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.RNAHelicesColourChooser;
69 import jalview.schemes.StrandColourScheme;
70 import jalview.schemes.TCoffeeColourScheme;
71 import jalview.schemes.TaylorColourScheme;
72 import jalview.schemes.TurnColourScheme;
73 import jalview.schemes.ZappoColourScheme;
74 import jalview.structure.StructureSelectionManager;
75 import jalview.structures.models.AAStructureBindingModel;
76 import jalview.util.MappingUtils;
77 import jalview.util.MessageManager;
78 import jalview.viewmodel.AlignmentViewport;
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 viewport.updateStrucConsensus(alignPanel);
289 if (viewport.getAlignment().hasRNAStructure())
291 RNAHelixColour.setEnabled(true);
295 RNAHelixColour.setEnabled(false);
300 RNAHelixColour.setEnabled(false);
301 purinePyrimidineColour.setEnabled(false);
302 nucleotideColour.setEnabled(false);
304 // Some JVMS send keyevents to Top frame or lowest panel,
305 // Havent worked out why yet. So add to both this frame and seqCanvas for
307 this.addKeyListener(this);
308 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
309 alignPanel.idPanel.idCanvas.addKeyListener(this);
310 alignPanel.scalePanel.addKeyListener(this);
311 alignPanel.annotationPanel.addKeyListener(this);
312 alignPanel.annotationPanelHolder.addKeyListener(this);
313 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
314 alignPanel.alabels.addKeyListener(this);
316 setAnnotationsVisibility();
320 addToDisplay(embedded);
327 public void addToDisplay(boolean embedded)
329 createAlignFrameWindow(embedded);
331 alignPanel.adjustAnnotationHeight();
332 alignPanel.paintAlignment(true);
335 public AlignViewport getAlignViewport()
340 public SeqCanvas getSeqcanvas()
342 return alignPanel.seqPanel.seqCanvas;
346 * Load a features file onto the alignment
349 * file URL, content, or other resolvable path
351 * is protocol for accessing data referred to by file
354 public boolean parseFeaturesFile(String file, DataSourceType type)
356 return parseFeaturesFile(file, type, true);
360 * Load a features file onto the alignment
363 * file URL, content, or other resolvable path
365 * is protocol for accessing data referred to by file
366 * @param autoenabledisplay
367 * when true, display features flag will be automatically enabled if
368 * features are loaded
369 * @return true if data parsed as a features file
371 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
372 boolean autoenabledisplay)
374 boolean featuresFile = false;
377 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
378 .getFeatureRenderer().getFeatureColours();
379 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
380 "relaxedidmatch", false);
381 featuresFile = new FeaturesFile(file, sourceType).parse(
382 viewport.getAlignment(), colours, true, relaxedIdMatching);
383 } catch (Exception ex)
385 ex.printStackTrace();
390 if (autoenabledisplay)
392 viewport.setShowSequenceFeatures(true);
393 sequenceFeatures.setState(true);
395 if (alignPanel.seqPanel.seqCanvas.fr != null)
397 // update the min/max ranges where necessary
398 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
400 if (viewport.featureSettings != null)
402 viewport.featureSettings.refreshTable();
404 alignPanel.paintAlignment(true);
405 statusBar.setText(MessageManager
406 .getString("label.successfully_added_features_alignment"));
412 public void keyPressed(KeyEvent evt)
414 if (viewport.cursorMode
415 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
416 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
417 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
418 && Character.isDigit(evt.getKeyChar()))
420 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
423 switch (evt.getKeyCode())
425 case 27: // escape key
426 deselectAllSequenceMenuItem_actionPerformed();
428 alignPanel.alabels.cancelDrag();
431 if (evt.isControlDown() || evt.isMetaDown())
433 cut_actionPerformed();
437 if (viewport.cursorMode && !evt.isControlDown())
439 alignPanel.seqPanel.setCursorColumn();
441 if (evt.isControlDown() || evt.isMetaDown())
443 copy_actionPerformed();
447 if (evt.isControlDown())
449 paste(evt.isShiftDown());
453 if (evt.isControlDown() || evt.isMetaDown())
455 selectAllSequenceMenuItem_actionPerformed();
458 case KeyEvent.VK_DOWN:
459 if (viewport.cursorMode)
461 alignPanel.seqPanel.moveCursor(0, 1);
465 moveSelectedSequences(false);
470 if (viewport.cursorMode)
472 alignPanel.seqPanel.moveCursor(0, -1);
476 moveSelectedSequences(true);
480 case KeyEvent.VK_LEFT:
