to open structure: "
4103 if (applet.useXtrnalSviewer)
4105 // register the association(s) and quit, don't create any windows.
4106 if (StructureSelectionManager.getStructureSelectionManager(applet)
4107 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4109 System.err.println("Failed to map " + pdb.getFile() + " ("
4110 + protocol + ") to any sequences");
4114 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4116 // can only do alignments with Jmol
4117 // find the last jmol window assigned to this alignment
4118 AppletJmol ajm = null, tajm;
4119 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4120 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4122 tajm = (AppletJmol) jmols.elementAt(i);
4123 if (tajm.ap.alignFrame == this)
4132 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4133 // try and add the pdb structure
4138 // otherwise, create a new window
4139 if (applet.jmolAvailable)
4141 new AppletJmol(pdb, seqs, chains, alignPanel,
4143 applet.lastFrameX += 40;
4144 applet.lastFrameY += 40;
4148 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4153 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4154 SequenceI[][] seqs, String[][] chains, String[] protocols)
4156 // TODO Auto-generated method stub
4157 System.err.println("Aligned Structure View: Not yet implemented.");
4161 * modify the current selection, providing the user has not made a selection
4165 * - sequences from this alignment
4167 * - columns to be selected on the alignment
4169 public void select(SequenceGroup sel, ColumnSelection csel)
4171 alignPanel.seqPanel.selection(sel, csel, null);
4174 public void scrollTo(int row, int column)
4176 alignPanel.seqPanel.scrollTo(row, column);
4179 public void scrollToRow(int row)
4181 alignPanel.seqPanel.scrollToRow(row);
4184 public void scrollToColumn(int column)
4186 alignPanel.seqPanel.scrollToColumn(column);
4190 * @return the alignments unique ID.
4192 public String getSequenceSetId()
4194 return viewport.getSequenceSetId();
4198 * Load the (T-Coffee) score file from the specified url
4201 * File/URL/T-COFFEE score file contents
4202 * @throws IOException
4203 * @return true if alignment was annotated with data from source
4205 public boolean loadScoreFile(String source) throws IOException
4208 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4209 AppletFormatAdapter.checkProtocol(source));
4210 if (!file.isValid())
4212 // TODO: raise dialog for gui
4213 System.err.println("Problems parsing T-Coffee scores: "
4214 + file.getWarningMessage());
4215 System.err.println("Origin was:\n" + source);
4220 * check that the score matrix matches the alignment dimensions
4223 if ((aln = viewport.getAlignment()) != null
4224 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4227 // TODO: raise a dialog box here rather than bomb out.
4229 .println("The scores matrix does not match the alignment dimensions");
4233 // TODO add parameter to indicate if matching should be done
4234 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4236 alignPanel.fontChanged();
4237 tcoffeeColour.setEnabled(true);
4238 // switch to this color
4239 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4244 System.err.println("Problems resolving T-Coffee scores:");
4245 if (file.getWarningMessage() != null)
4247 System.err.println(file.getWarningMessage());
4253 public SplitFrame getSplitFrame()
4255 return this.splitFrame;
4258 public void setSplitFrame(SplitFrame sf)
4260 this.splitFrame = sf;
4263 // may not need this
4265 public void setShowSeqFeatures(boolean b)
4267 // showSeqFeatures.setSelected(b);
4268 viewport.setShowSequenceFeatures(b);
4273 public void setMenusForViewport()
4275 // setMenusFromViewport(viewport);
4280 public void refreshFeatureUI(boolean enableIfNecessary)
4282 if (enableIfNecessary)
4284 sequenceFeatures.setState(true);
4285 alignPanel.av.setShowSequenceFeatures(true);
4290 public FeatureSettingsControllerI getFeatureSettingsUI()
4292 return alignPanel.av.featureSettings;