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.FileFormatI;
56 import jalview.io.FileFormats;
57 import jalview.io.TCoffeeScoreFile;
58 import jalview.schemes.Blosum62ColourScheme;
59 import jalview.schemes.BuriedColourScheme;
60 import jalview.schemes.ClustalxColourScheme;
61 import jalview.schemes.ColourSchemeI;
62 import jalview.schemes.HelixColourScheme;
63 import jalview.schemes.HydrophobicColourScheme;
64 import jalview.schemes.NucleotideColourScheme;
65 import jalview.schemes.PIDColourScheme;
66 import jalview.schemes.PurinePyrimidineColourScheme;
67 import jalview.schemes.RNAHelicesColour;
68 import jalview.schemes.StrandColourScheme;
69 import jalview.schemes.TCoffeeColourScheme;
70 import jalview.schemes.TaylorColourScheme;
71 import jalview.schemes.TurnColourScheme;
72 import jalview.schemes.ZappoColourScheme;
73 import jalview.structure.StructureSelectionManager;
74 import jalview.structures.models.AAStructureBindingModel;
75 import jalview.util.MappingUtils;
76 import jalview.util.MessageManager;
77 import jalview.viewmodel.AlignmentViewport;
78 import jalview.viewmodel.ViewportRanges;
80 import java.awt.BorderLayout;
81 import java.awt.Canvas;
82 import java.awt.CheckboxMenuItem;
83 import java.awt.Color;
84 import java.awt.FlowLayout;
86 import java.awt.FontMetrics;
87 import java.awt.Frame;
88 import java.awt.Graphics;
89 import java.awt.Label;
91 import java.awt.MenuBar;
92 import java.awt.MenuItem;
93 import java.awt.Panel;
94 import java.awt.event.ActionEvent;
95 import java.awt.event.ActionListener;
96 import java.awt.event.FocusEvent;
97 import java.awt.event.FocusListener;
98 import java.awt.event.ItemEvent;
99 import java.awt.event.ItemListener;
100 import java.awt.event.KeyEvent;
101 import java.awt.event.KeyListener;
102 import java.awt.event.WindowAdapter;
103 import java.awt.event.WindowEvent;
104 import java.io.IOException;
106 import java.net.URLEncoder;
107 import java.util.Arrays;
108 import java.util.Deque;
109 import java.util.HashMap;
110 import java.util.List;
111 import java.util.Map;
112 import java.util.StringTokenizer;
113 import java.util.Vector;
115 import org.jmol.viewer.Viewer;
117 public class AlignFrame extends EmbmenuFrame implements ActionListener,
118 ItemListener, KeyListener, AlignViewControllerGuiI
120 public AlignViewControllerI avc;
122 public AlignmentPanel alignPanel;
124 public AlignViewport viewport;
126 // width and height may be overridden by applet parameters
127 int frameWidth = 700;
129 int frameHeight = 500;
131 String jalviewServletURL;
134 * Flag for showing autocalculated consensus above or below other consensus
137 private boolean showAutoCalculatedAbove;
139 private SequenceAnnotationOrder annotationSortOrder;
142 * Constructor that creates the frame and adds it to the display.
149 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
152 this(al, applet, title, embedded, true);
156 * Constructor that optionally allows the frame to be displayed or only
163 * @param addToDisplay
165 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
166 boolean embedded, boolean addToDisplay)
168 this(al, null, null, applet, title, embedded, addToDisplay);
171 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
172 ColumnSelection columnSelection, JalviewLite applet,
173 String title, boolean embedded)
175 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
178 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
179 ColumnSelection columnSelection, JalviewLite applet,
180 String title, boolean embedded, boolean addToDisplay)
184 jalviewServletURL = applet.getParameter("APPLICATION_URL");
190 } catch (Exception ex)
192 ex.printStackTrace();
194 // need to get window geometry before we calculate alignment layout
200 param = applet.getParameter("windowWidth");
203 int width = Integer.parseInt(param);
206 param = applet.getParameter("windowHeight");
209 int height = Integer.parseInt(param);
210 frameHeight = height;
212 } catch (Exception ex)
216 viewport = new AlignViewport(al, applet);
218 if (hiddenSeqs != null && hiddenSeqs.length > 0)
220 viewport.hideSequence(hiddenSeqs);
222 if (columnSelection != null)
224 viewport.setColumnSelection(columnSelection);
226 viewport.setScaleAboveWrapped(scaleAbove.getState());
228 alignPanel = new AlignmentPanel(this, viewport);
229 avc = new jalview.controller.AlignViewController(this, viewport,
231 viewport.updateConservation(alignPanel);
232 viewport.updateConsensus(alignPanel);
234 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
235 followMouseOverFlag.setState(viewport.isFollowHighlight());
236 showGroupConsensus.setState(viewport.isShowGroupConsensus());
237 showGroupConservation.setState(viewport.isShowGroupConservation());
238 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
239 showSequenceLogo.setState(viewport.isShowSequenceLogo());
240 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
241 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
242 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
243 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
244 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
245 showAlignmentAnnotations.setState(true);
246 showSequenceAnnotations.setState(false);
248 seqLimits.setState(viewport.getShowJVSuffix());
252 String param = applet.getParameter("sortBy");
255 if (param.equalsIgnoreCase("Id"))
257 sortIDMenuItem_actionPerformed();
259 else if (param.equalsIgnoreCase("Pairwise Identity"))
261 sortPairwiseMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Length"))
265 sortLengthMenuItem_actionPerformed();
269 param = applet.getParameter("wrap");
272 if (param.equalsIgnoreCase("true"))
274 wrapMenuItem.setState(true);
275 wrapMenuItem_actionPerformed();
278 param = applet.getParameter("centrecolumnlabels");
281 centreColumnLabelFlag.setState(true);
282 centreColumnLabelFlag_stateChanged();
286 if (viewport.getAlignment().isNucleotide())
288 conservationMenuItem.setEnabled(false);
289 clustalColour.setEnabled(false);
290 BLOSUM62Colour.setEnabled(false);
291 zappoColour.setEnabled(false);
292 taylorColour.setEnabled(false);
293 hydrophobicityColour.setEnabled(false);
294 helixColour.setEnabled(false);
295 strandColour.setEnabled(false);
296 turnColour.setEnabled(false);
297 buriedColour.setEnabled(false);
298 viewport.updateStrucConsensus(alignPanel);
299 if (viewport.getAlignment().hasRNAStructure())
301 RNAHelixColour.setEnabled(true);
305 RNAHelixColour.setEnabled(false);
310 RNAHelixColour.setEnabled(false);
311 purinePyrimidineColour.setEnabled(false);
312 nucleotideColour.setEnabled(false);
314 // Some JVMS send keyevents to Top frame or lowest panel,
315 // Havent worked out why yet. So add to both this frame and seqCanvas for
317 this.addKeyListener(this);
318 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
319 alignPanel.idPanel.idCanvas.addKeyListener(this);
320 alignPanel.scalePanel.addKeyListener(this);
321 alignPanel.annotationPanel.addKeyListener(this);
322 alignPanel.annotationPanelHolder.addKeyListener(this);
323 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
324 alignPanel.alabels.addKeyListener(this);
326 setAnnotationsVisibility();
330 addToDisplay(embedded);
337 public void addToDisplay(boolean embedded)
339 createAlignFrameWindow(embedded);
341 alignPanel.adjustAnnotationHeight();
342 alignPanel.paintAlignment(true);
345 public AlignViewport getAlignViewport()
350 public SeqCanvas getSeqcanvas()
352 return alignPanel.seqPanel.seqCanvas;
356 * Load a features file onto the alignment
359 * file URL, content, or other resolvable path
361 * is protocol for accessing data referred to by file
364 public boolean parseFeaturesFile(String file, DataSourceType type)
366 return parseFeaturesFile(file, type, true);
370 * Load a features file onto the alignment
373 * file URL, content, or other resolvable path
375 * is protocol for accessing data referred to by file
376 * @param autoenabledisplay
377 * when true, display features flag will be automatically enabled if
378 * features are loaded
379 * @return true if data parsed as a features file
381 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
382 boolean autoenabledisplay)
384 boolean featuresFile = false;
387 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
388 .getFeatureRenderer().getFeatureColours();
389 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
390 "relaxedidmatch", false);
391 featuresFile = new FeaturesFile(file, sourceType).parse(
392 viewport.getAlignment(), colours, true, relaxedIdMatching);
393 } catch (Exception ex)
395 ex.printStackTrace();
400 if (autoenabledisplay)
402 viewport.setShowSequenceFeatures(true);
403 sequenceFeatures.setState(true);
405 if (alignPanel.seqPanel.seqCanvas.fr != null)
407 // update the min/max ranges where necessary
408 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
410 if (viewport.featureSettings != null)
412 viewport.featureSettings.refreshTable();
414 alignPanel.paintAlignment(true);
415 statusBar.setText(MessageManager
416 .getString("label.successfully_added_features_alignment"));
422 public void keyPressed(KeyEvent evt)
424 ViewportRanges ranges = viewport.getRanges();
426 if (viewport.cursorMode
427 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
428 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
429 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
430 && Character.isDigit(evt.getKeyChar()))
432 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
435 switch (evt.getKeyCode())
437 case 27: // escape key
438 deselectAllSequenceMenuItem_actionPerformed();
440 alignPanel.alabels.cancelDrag();
443 if (evt.isControlDown() || evt.isMetaDown())
445 cut_actionPerformed();
449 if (viewport.cursorMode && !evt.isControlDown())
451 alignPanel.seqPanel.setCursorColumn();
453 if (evt.isControlDown() || evt.isMetaDown())
455 copy_actionPerformed();
459 if (evt.isControlDown())
461 paste(evt.isShiftDown());
465 if (evt.isControlDown() || evt.isMetaDown())
467 selectAllSequenceMenuItem_actionPerformed();
470 case KeyEvent.VK_DOWN:
471 if (viewport.cursorMode)
473 alignPanel.seqPanel.moveCursor(0, 1);
477 moveSelectedSequences(false);
482 if (viewport.cursorMode)
484 alignPanel.seqPanel.moveCursor(0, -1);
488 moveSelectedSequences(true);
492 case KeyEvent.VK_LEFT:
493 if (evt.isAltDown() || !viewport.cursorMode)
495 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
499 alignPanel.seqPanel.moveCursor(-1, 0);
503 case KeyEvent.VK_RIGHT:
504 if (evt.isAltDown() || !viewport.cursorMode)
506 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
510 alignPanel.seqPanel.moveCursor(1, 0);
514 case KeyEvent.VK_SPACE:
515 if (viewport.cursorMode)
517 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
518 || evt.isShiftDown() || evt.isAltDown());
522 case KeyEvent.VK_DELETE:
523 case KeyEvent.VK_BACK_SPACE:
524 if (viewport.cursorMode)
526 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
527 || evt.isShiftDown() || evt.isAltDown());
531 cut_actionPerformed();
532 alignPanel.seqPanel.seqCanvas.repaint();
537 if (viewport.cursorMode)
539 alignPanel.seqPanel.setCursorRow();
543 if (viewport.cursorMode)
545 alignPanel.seqPanel.setCursorPosition();
549 case KeyEvent.VK_ENTER:
550 case KeyEvent.VK_COMMA:
551 if (viewport.cursorMode)
553 alignPanel.seqPanel.setCursorRowAndColumn();
558 if (viewport.cursorMode)
560 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
564 if (viewport.cursorMode)
566 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
571 viewport.cursorMode = !viewport.cursorMode;
572 statusBar.setText(MessageManager.formatMessage(
573 "label.keyboard_editing_mode",
574 new String[] { (viewport.cursorMode ? "on" : "off") }));
575 if (viewport.cursorMode)
577 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
578 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
583 if (evt.isControlDown())
585 findMenuItem_actionPerformed();
591 boolean toggleSeqs = !evt.isControlDown();
592 boolean toggleCols = !evt.isShiftDown();
593 toggleHiddenRegions(toggleSeqs, toggleCols);
597 case KeyEvent.VK_PAGE_UP:
598 if (viewport.getWrapAlignment())
600 ranges.scrollUp(true);
608 case KeyEvent.VK_PAGE_DOWN:
609 if (viewport.getWrapAlignment())
611 ranges.scrollUp(false);
620 if (evt.isControlDown())
622 undoMenuItem_actionPerformed();
627 if (evt.isControlDown())
629 redoMenuItem_actionPerformed();
634 if (evt.isControlDown())
641 if (evt.isControlDown())
643 trimAlignment(false);
648 if (evt.isControlDown())
650 if (evt.isShiftDown())
652 this.removeAllGapsMenuItem_actionPerformed();
656 removeGappedColumnMenuItem_actionPerformed();
661 if (evt.isControlDown())
665 invertColSel_actionPerformed();
669 invertSequenceMenuItem_actionPerformed();
675 if (evt.isControlDown())
677 if (evt.isShiftDown())
679 this.unGroup_actionPerformed();
683 this.createGroup_actionPerformed();
689 if (evt.isControlDown())
691 this.deleteGroups_actionPerformed();
696 if (evt.isControlDown())
703 alignPanel.paintAlignment(true);
707 * called by key handler and the hide all/show all menu items
712 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
714 boolean hide = false;
715 SequenceGroup sg = viewport.getSelectionGroup();
716 if (!toggleSeqs && !toggleCols)
718 // Hide everything by the current selection - this is a hack - we do the
719 // invert and then hide
720 // first check that there will be visible columns after the invert.
721 if (viewport.hasSelectedColumns()
722 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
725 // now invert the sequence set, if required - empty selection implies
726 // that no hiding is required.
729 invertSequenceMenuItem_actionPerformed();
730 sg = viewport.getSelectionGroup();
734 viewport.expandColSelection(sg, true);
735 // finally invert the column selection and get the new sequence
736 // selection and indicate it should be hidden.
737 invertColSel_actionPerformed();
744 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
747 viewport.hideAllSelectedSeqs();
749 else if (!(toggleCols && viewport.hasSelectedColumns()))
751 viewport.showAllHiddenSeqs();
757 if (viewport.hasSelectedColumns())
759 viewport.hideSelectedColumns();
762 viewport.setSelectionGroup(sg);
767 viewport.showAllHiddenColumns();
769 viewport.sendSelection();
774 public void keyReleased(KeyEvent evt)
779 public void keyTyped(KeyEvent evt)
784 public void itemStateChanged(ItemEvent evt)
786 final Object source = evt.getSource();
787 if (source == displayNonconservedMenuItem)
789 displayNonconservedMenuItem_actionPerformed();
791 else if (source == colourTextMenuItem)
793 colourTextMenuItem_actionPerformed();
795 else if (source == wrapMenuItem)
797 wrapMenuItem_actionPerformed();
799 else if (source == scaleAbove)
801 viewport.setScaleAboveWrapped(scaleAbove.getState());
803 else if (source == scaleLeft)
805 viewport.setScaleLeftWrapped(scaleLeft.getState());
807 else if (source == scaleRight)
809 viewport.setScaleRightWrapped(scaleRight.getState());
811 else if (source == seqLimits)
813 seqLimits_itemStateChanged();
815 else if (source == viewBoxesMenuItem)
817 viewport.setShowBoxes(viewBoxesMenuItem.getState());
819 else if (source == viewTextMenuItem)
821 viewport.setShowText(viewTextMenuItem.getState());
823 else if (source == renderGapsMenuItem)
825 viewport.setRenderGaps(renderGapsMenuItem.getState());
827 else if (source == annotationPanelMenuItem)
829 boolean showAnnotations = annotationPanelMenuItem.getState();
830 showAlignmentAnnotations.setEnabled(showAnnotations);
831 showSequenceAnnotations.setEnabled(showAnnotations);
832 viewport.setShowAnnotation(showAnnotations);
833 alignPanel.setAnnotationVisible(showAnnotations);
835 else if (source == sequenceFeatures)
837 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
838 alignPanel.seqPanel.seqCanvas.repaint();
840 else if (source == showAlignmentAnnotations)
842 setAnnotationsVisibility();
844 else if (source == showSequenceAnnotations)
846 setAnnotationsVisibility();
848 else if (source == sortAnnBySequence)
850 boolean newState = sortAnnBySequence.getState();
851 sortAnnByLabel.setState(false);
852 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
853 : SequenceAnnotationOrder.NONE);
854 setViewportAnnotationOrder();
856 else if (source == sortAnnByLabel)
858 boolean newState = sortAnnByLabel.getState();
859 sortAnnBySequence.setState(false);
860 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
861 : SequenceAnnotationOrder.NONE);
862 setViewportAnnotationOrder();
864 else if (source == showAutoFirst)
866 showAutoLast.setState(!showAutoFirst.getState());
867 setShowAutoCalculatedAbove(showAutoFirst.getState());
868 setViewportAnnotationOrder();
870 else if (source == showAutoLast)
872 showAutoFirst.setState(!showAutoLast.getState());
873 setShowAutoCalculatedAbove(showAutoFirst.getState());
874 setViewportAnnotationOrder();
876 else if (source == conservationMenuItem)
878 conservationMenuItem_actionPerformed();
880 else if (source == abovePIDThreshold)
882 abovePIDThreshold_actionPerformed();
884 else if (source == applyToAllGroups)
886 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
888 else if (source == autoCalculate)
890 viewport.autoCalculateConsensus = autoCalculate.getState();
892 else if (source == sortByTree)
894 viewport.sortByTree = sortByTree.getState();
896 else if (source == this.centreColumnLabelFlag)
898 centreColumnLabelFlag_stateChanged();
900 else if (source == this.followMouseOverFlag)
902 mouseOverFlag_stateChanged();
904 else if (source == showGroupConsensus)
906 showGroupConsensus_actionPerformed();
908 else if (source == showGroupConservation)
910 showGroupConservation_actionPerformed();
912 else if (source == showSequenceLogo)
914 showSequenceLogo_actionPerformed();
916 else if (source == normSequenceLogo)
918 normSequenceLogo_actionPerformed();
920 else if (source == showConsensusHistogram)
922 showConsensusHistogram_actionPerformed();
924 else if (source == applyAutoAnnotationSettings)
926 applyAutoAnnotationSettings_actionPerformed();
928 alignPanel.paintAlignment(true);
932 * Set the visibility state of sequence-related and/or alignment-related
933 * annotations depending on checkbox selections, and repaint.
937 private void setAnnotationsVisibility()
939 boolean showForAlignment = showAlignmentAnnotations.getState();
940 boolean showForSequences = showSequenceAnnotations.getState();
941 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
943 for (AlignmentAnnotation aa : alignPanel.getAlignment()
944 .getAlignmentAnnotation())
946 boolean visible = (aa.sequenceRef == null ? showForAlignment
948 aa.visible = visible;
951 alignPanel.validateAnnotationDimensions(true);
956 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
958 this.annotationSortOrder = order;
962 * Set flags on the viewport that control annotation ordering
964 private void setViewportAnnotationOrder()
966 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
968 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
971 private void setShowAutoCalculatedAbove(boolean showAbove)
973 this.showAutoCalculatedAbove = showAbove;
976 private void mouseOverFlag_stateChanged()
978 viewport.setFollowHighlight(followMouseOverFlag.getState());
979 // TODO: could kick the scrollTo mechanism to reset view for current
983 private void centreColumnLabelFlag_stateChanged()
985 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
986 this.alignPanel.annotationPanel.repaint();
990 public void actionPerformed(ActionEvent evt)
992 viewport.applet.currentAlignFrame = this;
994 Object source = evt.getSource();
996 if (source == inputText)
998 inputText_actionPerformed();
1000 else if (source == loadTree)
1002 loadTree_actionPerformed();
1004 else if (source == loadApplication)
1006 launchFullApplication();
1008 else if (source == loadAnnotations)
1012 else if (source == outputAnnotations)
1014 outputAnnotations(true);
1016 else if (source == outputFeatures)
1018 outputFeatures(true, "Jalview");
1020 else if (source == closeMenuItem)
1022 closeMenuItem_actionPerformed();
1024 else if (source == copy)
1026 copy_actionPerformed();
1028 else if (source == undoMenuItem)
1030 undoMenuItem_actionPerformed();
1032 else if (source == redoMenuItem)
1034 redoMenuItem_actionPerformed();
1036 else if (source == inputText)
1038 inputText_actionPerformed();
1040 else if (source == closeMenuItem)
1042 closeMenuItem_actionPerformed();
1044 else if (source == undoMenuItem)
1046 undoMenuItem_actionPerformed();
1048 else if (source == redoMenuItem)
1050 redoMenuItem_actionPerformed();
1052 else if (source == copy)
1054 copy_actionPerformed();
1056 else if (source == pasteNew)
1058 pasteNew_actionPerformed();
1060 else if (source == pasteThis)
1062 pasteThis_actionPerformed();
1064 else if (source == cut)
1066 cut_actionPerformed();
1068 else if (source == delete)
1070 delete_actionPerformed();
1072 else if (source == createGroup)
1074 createGroup_actionPerformed();
1076 else if (source == unGroup)
1078 unGroup_actionPerformed();
1080 else if (source == grpsFromSelection)
1082 makeGrpsFromSelection_actionPerformed();
1084 else if (source == deleteGroups)
1086 deleteGroups_actionPerformed();
1088 else if (source == selectAllSequenceMenuItem)
1090 selectAllSequenceMenuItem_actionPerformed();
1092 else if (source == deselectAllSequenceMenuItem)
1094 deselectAllSequenceMenuItem_actionPerformed();
1096 else if (source == invertSequenceMenuItem)
1098 invertSequenceMenuItem_actionPerformed();
1099 // uncomment to slave sequence selections in split frame
1100 // viewport.sendSelection();
1102 else if (source == invertColSel)
1104 viewport.invertColumnSelection();
1105 alignPanel.paintAlignment(true);
1106 viewport.sendSelection();
1108 else if (source == remove2LeftMenuItem)
1110 trimAlignment(true);
1112 else if (source == remove2RightMenuItem)
1114 trimAlignment(false);
1116 else if (source == removeGappedColumnMenuItem)
1118 removeGappedColumnMenuItem_actionPerformed();
1120 else if (source == removeAllGapsMenuItem)
1122 removeAllGapsMenuItem_actionPerformed();
1124 else if (source == findMenuItem)
1126 findMenuItem_actionPerformed();
1128 else if (source == font)
1130 new FontChooser(alignPanel);
1132 else if (source == newView)
1136 else if (source == showColumns)
1138 viewport.showAllHiddenColumns();
1139 alignPanel.paintAlignment(true);
1140 viewport.sendSelection();
1142 else if (source == showSeqs)
1144 viewport.showAllHiddenSeqs();
1145 alignPanel.paintAlignment(true);
1146 // uncomment if we want to slave sequence selections in split frame
1147 // viewport.sendSelection();
1149 else if (source == hideColumns)
1151 viewport.hideSelectedColumns();
1152 alignPanel.paintAlignment(true);
1153 viewport.sendSelection();
1155 else if (source == hideSequences
1156 && viewport.getSelectionGroup() != null)
1158 viewport.hideAllSelectedSeqs();
1159 alignPanel.paintAlignment(true);
1160 // uncomment if we want to slave sequence selections in split frame
1161 // viewport.sendSelection();
1163 else if (source == hideAllButSelection)
1165 toggleHiddenRegions(false, false);
1166 alignPanel.paintAlignment(true);
1167 viewport.sendSelection();
1169 else if (source == hideAllSelection)
1171 SequenceGroup sg = viewport.getSelectionGroup();
1172 viewport.expandColSelection(sg, false);
1173 viewport.hideAllSelectedSeqs();
1174 viewport.hideSelectedColumns();
1175 alignPanel.paintAlignment(true);
1176 viewport.sendSelection();
1178 else if (source == showAllHidden)
1180 viewport.showAllHiddenColumns();
1181 viewport.showAllHiddenSeqs();
1182 alignPanel.paintAlignment(true);
1183 viewport.sendSelection();
1185 else if (source == showGroupConsensus)
1187 showGroupConsensus_actionPerformed();
1189 else if (source == showGroupConservation)
1191 showGroupConservation_actionPerformed();
1193 else if (source == showSequenceLogo)
1195 showSequenceLogo_actionPerformed();
1197 else if (source == normSequenceLogo)
1199 normSequenceLogo_actionPerformed();
1201 else if (source == showConsensusHistogram)
1203 showConsensusHistogram_actionPerformed();
1205 else if (source == applyAutoAnnotationSettings)
1207 applyAutoAnnotationSettings_actionPerformed();
1209 else if (source == featureSettings)
1211 new FeatureSettings(alignPanel);
1213 else if (source == alProperties)
1215 StringBuffer contents = new jalview.io.AlignmentProperties(
1216 viewport.getAlignment()).formatAsString();
1217 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1218 cap.setText(contents.toString());
1219 Frame frame = new Frame();
1221 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1222 "label.alignment_properties", new String[] { getTitle() }),
1225 else if (source == overviewMenuItem)
1227 overviewMenuItem_actionPerformed();
1229 else if (source == noColourmenuItem)
1233 else if (source == clustalColour)
1235 abovePIDThreshold.setState(false);
1236 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1238 else if (source == zappoColour)
1240 changeColour(new ZappoColourScheme());
1242 else if (source == taylorColour)
1244 changeColour(new TaylorColourScheme());
1246 else if (source == hydrophobicityColour)
1248 changeColour(new HydrophobicColourScheme());
1250 else if (source == helixColour)
1252 changeColour(new HelixColourScheme());
1254 else if (source == strandColour)
1256 changeColour(new StrandColourScheme());
1258 else if (source == turnColour)
1260 changeColour(new TurnColourScheme());
1262 else if (source == buriedColour)
1264 changeColour(new BuriedColourScheme());
1266 else if (source == nucleotideColour)
1268 changeColour(new NucleotideColourScheme());
1270 else if (source == purinePyrimidineColour)
1272 changeColour(new PurinePyrimidineColourScheme());
1274 // else if (source == RNAInteractionColour)
1276 // changeColour(new RNAInteractionColourScheme());
1278 else if (source == RNAHelixColour)
1280 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1281 // new RNAHelicesColourChooser(viewport, alignPanel);
1283 else if (source == modifyPID)
1285 modifyPID_actionPerformed();
1287 else if (source == modifyConservation)
1289 modifyConservation_actionPerformed();
1291 else if (source == userDefinedColour)
1293 new UserDefinedColours(alignPanel, null);
1295 else if (source == PIDColour)
1297 changeColour(new PIDColourScheme());
1299 else if (source == BLOSUM62Colour)
1301 changeColour(new Blosum62ColourScheme());
1303 else if (source == tcoffeeColour)
1305 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1307 else if (source == annotationColour)
1309 new AnnotationColourChooser(viewport, alignPanel);
1311 else if (source == annotationColumnSelection)
1313 new AnnotationColumnChooser(viewport, alignPanel);
1315 else if (source == sortPairwiseMenuItem)
1317 sortPairwiseMenuItem_actionPerformed();
1319 else if (source == sortIDMenuItem)
1321 sortIDMenuItem_actionPerformed();
1323 else if (source == sortLengthMenuItem)
1325 sortLengthMenuItem_actionPerformed();
1327 else if (source == sortGroupMenuItem)
1329 sortGroupMenuItem_actionPerformed();
1331 else if (source == removeRedundancyMenuItem)
1333 removeRedundancyMenuItem_actionPerformed();
1335 else if (source == pairwiseAlignmentMenuItem)
1337 pairwiseAlignmentMenuItem_actionPerformed();
1339 else if (source == PCAMenuItem)
1341 PCAMenuItem_actionPerformed();
1343 else if (source == averageDistanceTreeMenuItem)
1345 averageDistanceTreeMenuItem_actionPerformed();
1347 else if (source == neighbourTreeMenuItem)
1349 neighbourTreeMenuItem_actionPerformed();
1351 else if (source == njTreeBlosumMenuItem)
1353 njTreeBlosumMenuItem_actionPerformed();
1355 else if (source == avDistanceTreeBlosumMenuItem)
1357 avTreeBlosumMenuItem_actionPerformed();
1359 else if (source == documentation)
1361 documentation_actionPerformed();
1363 else if (source == about)
1365 about_actionPerformed();
1370 public void inputText_actionPerformed()
1372 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1373 Frame frame = new Frame();
1375 jalview.bin.JalviewLite.addFrame(frame,
1376 MessageManager.getString("label.input_cut_paste"), 500, 500);
1379 protected void outputText_actionPerformed(ActionEvent e)
1381 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1382 Frame frame = new Frame();
1384 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1385 "label.alignment_output_command",
1386 new Object[] { e.getActionCommand() }), 600, 500);
1388 FileFormatI fileFormat = FileFormats.getInstance().forName(
1389 e.getActionCommand());
1390 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1391 fileFormat, viewport.getAlignment(),
1392 viewport.getShowJVSuffix()));
1395 public void loadAnnotations()
1397 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1398 cap.setText(MessageManager
1399 .getString("label.paste_features_annotations_Tcoffee_here"));
1400 cap.setAnnotationImport();
1401 Frame frame = new Frame();
1403 jalview.bin.JalviewLite.addFrame(frame,
1404 MessageManager.getString("action.paste_annotations"), 400, 300);
1408 public String outputAnnotations(boolean displayTextbox)
1410 String annotation = new AnnotationFile()
1411 .printAnnotationsForView(viewport);
1415 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1416 Frame frame = new Frame();
1418 jalview.bin.JalviewLite.addFrame(frame,
1419 MessageManager.getString("label.annotations"), 600, 500);
1420 cap.setText(annotation);
1426 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1428 if (alignPanel.getFeatureRenderer() != null
1429 && viewport.getFeaturesDisplayed() != null)
1431 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1437 public String outputFeatures(boolean displayTextbox, String format)
1440 FeaturesFile formatter = new FeaturesFile();
1441 if (format.equalsIgnoreCase("Jalview"))
1443 features = formatter.printJalviewFormat(viewport.getAlignment()
1444 .getSequencesArray(), getDisplayedFeatureCols());
1448 features = formatter.printGffFormat(viewport.getAlignment()
1449 .getSequencesArray(), getDisplayedFeatureCols());
1454 boolean frimport = false;
1455 if (features == null || features.equals("No Features Visible"))
1457 features = "# No features visible - paste some and import them here.";
1461 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1464 cap.setAnnotationImport();
1466 Frame frame = new Frame();
1468 jalview.bin.JalviewLite.addFrame(frame,
1469 MessageManager.getString("label.features"), 600, 500);
1470 cap.setText(features);
1474 if (features == null)
1483 void launchFullApplication()
1485 StringBuffer url = new StringBuffer(jalviewServletURL);
1487 // allow servlet parameters to be passed in applet parameter
1488 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1490 url.append(firstSep);
1493 + appendProtocol(viewport.applet.getParameter("file")));
1495 if (viewport.applet.getParameter("features") != null)
1497 url.append("&features=");
1498 url.append(appendProtocol(viewport.applet.getParameter("features")));
1501 if (viewport.applet.getParameter("annotations") != null)
1503 url.append("&annotations=");
1504 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1507 if (viewport.applet.getParameter("jnetfile") != null
1508 || viewport.applet.getParameter("jpredfile") != null)
1510 url.append("&annotations=");
1511 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1512 .getParameter("jnetfile") : viewport.applet
1513 .getParameter("jpredfile")));
1516 if (viewport.applet.getParameter("defaultColour") != null)
1518 url.append("&colour="
1519 + removeWhiteSpace(viewport.applet
1520 .getParameter("defaultColour")));
1523 if (viewport.applet.getParameter("userDefinedColour") != null)
1525 url.append("&colour="
1526 + removeWhiteSpace(viewport.applet
1527 .getParameter("userDefinedColour")));
1529 if (viewport.applet.getParameter("tree") != null)
1532 + appendProtocol(viewport.applet.getParameter("tree")));
1534 if (viewport.applet.getParameter("treeFile") != null)
1537 + appendProtocol(viewport.applet.getParameter("treeFile")));
1540 showURL(url.toString(), "FULL_APP");
1543 String removeWhiteSpace(String colour)
1545 StringBuffer sb = new StringBuffer();
1546 for (int i = 0; i < colour.length(); i++)
1548 if (Character.isWhitespace(colour.charAt(i)))
1554 sb.append(colour.charAt(i));
1558 return sb.toString();
1561 String appendProtocol(String url)
1566 url = URLEncoder.encode(url);
1569 * When we finally deprecate 1.1 compatibility, we can start to use
1570 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1571 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1572 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1573 * ex.printStackTrace(); }
1575 catch (java.net.MalformedURLException ex)
1577 url = viewport.applet.getCodeBase() + url;
1582 public void closeMenuItem_actionPerformed()
1584 PaintRefresher.RemoveComponent(alignPanel);
1585 if (alignPanel.seqPanel != null
1586 && alignPanel.seqPanel.seqCanvas != null)
1588 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1590 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1592 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1595 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1610 void updateEditMenuBar()
1613 if (viewport.getHistoryList().size() > 0)
1615 undoMenuItem.setEnabled(true);
1616 CommandI command = viewport.getHistoryList().peek();
1617 undoMenuItem.setLabel(MessageManager.formatMessage(
1618 "label.undo_command",
1619 new Object[] { command.getDescription() }));
1623 undoMenuItem.setEnabled(false);
1624 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1627 if (viewport.getRedoList().size() > 0)
1629 redoMenuItem.setEnabled(true);
1631 CommandI command = viewport.getRedoList().peek();
1632 redoMenuItem.setLabel(MessageManager.formatMessage(
1633 "label.redo_command",
1634 new Object[] { command.getDescription() }));
1638 redoMenuItem.setEnabled(false);
1639 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1647 public void addHistoryItem(CommandI command)
1649 if (command.getSize() > 0)
1651 viewport.addToHistoryList(command);
1652 viewport.clearRedoList();
1653 updateEditMenuBar();
1654 viewport.updateHiddenColumns();
1659 * TODO: JAL-1104 DOCUMENT ME!
1664 protected void undoMenuItem_actionPerformed()
1666 if (viewport.getHistoryList().isEmpty())
1671 CommandI command = viewport.getHistoryList().pop();
1672 viewport.addToRedoList(command);
1673 command.undoCommand(null);
1675 AlignmentViewport originalSource = getOriginatingSource(command);
1677 if (originalSource != viewport)
1680 .println("Warning: Viewport object mismatch whilst undoing");
1682 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1683 // viewport.getColumnSelection().getHiddenColumns()
1685 updateEditMenuBar();
1686 originalSource.firePropertyChange("alignment", null, originalSource
1687 .getAlignment().getSequences());
1691 * TODO: JAL-1104 DOCUMENT ME!
1696 protected void redoMenuItem_actionPerformed()
1698 if (viewport.getRedoList().isEmpty())
1703 CommandI command = viewport.getRedoList().pop();
1704 viewport.addToHistoryList(command);
1705 command.doCommand(null);
1707 AlignmentViewport originalSource = getOriginatingSource(command);
1709 if (originalSource != viewport)
1712 .println("Warning: Viewport object mismatch whilst re-doing");
1714 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1715 // viewport.getColumnSelection().getHiddenColumns()
1718 updateEditMenuBar();
1719 originalSource.firePropertyChange("alignment", null, originalSource
1720 .getAlignment().getSequences());
1723 AlignmentViewport getOriginatingSource(CommandI command)
1725 AlignmentViewport originalSource = null;
1726 // For sequence removal and addition, we need to fire
1727 // the property change event FROM the viewport where the
1728 // original alignment was altered
1729 AlignmentI al = null;
1730 if (command instanceof EditCommand)
1732 EditCommand editCommand = (EditCommand) command;
1733 al = editCommand.getAlignment();
1734 Vector comps = (Vector) PaintRefresher.components.get(viewport
1735 .getSequenceSetId());
1736 for (int i = 0; i < comps.size(); i++)
1738 if (comps.elementAt(i) instanceof AlignmentPanel)
1740 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1742 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1749 if (originalSource == null)
1751 // The original view is closed, we must validate
1752 // the current view against the closed view first
1755 PaintRefresher.validateSequences(al, viewport.getAlignment());
1758 originalSource = viewport;
1761 return originalSource;
1765 * Move the currently selected sequences up or down one position in the
1770 public void moveSelectedSequences(boolean up)
1772 SequenceGroup sg = viewport.getSelectionGroup();
1777 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1778 up ? null : viewport.getHiddenRepSequences(), up);
1779 alignPanel.paintAlignment(true);
1782 * Also move cDNA/protein complement sequences
1784 AlignViewportI complement = viewport.getCodingComplement();
1785 if (complement != null)
1787 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1788 viewport, complement);
1789 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1790 up ? null : complement.getHiddenRepSequences(), up);
1791 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1795 synchronized void slideSequences(boolean right, int size)
1797 List<SequenceI> sg = new Vector<SequenceI>();
1798 if (viewport.cursorMode)
1800 sg.add(viewport.getAlignment().getSequenceAt(
1801 alignPanel.seqPanel.seqCanvas.cursorY));
1803 else if (viewport.getSelectionGroup() != null
1804 && viewport.getSelectionGroup().getSize() != viewport
1805 .getAlignment().getHeight())
1807 sg = viewport.getSelectionGroup().getSequences(
1808 viewport.getHiddenRepSequences());
1816 Vector<SequenceI> invertGroup = new Vector();
1818 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1820 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1822 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1826 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1828 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1830 for (int i = 0; i < invertGroup.size(); i++)
1832 seqs2[i] = invertGroup.elementAt(i);
1835 SlideSequencesCommand ssc;
1838 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1839 size, viewport.getGapCharacter());
1843 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1844 size, viewport.getGapCharacter());
1847 int groupAdjustment = 0;
1848 if (ssc.getGapsInsertedBegin() && right)
1850 if (viewport.cursorMode)
1852 alignPanel.seqPanel.moveCursor(size, 0);
1856 groupAdjustment = size;
1859 else if (!ssc.getGapsInsertedBegin() && !right)
1861 if (viewport.cursorMode)
1863 alignPanel.seqPanel.moveCursor(-size, 0);
1867 groupAdjustment = -size;
1871 if (groupAdjustment != 0)
1873 viewport.getSelectionGroup().setStartRes(
1874 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1875 viewport.getSelectionGroup().setEndRes(
1876 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1879 boolean appendHistoryItem = false;
1880 Deque<CommandI> historyList = viewport.getHistoryList();
1881 if (historyList != null && historyList.size() > 0
1882 && historyList.peek() instanceof SlideSequencesCommand)
1884 appendHistoryItem = ssc
1885 .appendSlideCommand((SlideSequencesCommand) historyList
1889 if (!appendHistoryItem)
1891 addHistoryItem(ssc);
1897 static StringBuffer copiedSequences;
1899 static Vector copiedHiddenColumns;
1901 protected void copy_actionPerformed()
1903 if (viewport.getSelectionGroup() == null)
1908 SequenceGroup sg = viewport.getSelectionGroup();
1909 copiedSequences = new StringBuffer();
1910 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1911 for (int i = 0; i < sg.getSize(); i++)
1913 SequenceI seq = sg.getSequenceAt(i);
1914 int index = viewport.getAlignment().findIndex(seq);
1915 orderedSeqs.put(index, seq);
1918 int index = 0, startRes, endRes;
1921 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1923 copiedHiddenColumns = new Vector();
1924 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1925 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1927 copiedHiddenColumns.addElement(new int[] {
1928 region[0] - hiddenOffset, region[1] - hiddenOffset });
1933 copiedHiddenColumns = null;
1936 for (int i = 0; i < sg.getSize(); i++)
1938 SequenceI seq = null;
1942 if (orderedSeqs.containsKey(index))
1944 seq = orderedSeqs.get(index);
1955 // Returns residue following index if gap
1956 startRes = seq.findPosition(sg.getStartRes());
1959 // Need to find the residue preceeding index if gap
1962 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1964 ch = seq.getCharAt(j);
1965 if (!jalview.util.Comparison.isGap((ch)))
1973 endRes += seq.getStart() - 1;
1976 copiedSequences.append(seq.getName()
1982 + seq.getSequenceAsString(sg.getStartRes(),
1983 sg.getEndRes() + 1) + "\n");
1988 protected void pasteNew_actionPerformed()
1993 protected void pasteThis_actionPerformed()
1998 void paste(boolean newAlignment)
2003 if (copiedSequences == null)
2008 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2009 Vector seqs = new Vector();
2010 while (st.hasMoreElements())
2012 String name = st.nextToken();
2013 int start = Integer.parseInt(st.nextToken());
2014 int end = Integer.parseInt(st.nextToken());
2015 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2017 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2018 for (int i = 0; i < seqs.size(); i++)
2020 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2025 String newtitle = MessageManager
2026 .getString("label.copied_sequences");
2027 if (getTitle().startsWith(
2028 MessageManager.getString("label.copied_sequences")))
2030 newtitle = getTitle();
2034 newtitle = newtitle.concat(MessageManager.formatMessage(
2035 "label.from_msname", new String[] { getTitle() }));
2037 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2038 viewport.applet, newtitle, false);
2039 if (copiedHiddenColumns != null)
2041 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2043 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2044 af.viewport.hideColumns(region[0], region[1]);
2048 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2053 addSequences(newSeqs);
2056 } catch (Exception ex)
2058 } // could be anything being pasted in here
2062 void addSequences(SequenceI[] seqs)
2064 for (int i = 0; i < seqs.length; i++)
2066 viewport.getAlignment().addSequence(seqs[i]);
2070 addHistoryItem(new EditCommand(
2071 MessageManager.getString("label.add_sequences"), Action.PASTE,
2072 seqs, 0, viewport.getAlignment().getWidth(),
2073 viewport.getAlignment()));
2075 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2076 viewport.getAlignment().getWidth();
2077 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2082 protected void cut_actionPerformed()
2084 copy_actionPerformed();
2085 delete_actionPerformed();
2088 protected void delete_actionPerformed()
2091 SequenceGroup sg = viewport.getSelectionGroup();
2097 Vector seqs = new Vector();
2099 for (int i = 0; i < sg.getSize(); i++)
2101 seq = sg.getSequenceAt(i);
2102 seqs.addElement(seq);
2106 * If the cut affects all sequences, warn, remove highlighted columns
2108 if (sg.getSize() == viewport.getAlignment().getHeight())
2110 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2111 .getAlignment().getWidth()) ? true : false;
2112 if (isEntireAlignWidth)
2114 String title = MessageManager.getString("label.delete_all");
2115 Panel infoPanel = new Panel();
2116 infoPanel.setLayout(new FlowLayout());
2118 .add(new Label(MessageManager.getString("warn.delete_all")));
2120 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2121 dialog.setMainPanel(infoPanel);
2122 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2123 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2124 dialog.setVisible(true);
2131 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2132 sg.getEndRes() + 1);
2135 SequenceI[] cut = new SequenceI[seqs.size()];
2136 for (int i = 0; i < seqs.size(); i++)
2138 cut[i] = (SequenceI) seqs.elementAt(i);
2142 * //ADD HISTORY ITEM
2144 addHistoryItem(new EditCommand(
2145 MessageManager.getString("label.cut_sequences"), Action.CUT,
2146 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2147 viewport.getAlignment()));
2149 viewport.setSelectionGroup(null);
2150 viewport.getAlignment().deleteGroup(sg);
2152 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2155 if (viewport.getAlignment().getHeight() < 1)
2157 this.setVisible(false);
2159 viewport.sendSelection();
2163 * group consensus toggled
2166 protected void showGroupConsensus_actionPerformed()
2168 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2169 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174 * group conservation toggled.
2176 protected void showGroupConservation_actionPerformed()
2178 viewport.setShowGroupConservation(showGroupConservation.getState());
2179 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2186 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2187 * .event.ActionEvent)
2189 protected void showConsensusHistogram_actionPerformed()
2191 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2192 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2199 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2200 * .event.ActionEvent)
2202 protected void showSequenceLogo_actionPerformed()
2204 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2205 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2208 protected void normSequenceLogo_actionPerformed()
2210 showSequenceLogo.setState(true);
2211 viewport.setShowSequenceLogo(true);
2212 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2213 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2216 protected void applyAutoAnnotationSettings_actionPerformed()
2218 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2221 protected void makeGrpsFromSelection_actionPerformed()
2223 if (avc.makeGroupsFromSelection())
2225 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2226 alignPanel.updateAnnotation();
2227 alignPanel.paintAlignment(true);
2231 protected void createGroup_actionPerformed()
2236 protected void unGroup_actionPerformed()
2240 alignPanel.alignmentChanged();
2244 protected void deleteGroups_actionPerformed()
2246 if (avc.deleteGroups())
2248 alignPanel.alignmentChanged();
2252 public void selectAllSequenceMenuItem_actionPerformed()
2254 SequenceGroup sg = new SequenceGroup();
2255 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2257 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2259 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2260 viewport.setSelectionGroup(sg);
2261 // JAL-2034 - should delegate to
2262 // alignPanel to decide if overview needs
2264 alignPanel.paintAlignment(false);
2265 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2266 viewport.sendSelection();
2269 public void deselectAllSequenceMenuItem_actionPerformed()
2271 if (viewport.cursorMode)
2273 alignPanel.seqPanel.keyboardNo1 = null;
2274 alignPanel.seqPanel.keyboardNo2 = null;
2276 viewport.setSelectionGroup(null);
2277 viewport.getColumnSelection().clear();
2278 viewport.setSelectionGroup(null);
2279 alignPanel.idPanel.idCanvas.searchResults = null;
2280 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2281 // JAL-2034 - should delegate to
2282 // alignPanel to decide if overview needs
2284 alignPanel.paintAlignment(false);
2285 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2286 viewport.sendSelection();
2289 public void invertSequenceMenuItem_actionPerformed()
2291 SequenceGroup sg = viewport.getSelectionGroup();
2292 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2294 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2297 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2298 viewport.sendSelection();
2301 public void invertColSel_actionPerformed()
2303 viewport.invertColumnSelection();
2304 alignPanel.paintAlignment(true);
2305 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2306 viewport.sendSelection();
2309 void trimAlignment(boolean trimLeft)
2311 AlignmentI al = viewport.getAlignment();
2312 ViewportRanges ranges = viewport.getRanges();
2313 ColumnSelection colSel = viewport.getColumnSelection();
2316 if (!colSel.isEmpty())
2320 column = colSel.getMin();
2324 column = colSel.getMax();
2328 if (viewport.getSelectionGroup() != null)
2330 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2331 viewport.getHiddenRepSequences());
2335 seqs = al.getSequencesArray();
2338 TrimRegionCommand trimRegion;
2341 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2343 ranges.setStartRes(0);
2347 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2351 statusBar.setText(MessageManager.formatMessage(
2352 "label.removed_columns",
2353 new String[] { Integer.valueOf(trimRegion.getSize())
2355 addHistoryItem(trimRegion);
2357 for (SequenceGroup sg : al.getGroups())
2359 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2360 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2366 viewport.firePropertyChange("alignment", null, al.getSequences());
2370 public void removeGappedColumnMenuItem_actionPerformed()
2372 AlignmentI al = viewport.getAlignment();
2373 ViewportRanges ranges = viewport.getRanges();
2375 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2378 if (viewport.getSelectionGroup() != null)
2380 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2381 viewport.getHiddenRepSequences());
2382 start = viewport.getSelectionGroup().getStartRes();
2383 end = viewport.getSelectionGroup().getEndRes();
2387 seqs = viewport.getAlignment().getSequencesArray();
2390 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2391 "Remove Gapped Columns", seqs, start, end,
2392 viewport.getAlignment());
2394 addHistoryItem(removeGapCols);
2396 statusBar.setText(MessageManager.formatMessage(
2397 "label.removed_empty_columns",
2398 new String[] { Integer.valueOf(removeGapCols.getSize())
2401 // This is to maintain viewport position on first residue
2402 // of first sequence
2403 SequenceI seq = al.getSequenceAt(0);
2404 int startRes = seq.findPosition(ranges.getStartRes());
2405 // ShiftList shifts;
2406 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2407 // edit.alColumnChanges=shifts.getInverse();
2408 // if (viewport.hasHiddenColumns)
2409 // viewport.getColumnSelection().compensateForEdits(shifts);
2410 ranges.setStartRes(seq.findIndex(startRes) - 1);
2411 viewport.firePropertyChange("alignment", null, al.getSequences());
2415 public void removeAllGapsMenuItem_actionPerformed()
2417 AlignmentI al = viewport.getAlignment();
2418 ViewportRanges ranges = viewport.getRanges();
2420 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2423 if (viewport.getSelectionGroup() != null)
2425 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2426 viewport.getHiddenRepSequences());
2427 start = viewport.getSelectionGroup().getStartRes();
2428 end = viewport.getSelectionGroup().getEndRes();
2432 seqs = viewport.getAlignment().getSequencesArray();
2435 // This is to maintain viewport position on first residue
2436 // of first sequence
2437 SequenceI seq = al.getSequenceAt(0);
2438 int startRes = seq.findPosition(ranges.getStartRes());
2440 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2443 ranges.setStartRes(seq.findIndex(startRes) - 1);
2445 viewport.firePropertyChange("alignment", null, al.getSequences());
2449 public void findMenuItem_actionPerformed()
2451 new Finder(alignPanel);
2455 * create a new view derived from the current view
2458 * @return frame for the new view
2460 public AlignFrame newView(String viewtitle)
2463 if (viewport.hasHiddenRows())
2465 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2466 .getFullAlignment().getSequencesArray());
2470 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2473 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2475 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2477 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2479 newal.addAnnotation(viewport.getAlignment()
2480 .getAlignmentAnnotation()[i]);
2485 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2487 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2488 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2489 PaintRefresher.Register(newaf.alignPanel,
2490 newaf.alignPanel.av.getSequenceSetId());
2492 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2493 newaf.alignPanel.av.getSequenceSetId());
2494 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2495 newaf.alignPanel.av.getSequenceSetId());
2497 Vector comps = (Vector) PaintRefresher.components.get(viewport
2498 .getSequenceSetId());
2500 for (int i = 0; i < comps.size(); i++)
2502 if (comps.elementAt(i) instanceof AlignmentPanel)
2508 String title = new String(this.getTitle());
2509 if (viewtitle != null)
2511 title = viewtitle + " ( " + title + ")";
2515 if (title.indexOf("(View") > -1)
2517 title = title.substring(0, title.indexOf("(View"));
2519 title += "(View " + viewSize + ")";
2522 newaf.setTitle(title.toString());
2524 newaf.viewport.setHistoryList(viewport.getHistoryList());
2525 newaf.viewport.setRedoList(viewport.getRedoList());
2531 * @return list of feature groups on the view
2533 public String[] getFeatureGroups()
2535 FeatureRenderer fr = null;
2536 if (alignPanel != null
2537 && (fr = alignPanel.getFeatureRenderer()) != null)
2539 List<String> gps = fr.getFeatureGroups();
2540 String[] _gps = gps.toArray(new String[gps.size()]);
2547 * get sequence feature groups that are hidden or shown
2553 public String[] getFeatureGroupsOfState(boolean visible)
2555 FeatureRenderer fr = null;
2556 if (alignPanel != null
2557 && (fr = alignPanel.getFeatureRenderer()) != null)
2559 List<String> gps = fr.getGroups(visible);
2560 String[] _gps = gps.toArray(new String[gps.size()]);
2567 * Change the display state for the given feature groups
2570 * list of group strings
2572 * visible or invisible
2574 public void setFeatureGroupState(String[] groups, boolean state)
2576 FeatureRenderer fr = null;
2577 this.sequenceFeatures.setState(true);
2578 viewport.setShowSequenceFeatures(true);
2579 if (alignPanel != null
2580 && (fr = alignPanel.getFeatureRenderer()) != null)
2583 fr.setGroupVisibility(Arrays.asList(groups), state);
2584 alignPanel.seqPanel.seqCanvas.repaint();
2585 if (alignPanel.overviewPanel != null)
2587 alignPanel.overviewPanel.updateOverviewImage();
2592 public void seqLimits_itemStateChanged()
2594 viewport.setShowJVSuffix(seqLimits.getState());
2595 alignPanel.fontChanged();
2596 alignPanel.paintAlignment(true);
2599 protected void colourTextMenuItem_actionPerformed()
2601 viewport.setColourText(colourTextMenuItem.getState());
2602 alignPanel.paintAlignment(true);
2605 protected void displayNonconservedMenuItem_actionPerformed()
2607 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2608 alignPanel.paintAlignment(true);
2611 protected void wrapMenuItem_actionPerformed()
2613 viewport.setWrapAlignment(wrapMenuItem.getState());
2614 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2615 scaleAbove.setEnabled(wrapMenuItem.getState());
2616 scaleLeft.setEnabled(wrapMenuItem.getState());
2617 scaleRight.setEnabled(wrapMenuItem.getState());
2618 alignPanel.paintAlignment(true);
2621 public void overviewMenuItem_actionPerformed()
2623 if (alignPanel.overviewPanel != null)
2628 Frame frame = new Frame();
2629 OverviewPanel overview = new OverviewPanel(alignPanel);
2630 frame.add(overview);
2631 // +50 must allow for applet frame window
2632 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2633 "label.overview_params", new String[] { this.getTitle() }),
2634 overview.getPreferredSize().width,
2635 overview.getPreferredSize().height + 50);
2638 final AlignmentPanel ap = alignPanel;
2639 frame.addWindowListener(new WindowAdapter()
2642 public void windowClosing(WindowEvent e)
2646 ap.setOverviewPanel(null);
2651 alignPanel.setOverviewPanel(overview);
2656 public void changeColour(ColourSchemeI cs)
2658 viewport.setGlobalColourScheme(cs);
2660 alignPanel.paintAlignment(true);
2663 protected void modifyPID_actionPerformed()
2665 if (viewport.getAbovePIDThreshold()
2666 && viewport.getGlobalColourScheme() != null)
2668 SliderPanel.setPIDSliderSource(alignPanel,
2669 viewport.getResidueShading(), alignPanel.getViewName());
2670 SliderPanel.showPIDSlider();
2674 protected void modifyConservation_actionPerformed()
2676 if (viewport.getConservationSelected()
2677 && viewport.getGlobalColourScheme() != null)
2679 SliderPanel.setConservationSlider(alignPanel,
2680 viewport.getResidueShading(), alignPanel.getViewName());
2681 SliderPanel.showConservationSlider();
2685 protected void conservationMenuItem_actionPerformed()
2687 boolean selected = conservationMenuItem.getState();
2688 modifyConservation.setEnabled(selected);
2689 viewport.setConservationSelected(selected);
2690 viewport.getResidueShading().setConservationApplied(selected);
2692 changeColour(viewport.getGlobalColourScheme());
2696 modifyConservation_actionPerformed();
2700 SliderPanel.hideConservationSlider();
2704 public void abovePIDThreshold_actionPerformed()
2706 boolean selected = abovePIDThreshold.getState();
2707 modifyPID.setEnabled(selected);
2708 viewport.setAbovePIDThreshold(selected);
2711 viewport.getResidueShading().setThreshold(0,
2712 viewport.isIgnoreGapsConsensus());
2715 changeColour(viewport.getGlobalColourScheme());
2719 modifyPID_actionPerformed();
2723 SliderPanel.hidePIDSlider();
2727 public void sortPairwiseMenuItem_actionPerformed()
2729 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2731 .getAlignment().getSequenceAt(0), null);
2733 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2734 viewport.getAlignment()));
2735 alignPanel.paintAlignment(true);
2738 public void sortIDMenuItem_actionPerformed()
2740 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741 AlignmentSorter.sortByID(viewport.getAlignment());
2742 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2743 viewport.getAlignment()));
2744 alignPanel.paintAlignment(true);
2747 public void sortLengthMenuItem_actionPerformed()
2749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750 AlignmentSorter.sortByLength(viewport.getAlignment());
2751 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2752 viewport.getAlignment()));
2753 alignPanel.paintAlignment(true);
2756 public void sortGroupMenuItem_actionPerformed()
2758 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2759 AlignmentSorter.sortByGroup(viewport.getAlignment());
2760 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2761 viewport.getAlignment()));
2762 alignPanel.paintAlignment(true);
2766 public void removeRedundancyMenuItem_actionPerformed()
2768 new RedundancyPanel(alignPanel);
2771 public void pairwiseAlignmentMenuItem_actionPerformed()
2773 if (viewport.getSelectionGroup() != null
2774 && viewport.getSelectionGroup().getSize() > 1)
2776 Frame frame = new Frame();
2777 frame.add(new PairwiseAlignPanel(alignPanel));
2778 jalview.bin.JalviewLite.addFrame(frame,
2779 MessageManager.getString("action.pairwise_alignment"), 600,
2784 public void PCAMenuItem_actionPerformed()
2786 // are the sequences aligned?
2787 if (!viewport.getAlignment().isAligned(false))
2790 int Width = viewport.getAlignment().getWidth();
2792 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2794 current = viewport.getAlignment().getSequenceAt(i);
2796 if (current.getLength() < Width)
2798 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2801 alignPanel.paintAlignment(true);
2804 if ((viewport.getSelectionGroup() != null
2805 && viewport.getSelectionGroup().getSize() < 4 && viewport
2806 .getSelectionGroup().getSize() > 0)
2807 || viewport.getAlignment().getHeight() < 4)
2814 new PCAPanel(viewport);
2815 } catch (java.lang.OutOfMemoryError ex)
2821 public void averageDistanceTreeMenuItem_actionPerformed()
2823 NewTreePanel("AV", "PID", "Average distance tree using PID");
2826 public void neighbourTreeMenuItem_actionPerformed()
2828 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2831 protected void njTreeBlosumMenuItem_actionPerformed()
2833 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2836 protected void avTreeBlosumMenuItem_actionPerformed()
2838 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2841 void NewTreePanel(String type, String pwType, String title)
2843 // are the sequences aligned?
2844 if (!viewport.getAlignment().isAligned(false))
2847 int Width = viewport.getAlignment().getWidth();
2849 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2851 current = viewport.getAlignment().getSequenceAt(i);
2853 if (current.getLength() < Width)
2855 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2858 alignPanel.paintAlignment(true);
2862 if ((viewport.getSelectionGroup() != null && viewport
2863 .getSelectionGroup().getSize() > 1)
2864 || (viewport.getAlignment().getHeight() > 1))
2866 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2868 addTreeMenuItem(tp, title);
2870 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2874 void loadTree_actionPerformed()
2876 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2877 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2878 cap.setTreeImport();
2879 Frame frame = new Frame();
2881 jalview.bin.JalviewLite.addFrame(frame,
2882 MessageManager.getString("label.paste_newick_file"), 400, 300);
2885 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2887 TreePanel tp = new TreePanel(alignPanel, treeFile,
2888 MessageManager.getString("label.load_tree_from_file"), tree);
2889 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2890 addTreeMenuItem(tp, treeFile);
2894 * sort the alignment using the given treePanel
2897 * tree used to sort view
2899 * string used for undo event name
2901 public void sortByTree(TreePanel treePanel, String title)
2903 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2905 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2906 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2907 // HistoryItem.SORT));
2908 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2909 "label.order_by_params", new String[] { title }), oldOrder,
2910 viewport.getAlignment()));
2911 alignPanel.paintAlignment(true);
2915 * Do any automatic reordering of the alignment and add the necessary bits to
2916 * the menu structure for the new tree
2921 protected void addTreeMenuItem(final TreePanel treePanel,
2924 final MenuItem item = new MenuItem(title);
2925 sortByTreeMenu.add(item);
2926 item.addActionListener(new java.awt.event.ActionListener()
2929 public void actionPerformed(ActionEvent evt)
2931 sortByTree(treePanel, title); // treePanel.getTitle());
2935 treePanel.addWindowListener(new WindowAdapter()
2938 public void windowOpened(WindowEvent e)
2940 if (viewport.sortByTree)
2942 sortByTree(treePanel, title);
2944 super.windowOpened(e);
2948 public void windowClosing(WindowEvent e)
2950 sortByTreeMenu.remove(item);
2955 public boolean sortBy(AlignmentOrder alorder, String undoname)
2957 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2958 if (viewport.applet.debug)
2960 System.err.println("Sorting " + alorder.getOrder().size()
2961 + " in alignment '" + getTitle() + "'");
2963 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2964 if (undoname != null)
2966 addHistoryItem(new OrderCommand(undoname, oldOrder,
2967 viewport.getAlignment()));
2969 alignPanel.paintAlignment(true);
2973 protected void documentation_actionPerformed()
2975 alignPanel.av.applet.openJalviewHelpUrl();
2978 protected void about_actionPerformed()
2981 class AboutPanel extends Canvas
2987 public AboutPanel(String version, String builddate)
2989 this.version = version;
2990 this.builddate = builddate;
2994 public void paint(Graphics g)
2996 g.setColor(Color.white);
2997 g.fillRect(0, 0, getSize().width, getSize().height);
2998 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2999 FontMetrics fm = g.getFontMetrics();
3000 int fh = fm.getHeight();
3002 g.setColor(Color.black);
3003 // TODO: update this text for each release or centrally store it for
3004 // lite and application
3005 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3006 g.drawString(MessageManager.formatMessage(
3007 "label.jalviewLite_release", new String[] { version }), x,
3009 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3010 g.drawString(MessageManager.formatMessage(
3011 "label.jaview_build_date", new String[] { builddate }), x,
3013 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3014 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3016 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3017 x + 50, y += fh + 8);
3019 MessageManager.getString("label.jalview_dev_managers"), x,
3021 g.drawString(MessageManager
3022 .getString("label.jalview_distribution_lists"), x, y += fh);
3023 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3026 MessageManager.getString("label.jalview_cite_1_authors"),
3029 MessageManager.getString("label.jalview_cite_1_title"), x,
3031 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3036 Frame frame = new Frame();
3037 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3039 jalview.bin.JalviewLite.addFrame(frame,
3040 MessageManager.getString("label.jalview"), 580, 220);
3044 public void showURL(String url, String target)
3046 if (viewport.applet == null)
3048 System.out.println("Not running as applet - no browser available.");
3052 viewport.applet.showURL(url, target);
3056 // ////////////////////////////////////////////////////////////////////////////////
3057 // JBuilder Graphics here
3059 MenuBar alignFrameMenuBar = new MenuBar();
3061 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3063 MenuItem loadApplication = new MenuItem(
3064 MessageManager.getString("label.view_full_application"));
3066 MenuItem loadTree = new MenuItem(
3067 MessageManager.getString("label.load_associated_tree"));
3069 MenuItem loadAnnotations = new MenuItem(
3070 MessageManager.getString("label.load_features_annotations"));
3072 MenuItem outputFeatures = new MenuItem(
3073 MessageManager.getString("label.export_features"));
3075 MenuItem outputAnnotations = new MenuItem(
3076 MessageManager.getString("label.export_annotations"));
3078 MenuItem closeMenuItem = new MenuItem(
3079 MessageManager.getString("action.close"));
3081 MenuItem selectAllSequenceMenuItem = new MenuItem(
3082 MessageManager.getString("action.select_all"));
3084 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3085 MessageManager.getString("action.deselect_all"));
3087 MenuItem invertSequenceMenuItem = new MenuItem(
3088 MessageManager.getString("action.invert_selection"));
3090 MenuItem remove2LeftMenuItem = new MenuItem();
3092 MenuItem remove2RightMenuItem = new MenuItem();
3094 MenuItem removeGappedColumnMenuItem = new MenuItem();
3096 MenuItem removeAllGapsMenuItem = new MenuItem();
3098 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3100 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3102 MenuItem sortPairwiseMenuItem = new MenuItem();
3104 MenuItem sortIDMenuItem = new MenuItem();
3106 MenuItem sortLengthMenuItem = new MenuItem();
3108 MenuItem sortGroupMenuItem = new MenuItem();
3110 MenuItem removeRedundancyMenuItem = new MenuItem();
3112 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3114 MenuItem PCAMenuItem = new MenuItem();
3116 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3118 MenuItem neighbourTreeMenuItem = new MenuItem();
3120 BorderLayout borderLayout1 = new BorderLayout();
3122 public Label statusBar = new Label();
3124 MenuItem clustalColour = new MenuItem();
3126 MenuItem zappoColour = new MenuItem();
3128 MenuItem taylorColour = new MenuItem();
3130 MenuItem hydrophobicityColour = new MenuItem();
3132 MenuItem helixColour = new MenuItem();
3134 MenuItem strandColour = new MenuItem();
3136 MenuItem turnColour = new MenuItem();
3138 MenuItem buriedColour = new MenuItem();
3140 MenuItem purinePyrimidineColour = new MenuItem();
3142 // MenuItem RNAInteractionColour = new MenuItem();
3144 MenuItem RNAHelixColour = new MenuItem();
3146 MenuItem userDefinedColour = new MenuItem();
3148 MenuItem PIDColour = new MenuItem();
3150 MenuItem BLOSUM62Colour = new MenuItem();
3152 MenuItem tcoffeeColour = new MenuItem();
3154 MenuItem njTreeBlosumMenuItem = new MenuItem();
3156 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3158 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3160 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3162 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3164 MenuItem alProperties = new MenuItem(
3165 MessageManager.getString("label.alignment_props"));
3167 MenuItem overviewMenuItem = new MenuItem();
3169 MenuItem undoMenuItem = new MenuItem();
3171 MenuItem redoMenuItem = new MenuItem();
3173 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3175 MenuItem noColourmenuItem = new MenuItem();
3177 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3179 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3181 MenuItem findMenuItem = new MenuItem();
3183 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3185 MenuItem nucleotideColour = new MenuItem();
3187 MenuItem deleteGroups = new MenuItem();
3189 MenuItem grpsFromSelection = new MenuItem();
3191 MenuItem createGroup = new MenuItem();
3193 MenuItem unGroup = new MenuItem();
3195 MenuItem delete = new MenuItem();
3197 MenuItem copy = new MenuItem();
3199 MenuItem cut = new MenuItem();
3201 Menu pasteMenu = new Menu();
3203 MenuItem pasteNew = new MenuItem();
3205 MenuItem pasteThis = new MenuItem();
3207 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3209 MenuItem font = new MenuItem();
3211 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3213 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3215 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3217 MenuItem modifyPID = new MenuItem();
3219 MenuItem modifyConservation = new MenuItem();
3221 CheckboxMenuItem autoCalculate = null;
3223 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3224 "Sort Alignment With New Tree", true);
3226 Menu sortByTreeMenu = new Menu();
3228 MenuItem inputText = new MenuItem();
3230 MenuItem documentation = new MenuItem();
3232 MenuItem about = new MenuItem();
3234 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3236 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3238 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3240 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3242 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3244 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3246 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3248 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3250 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3253 * Initialise menus and other items
3257 private void jbInit() throws Exception
3259 setMenuBar(alignFrameMenuBar);
3262 * Configure File menu items and actions
3265 .setLabel(MessageManager.getString("label.input_from_textbox"));
3266 inputText.addActionListener(this);
3267 Menu outputTextboxMenu = new Menu(
3268 MessageManager.getString("label.out_to_textbox"));
3269 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3271 MenuItem item = new MenuItem(ff);
3273 item.addActionListener(new java.awt.event.ActionListener()
3276 public void actionPerformed(ActionEvent e)
3278 outputText_actionPerformed(e);
3282 outputTextboxMenu.add(item);
3284 closeMenuItem.addActionListener(this);
3285 loadApplication.addActionListener(this);
3286 loadTree.addActionListener(this);
3287 loadAnnotations.addActionListener(this);
3288 outputFeatures.addActionListener(this);
3289 outputAnnotations.addActionListener(this);
3292 * Configure Edit menu items and actions
3294 undoMenuItem.setEnabled(false);
3295 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3296 undoMenuItem.addActionListener(this);
3297 redoMenuItem.setEnabled(false);
3298 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3299 redoMenuItem.addActionListener(this);
3300 copy.setLabel(MessageManager.getString("action.copy"));
3301 copy.addActionListener(this);
3302 cut.setLabel(MessageManager.getString("action.cut"));
3303 cut.addActionListener(this);
3304 delete.setLabel(MessageManager.getString("action.delete"));
3305 delete.addActionListener(this);
3306 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3307 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3308 pasteNew.addActionListener(this);
3309 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3310 pasteThis.addActionListener(this);
3311 remove2LeftMenuItem.setLabel(MessageManager
3312 .getString("action.remove_left"));
3313 remove2LeftMenuItem.addActionListener(this);
3314 remove2RightMenuItem.setLabel(MessageManager
3315 .getString("action.remove_right"));
3316 remove2RightMenuItem.addActionListener(this);
3317 removeGappedColumnMenuItem.setLabel(MessageManager
3318 .getString("action.remove_empty_columns"));
3319 removeGappedColumnMenuItem.addActionListener(this);
3320 removeAllGapsMenuItem.setLabel(MessageManager
3321 .getString("action.remove_all_gaps"));
3322 removeAllGapsMenuItem.addActionListener(this);
3323 removeRedundancyMenuItem.setLabel(MessageManager
3324 .getString("action.remove_redundancy"));
3325 removeRedundancyMenuItem.addActionListener(this);
3328 * Configure Select menu items and actions
3330 findMenuItem.setLabel(MessageManager.getString("action.find"));
3331 findMenuItem.addActionListener(this);
3332 selectAllSequenceMenuItem.addActionListener(this);
3333 deselectAllSequenceMenuItem.addActionListener(this);
3334 invertSequenceMenuItem.setLabel(MessageManager
3335 .getString("action.invert_sequence_selection"));
3336 invertSequenceMenuItem.addActionListener(this);
3337 invertColSel.setLabel(MessageManager
3338 .getString("action.invert_column_selection"));
3339 invertColSel.addActionListener(this);
3340 deleteGroups.setLabel(MessageManager
3341 .getString("action.undefine_groups"));
3342 deleteGroups.addActionListener(this);
3343 grpsFromSelection.setLabel(MessageManager
3344 .getString("action.make_groups_selection"));
3345 grpsFromSelection.addActionListener(this);
3346 createGroup.setLabel(MessageManager.getString("action.create_group"));
3347 createGroup.addActionListener(this);
3348 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3349 unGroup.addActionListener(this);
3351 annotationColumnSelection.setLabel(MessageManager
3352 .getString("action.select_by_annotation"));
3353 annotationColumnSelection.addActionListener(this);
3356 * Configure View menu items and actions
3358 newView.setLabel(MessageManager.getString("action.new_view"));
3359 newView.addActionListener(this);
3360 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3361 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3362 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3363 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3365 .setLabel(MessageManager.getString("label.selected_columns"));
3366 hideSequences.setLabel(MessageManager
3367 .getString("label.selected_sequences"));
3368 hideAllButSelection.setLabel(MessageManager
3369 .getString("label.all_but_selected_region"));
3370 hideAllSelection.setLabel(MessageManager
3371 .getString("label.selected_region"));
3372 showAllHidden.setLabel(MessageManager
3373 .getString("label.all_sequences_columns"));
3374 showColumns.addActionListener(this);
3375 showSeqs.addActionListener(this);
3376 hideColumns.addActionListener(this);
3377 hideSequences.addActionListener(this);
3378 hideAllButSelection.addActionListener(this);
3379 hideAllSelection.addActionListener(this);
3380 showAllHidden.addActionListener(this);
3381 featureSettings.setLabel(MessageManager
3382 .getString("action.feature_settings"));
3383 featureSettings.addActionListener(this);
3384 sequenceFeatures.setLabel(MessageManager
3385 .getString("label.show_sequence_features"));
3386 sequenceFeatures.addItemListener(this);
3387 sequenceFeatures.setState(false);
3388 followMouseOverFlag.setLabel(MessageManager
3389 .getString("label.automatic_scrolling"));
3390 followMouseOverFlag.addItemListener(this);
3391 alProperties.addActionListener(this);
3392 overviewMenuItem.setLabel(MessageManager
3393 .getString("label.overview_window"));
3394 overviewMenuItem.addActionListener(this);
3397 * Configure Annotations menu items and actions
3399 annotationPanelMenuItem.setLabel(MessageManager
3400 .getString("label.show_annotations"));
3401 annotationPanelMenuItem.addItemListener(this);
3402 showGroupConsensus.setLabel(MessageManager
3403 .getString("label.group_consensus"));
3404 showGroupConservation.setLabel(MessageManager
3405 .getString("label.group_conservation"));
3406 showConsensusHistogram.setLabel(MessageManager
3407 .getString("label.show_consensus_histogram"));
3408 showSequenceLogo.setLabel(MessageManager
3409 .getString("label.show_consensus_logo"));
3410 normSequenceLogo.setLabel(MessageManager
3411 .getString("label.norm_consensus_logo"));
3412 applyAutoAnnotationSettings.setLabel(MessageManager
3413 .getString("label.apply_all_groups"));
3414 applyAutoAnnotationSettings.setState(true);
3415 Menu autoAnnMenu = new Menu(
3416 MessageManager.getString("label.autocalculated_annotation"));
3417 showGroupConsensus.addItemListener(this);
3418 showGroupConservation.addItemListener(this);
3419 showConsensusHistogram.addItemListener(this);
3420 showSequenceLogo.addItemListener(this);
3421 normSequenceLogo.addItemListener(this);
3422 applyAutoAnnotationSettings.addItemListener(this);
3423 showAlignmentAnnotations = new CheckboxMenuItem(
3424 MessageManager.getString("label.show_all_al_annotations"));
3425 showSequenceAnnotations = new CheckboxMenuItem(
3426 MessageManager.getString("label.show_all_seq_annotations"));
3427 sortAnnBySequence = new CheckboxMenuItem(
3428 MessageManager.getString("label.sort_annotations_by_sequence"));
3429 sortAnnByLabel = new CheckboxMenuItem(
3430 MessageManager.getString("label.sort_annotations_by_label"));
3431 showAutoFirst = new CheckboxMenuItem(
3432 MessageManager.getString("label.show_first"));
3433 showAutoFirst.setState(false); // pending applet parameter
3434 setShowAutoCalculatedAbove(showAutoFirst.getState());
3435 showAutoLast = new CheckboxMenuItem(
3436 MessageManager.getString("label.show_last"));
3437 showAutoLast.setState(!showAutoFirst.getState());
3438 showAlignmentAnnotations.addItemListener(this);
3439 showSequenceAnnotations.addItemListener(this);
3440 sortAnnBySequence.addItemListener(this);
3441 sortAnnByLabel.addItemListener(this);
3442 showAutoFirst.addItemListener(this);
3443 showAutoLast.addItemListener(this);
3446 * Configure Format menu items and actions
3448 font.setLabel(MessageManager.getString("action.font"));
3449 font.addActionListener(this);
3450 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3451 scaleAbove.setState(true);
3452 scaleAbove.setEnabled(false);
3453 scaleAbove.addItemListener(this);
3454 scaleLeft.setEnabled(false);
3455 scaleLeft.setState(true);
3456 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3457 scaleLeft.addItemListener(this);
3458 scaleRight.setEnabled(false);
3459 scaleRight.setState(true);
3460 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3461 scaleRight.addItemListener(this);
3462 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3463 viewBoxesMenuItem.setState(true);
3464 viewBoxesMenuItem.addItemListener(this);
3465 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3466 viewTextMenuItem.setState(true);
3467 viewTextMenuItem.addItemListener(this);
3468 colourTextMenuItem.setLabel(MessageManager
3469 .getString("label.colour_text"));
3470 colourTextMenuItem.addItemListener(this);
3471 displayNonconservedMenuItem.setLabel(MessageManager
3472 .getString("label.show_non_conserved"));
3473 displayNonconservedMenuItem.addItemListener(this);
3474 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3475 wrapMenuItem.addItemListener(this);
3476 renderGapsMenuItem.setLabel(MessageManager
3477 .getString("action.show_gaps"));
3478 renderGapsMenuItem.setState(true);
3479 renderGapsMenuItem.addItemListener(this);
3480 centreColumnLabelFlag.setLabel(MessageManager
3481 .getString("label.centre_column_labels"));
3482 centreColumnLabelFlag.addItemListener(this);
3483 seqLimits.setState(true);
3484 seqLimits.setLabel(MessageManager
3485 .getString("label.show_sequence_limits"));
3486 seqLimits.addItemListener(this);
3489 * Configure Colour menu items and actions
3491 applyToAllGroups.setLabel(MessageManager
3492 .getString("label.apply_colour_to_all_groups"));
3493 applyToAllGroups.setState(true);
3494 applyToAllGroups.addItemListener(this);
3495 clustalColour.setLabel(MessageManager
3496 .getString("label.colourScheme_clustal"));
3497 clustalColour.addActionListener(this);
3498 zappoColour.setLabel(MessageManager
3499 .getString("label.colourScheme_zappo"));
3500 zappoColour.addActionListener(this);
3501 taylorColour.setLabel(MessageManager
3502 .getString("label.colourScheme_taylor"));
3503 taylorColour.addActionListener(this);
3504 hydrophobicityColour.setLabel(MessageManager
3505 .getString("label.colourScheme_hydrophobic"));
3506 hydrophobicityColour.addActionListener(this);
3507 helixColour.setLabel(MessageManager
3508 .getString("label.colourScheme_helix_propensity"));
3509 helixColour.addActionListener(this);
3510 strandColour.setLabel(MessageManager
3511 .getString("label.colourScheme_strand_propensity"));
3512 strandColour.addActionListener(this);
3513 turnColour.setLabel(MessageManager
3514 .getString("label.colourScheme_turn_propensity"));
3515 turnColour.addActionListener(this);
3516 buriedColour.setLabel(MessageManager
3517 .getString("label.colourScheme_buried_index"));
3518 buriedColour.addActionListener(this);
3519 purinePyrimidineColour.setLabel(MessageManager
3520 .getString("label.colourScheme_purine/pyrimidine"));
3521 purinePyrimidineColour.addActionListener(this);
3522 // RNAInteractionColour.setLabel(MessageManager
3523 // .getString("label.rna_interaction"));
3524 // RNAInteractionColour.addActionListener(this);
3525 RNAHelixColour.setLabel(MessageManager
3526 .getString("label.colourScheme_rna_helices"));
3527 RNAHelixColour.addActionListener(this);
3528 userDefinedColour.setLabel(MessageManager
3529 .getString("action.user_defined"));
3530 userDefinedColour.addActionListener(this);
3531 PIDColour.setLabel(MessageManager
3532 .getString("label.colourScheme_%_identity"));
3533 PIDColour.addActionListener(this);
3534 BLOSUM62Colour.setLabel(MessageManager
3535 .getString("label.colourScheme_blosum62"));
3536 BLOSUM62Colour.addActionListener(this);
3537 tcoffeeColour.setLabel(MessageManager
3538 .getString("label.colourScheme_t-coffee_scores"));
3539 // it will be enabled only if a score file is provided
3540 tcoffeeColour.setEnabled(false);
3541 tcoffeeColour.addActionListener(this);
3542 conservationMenuItem.setLabel(MessageManager
3543 .getString("action.by_conservation"));
3544 conservationMenuItem.addItemListener(this);
3545 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3546 noColourmenuItem.addActionListener(this);
3547 abovePIDThreshold.setLabel(MessageManager
3548 .getString("label.above_identity_threshold"));
3549 abovePIDThreshold.addItemListener(this);
3550 nucleotideColour.setLabel(MessageManager
3551 .getString("label.colourScheme_nucleotide"));
3552 nucleotideColour.addActionListener(this);
3553 modifyPID.setLabel(MessageManager
3554 .getString("label.modify_identity_threshold"));
3555 modifyPID.setEnabled(abovePIDThreshold.getState());
3556 modifyPID.addActionListener(this);
3557 modifyConservation.setLabel(MessageManager
3558 .getString("label.modify_conservation_threshold"));
3559 modifyConservation.setEnabled(conservationMenuItem.getState());
3560 modifyConservation.addActionListener(this);
3561 annotationColour.setLabel(MessageManager
3562 .getString("action.by_annotation"));
3563 annotationColour.addActionListener(this);
3566 * Configure Calculate menu items and actions
3568 sortPairwiseMenuItem.setLabel(MessageManager
3569 .getString("action.by_pairwise_id"));
3570 sortPairwiseMenuItem.addActionListener(this);
3571 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3572 sortIDMenuItem.addActionListener(this);
3573 sortLengthMenuItem.setLabel(MessageManager
3574 .getString("action.by_length"));
3575 sortLengthMenuItem.addActionListener(this);
3576 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3577 sortGroupMenuItem.addActionListener(this);
3578 pairwiseAlignmentMenuItem.setLabel(MessageManager
3579 .getString("action.pairwise_alignment"));
3580 pairwiseAlignmentMenuItem.addActionListener(this);
3581 PCAMenuItem.setLabel(MessageManager
3582 .getString("label.principal_component_analysis"));
3583 PCAMenuItem.addActionListener(this);
3584 autoCalculate = new CheckboxMenuItem(
3585 MessageManager.getString("label.autocalculate_consensus"), true);
3586 averageDistanceTreeMenuItem.setLabel(MessageManager
3587 .getString("label.average_distance_identity"));
3588 averageDistanceTreeMenuItem.addActionListener(this);
3589 neighbourTreeMenuItem.setLabel(MessageManager
3590 .getString("label.neighbour_joining_identity"));
3591 neighbourTreeMenuItem.addActionListener(this);
3592 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3593 .getString("label.average_distance_blosum62"));
3594 avDistanceTreeBlosumMenuItem.addActionListener(this);
3595 njTreeBlosumMenuItem.setLabel(MessageManager
3596 .getString("label.neighbour_blosum62"));
3597 njTreeBlosumMenuItem.addActionListener(this);
3598 sortByTreeMenu.setLabel(MessageManager
3599 .getString("action.by_tree_order"));
3600 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3601 Menu calculateTreeMenu = new Menu(
3602 MessageManager.getString("action.calculate_tree"));
3603 autoCalculate.addItemListener(this);
3604 sortByTree.addItemListener(this);
3607 * Configure Help menu items and actions
3609 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3610 documentation.setLabel(MessageManager.getString("label.documentation"));
3611 documentation.addActionListener(this);
3612 about.setLabel(MessageManager.getString("label.about"));
3613 about.addActionListener(this);
3616 * Add top level menus to frame
3618 alignFrameMenuBar.add(fileMenu);
3619 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3620 alignFrameMenuBar.add(editMenu);
3621 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3622 alignFrameMenuBar.add(selectMenu);
3623 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3624 alignFrameMenuBar.add(viewMenu);
3625 Menu annotationsMenu = new Menu(
3626 MessageManager.getString("action.annotations"));
3627 alignFrameMenuBar.add(annotationsMenu);
3628 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3629 alignFrameMenuBar.add(formatMenu);
3630 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3631 alignFrameMenuBar.add(colourMenu);
3632 Menu calculateMenu = new Menu(
3633 MessageManager.getString("action.calculate"));
3634 alignFrameMenuBar.add(calculateMenu);
3635 alignFrameMenuBar.add(helpMenu);
3640 fileMenu.add(inputText);
3641 fileMenu.add(loadTree);
3642 fileMenu.add(loadAnnotations);
3643 fileMenu.addSeparator();
3644 fileMenu.add(outputTextboxMenu);
3645 fileMenu.add(outputFeatures);
3646 fileMenu.add(outputAnnotations);
3647 if (jalviewServletURL != null)
3649 fileMenu.add(loadApplication);
3651 fileMenu.addSeparator();
3652 fileMenu.add(closeMenuItem);
3657 editMenu.add(undoMenuItem);
3658 editMenu.add(redoMenuItem);
3661 pasteMenu.add(pasteNew);
3662 pasteMenu.add(pasteThis);
3663 editMenu.add(pasteMenu);
3664 editMenu.add(delete);
3665 editMenu.addSeparator();
3666 editMenu.add(remove2LeftMenuItem);
3667 editMenu.add(remove2RightMenuItem);
3668 editMenu.add(removeGappedColumnMenuItem);
3669 editMenu.add(removeAllGapsMenuItem);
3670 editMenu.add(removeRedundancyMenuItem);
3675 selectMenu.add(findMenuItem);
3676 selectMenu.addSeparator();
3677 selectMenu.add(selectAllSequenceMenuItem);
3678 selectMenu.add(deselectAllSequenceMenuItem);
3679 selectMenu.add(invertSequenceMenuItem);
3680 selectMenu.add(invertColSel);
3681 selectMenu.add(createGroup);
3682 selectMenu.add(unGroup);
3683 selectMenu.add(grpsFromSelection);
3684 selectMenu.add(deleteGroups);
3685 selectMenu.add(annotationColumnSelection);
3690 viewMenu.add(newView);
3691 viewMenu.addSeparator();
3692 showMenu.add(showColumns);
3693 showMenu.add(showSeqs);
3694 showMenu.add(showAllHidden);
3695 viewMenu.add(showMenu);
3696 hideMenu.add(hideColumns);
3697 hideMenu.add(hideSequences);
3698 hideMenu.add(hideAllSelection);
3699 hideMenu.add(hideAllButSelection);
3700 viewMenu.add(hideMenu);
3701 viewMenu.addSeparator();
3702 viewMenu.add(followMouseOverFlag);
3703 viewMenu.addSeparator();
3704 viewMenu.add(sequenceFeatures);
3705 viewMenu.add(featureSettings);
3706 viewMenu.addSeparator();
3707 viewMenu.add(alProperties);
3708 viewMenu.addSeparator();
3709 viewMenu.add(overviewMenuItem);
3714 annotationsMenu.add(annotationPanelMenuItem);
3715 annotationsMenu.addSeparator();
3716 annotationsMenu.add(showAlignmentAnnotations);
3717 annotationsMenu.add(showSequenceAnnotations);
3718 annotationsMenu.add(sortAnnBySequence);
3719 annotationsMenu.add(sortAnnByLabel);
3720 annotationsMenu.addSeparator();
3721 autoAnnMenu.add(showAutoFirst);
3722 autoAnnMenu.add(showAutoLast);
3723 autoAnnMenu.addSeparator();
3724 autoAnnMenu.add(applyAutoAnnotationSettings);
3725 autoAnnMenu.add(showConsensusHistogram);
3726 autoAnnMenu.add(showSequenceLogo);
3727 autoAnnMenu.add(normSequenceLogo);
3728 autoAnnMenu.addSeparator();
3729 autoAnnMenu.add(showGroupConservation);
3730 autoAnnMenu.add(showGroupConsensus);
3731 annotationsMenu.add(autoAnnMenu);
3736 formatMenu.add(font);
3737 formatMenu.add(seqLimits);
3738 formatMenu.add(wrapMenuItem);
3739 formatMenu.add(scaleAbove);
3740 formatMenu.add(scaleLeft);
3741 formatMenu.add(scaleRight);
3742 formatMenu.add(viewBoxesMenuItem);
3743 formatMenu.add(viewTextMenuItem);
3744 formatMenu.add(colourTextMenuItem);
3745 formatMenu.add(displayNonconservedMenuItem);
3746 formatMenu.add(renderGapsMenuItem);
3747 formatMenu.add(centreColumnLabelFlag);
3752 colourMenu.add(applyToAllGroups);
3753 colourMenu.addSeparator();
3754 colourMenu.add(noColourmenuItem);
3755 colourMenu.add(clustalColour);
3756 colourMenu.add(BLOSUM62Colour);
3757 colourMenu.add(PIDColour);
3758 colourMenu.add(zappoColour);
3759 colourMenu.add(taylorColour);
3760 colourMenu.add(hydrophobicityColour);
3761 colourMenu.add(helixColour);
3762 colourMenu.add(strandColour);
3763 colourMenu.add(turnColour);
3764 colourMenu.add(buriedColour);
3765 colourMenu.add(nucleotideColour);
3766 colourMenu.add(purinePyrimidineColour);
3767 // colourMenu.add(RNAInteractionColour);
3768 colourMenu.add(tcoffeeColour);
3769 colourMenu.add(userDefinedColour);
3770 colourMenu.addSeparator();
3771 colourMenu.add(conservationMenuItem);
3772 colourMenu.add(modifyConservation);
3773 colourMenu.add(abovePIDThreshold);
3774 colourMenu.add(modifyPID);
3775 colourMenu.add(annotationColour);
3776 colourMenu.add(RNAHelixColour);
3781 sortMenu.add(sortIDMenuItem);
3782 sortMenu.add(sortLengthMenuItem);
3783 sortMenu.add(sortByTreeMenu);
3784 sortMenu.add(sortGroupMenuItem);
3785 sortMenu.add(sortPairwiseMenuItem);
3786 calculateMenu.add(sortMenu);
3787 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3788 calculateTreeMenu.add(neighbourTreeMenuItem);
3789 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3790 calculateTreeMenu.add(njTreeBlosumMenuItem);
3791 calculateMenu.add(calculateTreeMenu);
3792 calculateMenu.addSeparator();
3793 calculateMenu.add(pairwiseAlignmentMenuItem);
3794 calculateMenu.add(PCAMenuItem);
3795 calculateMenu.add(autoCalculate);
3796 calculateMenu.add(sortByTree);
3801 helpMenu.add(documentation);
3802 helpMenu.add(about);
3807 statusBar.setBackground(Color.white);
3808 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3809 statusBar.setText(MessageManager.getString("label.status_bar"));
3810 this.add(statusBar, BorderLayout.SOUTH);
3814 public void setStatus(String string)
3816 statusBar.setText(string);
3819 MenuItem featureSettings = new MenuItem();
3821 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3823 MenuItem annotationColour = new MenuItem();
3825 MenuItem annotationColumnSelection = new MenuItem();
3827 MenuItem invertColSel = new MenuItem();
3829 MenuItem showColumns = new MenuItem();
3831 MenuItem showSeqs = new MenuItem();
3833 MenuItem hideColumns = new MenuItem();
3835 MenuItem hideSequences = new MenuItem();
3837 MenuItem hideAllButSelection = new MenuItem();
3839 MenuItem hideAllSelection = new MenuItem();
3841 MenuItem showAllHidden = new MenuItem();
3843 MenuItem newView = new MenuItem();
3845 private CheckboxMenuItem showAlignmentAnnotations;
3847 private CheckboxMenuItem showSequenceAnnotations;
3849 private CheckboxMenuItem sortAnnBySequence;
3851 private CheckboxMenuItem sortAnnByLabel;
3853 private CheckboxMenuItem showAutoFirst;
3855 private CheckboxMenuItem showAutoLast;
3857 private SplitFrame splitFrame;
3860 * Attach the alignFrame panels after embedding menus, if necessary. This used
3861 * to be called setEmbedded, but is now creates the dropdown menus in a
3862 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3864 * @param reallyEmbedded
3865 * true to attach the view to the applet area on the page rather than
3868 public void createAlignFrameWindow(boolean reallyEmbedded)
3872 embedAlignFrameInApplet(viewport.applet);
3877 // test and embed menu bar if necessary.
3879 if (embedMenuIfNeeded(alignPanel))
3882 * adjust for status bar height too. ? pointless as overridden by layout
3885 alignPanel.setSize(getSize().width,
3886 getSize().height - statusBar.getHeight());
3888 add(statusBar, BorderLayout.SOUTH);
3889 add(alignPanel, BorderLayout.CENTER);
3890 // and register with the applet so it can pass external API calls to us
3891 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3897 * Add the components of this AlignFrame to the applet container.
3901 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3904 // Explicitly build the embedded menu panel for the on-page applet
3906 // view cannot be closed if its actually on the page
3907 fileMenu.remove(closeMenuItem);
3908 fileMenu.remove(3); // Remove Separator
3909 // construct embedded menu, using default font
3910 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3911 // and actually add the components to the applet area
3912 theApplet.setLayout(new BorderLayout());
3913 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3914 theApplet.add(statusBar, BorderLayout.SOUTH);
3915 // TODO should size be left to the layout manager?
3916 alignPanel.setSize(theApplet.getSize().width,
3917 theApplet.getSize().height - embeddedMenu.getHeight()
3918 - statusBar.getHeight());
3919 theApplet.add(alignPanel, BorderLayout.CENTER);
3920 final AlignFrame me = this;
3921 theApplet.addFocusListener(new FocusListener()
3925 public void focusLost(FocusEvent e)
3927 if (theApplet.currentAlignFrame == me)
3929 theApplet.currentAlignFrame = null;
3934 public void focusGained(FocusEvent e)
3936 theApplet.currentAlignFrame = me;
3939 theApplet.validate();
3943 * create a new binding between structures in an existing jmol viewer instance
3944 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3945 * this does not open a new Jmol window, or modify the display of the
3946 * structures in the original jmol window. Note This method doesn't work
3947 * without an additional javascript library to exchange messages between the
3948 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3951 * JmolViewer instance
3952 * @param sequenceIds
3953 * - sequence Ids to search for associations
3955 public SequenceStructureBinding addStructureViewInstance(
3956 Object jmolviewer, String[] sequenceIds)
3958 Viewer viewer = null;
3961 viewer = (Viewer) jmolviewer;
3962 } catch (ClassCastException ex)
3964 System.err.println("Unsupported viewer object :"
3965 + jmolviewer.getClass());
3969 System.err.println("Can't use this object as a structure viewer:"
3970 + jmolviewer.getClass());
3973 SequenceI[] seqs = null;
3974 if (sequenceIds == null || sequenceIds.length == 0)
3976 seqs = viewport.getAlignment().getSequencesArray();
3980 Vector sqi = new Vector();
3981 AlignmentI al = viewport.getAlignment();
3982 for (int sid = 0; sid < sequenceIds.length; sid++)
3984 SequenceI sq = al.findName(sequenceIds[sid]);
3992 seqs = new SequenceI[sqi.size()];
3993 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3995 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4003 AAStructureBindingModel jmv = null;
4004 // TODO: search for a jmv that involves viewer
4006 { // create a new viewer/jalview binding.
4007 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4014 * bind a pdb file to a sequence in the current view
4017 * - sequenceId within the dataset.
4018 * @param pdbEntryString
4019 * - the short name for the PDB file
4021 * - pdb file - either a URL or a valid PDB file.
4022 * @return true if binding was as success TODO: consider making an exception
4023 * structure for indicating when PDB parsing or sequenceId location
4026 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4029 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4030 boolean needtoadd = false;
4031 if (toaddpdb != null)
4033 Vector pdbe = toaddpdb.getAllPDBEntries();
4034 PDBEntry pdbentry = null;
4035 if (pdbe != null && pdbe.size() > 0)
4037 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4039 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4040 if (!pdbentry.getId().equals(pdbEntryString)
4041 && !pdbentry.getFile().equals(pdbFile))
4051 if (pdbentry == null)
4053 pdbentry = new PDBEntry();
4054 pdbentry.setId(pdbEntryString);
4055 pdbentry.setFile(pdbFile);
4056 needtoadd = true; // add this new entry to sequence.
4058 // resolve data source
4059 // TODO: this code should be a refactored to an io package
4060 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4061 pdbFile, FileFormat.PDB);
4062 if (protocol == null)
4068 pdbentry.setProperty("protocol", protocol);
4069 toaddpdb.addPDBId(pdbentry);
4070 alignPanel.getStructureSelectionManager()
4071 .registerPDBEntry(pdbentry);
4077 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4081 Vector sequences = new Vector();
4082 for (int i = 0; i < seqs.length; i++)
4084 if (seqs[i] != null)
4086 sequences.addElement(new Object[] { seqs[i],
4087 (chains != null) ? chains[i] : null });
4090 seqs = new SequenceI[sequences.size()];
4091 chains = new String[sequences.size()];
4092 for (int i = 0, isize = sequences.size(); i < isize; i++)
4094 Object[] oj = (Object[]) sequences.elementAt(i);
4096 seqs[i] = (SequenceI) oj[0];
4097 chains[i] = (String) oj[1];
4100 return new Object[] { seqs, chains };
4104 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4105 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4107 // Scrub any null sequences from the array
4108 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4109 seqs = (SequenceI[]) sqch[0];
4110 chains = (String[]) sqch[1];
4111 if (seqs == null || seqs.length == 0)
4114 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4116 if (protocol == null)
4118 String sourceType = (String) pdb.getProperty("protocol");
4121 protocol = DataSourceType.valueOf(sourceType);
4122 } catch (IllegalArgumentException e)
4126 if (protocol == null)
4128 System.err.println("Couldn't work out protocol to open structure: "
4133 if (applet.useXtrnalSviewer)
4135 // register the association(s) and quit, don't create any windows.
4136 if (StructureSelectionManager.getStructureSelectionManager(applet)
4137 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4139 System.err.println("Failed to map " + pdb.getFile() + " ("
4140 + protocol + ") to any sequences");
4144 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4146 // can only do alignments with Jmol
4147 // find the last jmol window assigned to this alignment
4148 AppletJmol ajm = null, tajm;
4149 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4150 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4152 tajm = (AppletJmol) jmols.elementAt(i);
4153 if (tajm.ap.alignFrame == this)
4162 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4163 // try and add the pdb structure
4168 // otherwise, create a new window
4169 if (applet.jmolAvailable)
4171 new AppletJmol(pdb, seqs, chains, alignPanel,
4173 applet.lastFrameX += 40;
4174 applet.lastFrameY += 40;
4178 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4183 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4184 SequenceI[][] seqs, String[][] chains, String[] protocols)
4186 // TODO Auto-generated method stub
4187 System.err.println("Aligned Structure View: Not yet implemented.");
4191 * modify the current selection, providing the user has not made a selection
4195 * - sequences from this alignment
4197 * - columns to be selected on the alignment
4199 public void select(SequenceGroup sel, ColumnSelection csel)
4201 alignPanel.seqPanel.selection(sel, csel, null);
4204 public void scrollTo(int row, int column)
4206 alignPanel.seqPanel.scrollTo(row, column);
4209 public void scrollToRow(int row)
4211 alignPanel.seqPanel.scrollToRow(row);
4214 public void scrollToColumn(int column)
4216 alignPanel.seqPanel.scrollToColumn(column);
4220 * @return the alignments unique ID.
4222 public String getSequenceSetId()
4224 return viewport.getSequenceSetId();
4228 * Load the (T-Coffee) score file from the specified url
4231 * File/URL/T-COFFEE score file contents
4232 * @throws IOException
4233 * @return true if alignment was annotated with data from source
4235 public boolean loadScoreFile(String source) throws IOException
4238 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4239 AppletFormatAdapter.checkProtocol(source));
4240 if (!file.isValid())
4242 // TODO: raise dialog for gui
4243 System.err.println("Problems parsing T-Coffee scores: "
4244 + file.getWarningMessage());
4245 System.err.println("Origin was:\n" + source);
4250 * check that the score matrix matches the alignment dimensions
4253 if ((aln = viewport.getAlignment()) != null
4254 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4257 // TODO: raise a dialog box here rather than bomb out.
4259 .println("The scores matrix does not match the alignment dimensions");
4263 // TODO add parameter to indicate if matching should be done
4264 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4266 alignPanel.fontChanged();
4267 tcoffeeColour.setEnabled(true);
4268 // switch to this color
4269 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4274 System.err.println("Problems resolving T-Coffee scores:");
4275 if (file.getWarningMessage() != null)
4277 System.err.println(file.getWarningMessage());
4283 public SplitFrame getSplitFrame()
4285 return this.splitFrame;
4288 public void setSplitFrame(SplitFrame sf)
4290 this.splitFrame = sf;
4293 // may not need this
4295 public void setShowSeqFeatures(boolean b)
4297 // showSeqFeatures.setSelected(b);
4298 viewport.setShowSequenceFeatures(b);
4303 public void setMenusForViewport()
4305 // setMenusFromViewport(viewport);
4310 public void refreshFeatureUI(boolean enableIfNecessary)
4312 if (enableIfNecessary)
4314 sequenceFeatures.setState(true);
4315 alignPanel.av.setShowSequenceFeatures(true);
4320 public FeatureSettingsControllerI getFeatureSettingsUI()
4322 return alignPanel.av.featureSettings;