481 if (evt.isAltDown() || !viewport.cursorMode)
483 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
487 alignPanel.seqPanel.moveCursor(-1, 0);
491 case KeyEvent.VK_RIGHT:
492 if (evt.isAltDown() || !viewport.cursorMode)
494 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
498 alignPanel.seqPanel.moveCursor(1, 0);
502 case KeyEvent.VK_SPACE:
503 if (viewport.cursorMode)
505 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
506 || evt.isShiftDown() || evt.isAltDown());
510 case KeyEvent.VK_DELETE:
511 case KeyEvent.VK_BACK_SPACE:
512 if (viewport.cursorMode)
514 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
515 || evt.isShiftDown() || evt.isAltDown());
519 cut_actionPerformed();
520 alignPanel.seqPanel.seqCanvas.repaint();
525 if (viewport.cursorMode)
527 alignPanel.seqPanel.setCursorRow();
531 if (viewport.cursorMode)
533 alignPanel.seqPanel.setCursorPosition();
537 case KeyEvent.VK_ENTER:
538 case KeyEvent.VK_COMMA:
539 if (viewport.cursorMode)
541 alignPanel.seqPanel.setCursorRowAndColumn();
546 if (viewport.cursorMode)
548 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
552 if (viewport.cursorMode)
554 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
559 viewport.cursorMode = !viewport.cursorMode;
560 statusBar.setText(MessageManager.formatMessage(
561 "label.keyboard_editing_mode",
562 new String[] { (viewport.cursorMode ? "on" : "off") }));
563 if (viewport.cursorMode)
565 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
566 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
571 if (evt.isControlDown())
573 findMenuItem_actionPerformed();
579 boolean toggleSeqs = !evt.isControlDown();
580 boolean toggleCols = !evt.isShiftDown();
581 toggleHiddenRegions(toggleSeqs, toggleCols);
585 case KeyEvent.VK_PAGE_UP:
586 if (viewport.getWrapAlignment())
588 alignPanel.scrollUp(true);
592 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
593 - viewport.endSeq + viewport.startSeq);
597 case KeyEvent.VK_PAGE_DOWN:
598 if (viewport.getWrapAlignment())
600 alignPanel.scrollUp(false);
604 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
605 + viewport.endSeq - viewport.startSeq);
610 if (evt.isControlDown())
612 undoMenuItem_actionPerformed();
617 if (evt.isControlDown())
619 redoMenuItem_actionPerformed();
624 if (evt.isControlDown())
631 if (evt.isControlDown())
633 trimAlignment(false);
638 if (evt.isControlDown())
640 if (evt.isShiftDown())
642 this.removeAllGapsMenuItem_actionPerformed();
646 removeGappedColumnMenuItem_actionPerformed();
651 if (evt.isControlDown())
655 invertColSel_actionPerformed();
659 invertSequenceMenuItem_actionPerformed();
665 if (evt.isControlDown())
667 if (evt.isShiftDown())
669 this.unGroup_actionPerformed();
673 this.createGroup_actionPerformed();
679 if (evt.isControlDown())
681 this.deleteGroups_actionPerformed();
686 if (evt.isControlDown())
693 alignPanel.paintAlignment(true);
697 * called by key handler and the hide all/show all menu items
702 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
704 boolean hide = false;
705 SequenceGroup sg = viewport.getSelectionGroup();
706 if (!toggleSeqs && !toggleCols)
708 // Hide everything by the current selection - this is a hack - we do the
709 // invert and then hide
710 // first check that there will be visible columns after the invert.
711 if (viewport.hasSelectedColumns()
712 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
715 // now invert the sequence set, if required - empty selection implies
716 // that no hiding is required.
719 invertSequenceMenuItem_actionPerformed();
720 sg = viewport.getSelectionGroup();
724 viewport.expandColSelection(sg, true);
725 // finally invert the column selection and get the new sequence
726 // selection and indicate it should be hidden.
727 invertColSel_actionPerformed();
734 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
737 viewport.hideAllSelectedSeqs();
739 else if (!(toggleCols && viewport.hasSelectedColumns()))
741 viewport.showAllHiddenSeqs();
747 if (viewport.hasSelectedColumns())
749 viewport.hideSelectedColumns();
752 viewport.setSelectionGroup(sg);
757 viewport.showAllHiddenColumns();
759 viewport.sendSelection();
764 public void keyReleased(KeyEvent evt)
769 public void keyTyped(KeyEvent evt)
774 public void itemStateChanged(ItemEvent evt)
776 final Object source = evt.getSource();
777 if (source == displayNonconservedMenuItem)
779 displayNonconservedMenuItem_actionPerformed();
781 else if (source == colourTextMenuItem)
783 colourTextMenuItem_actionPerformed();
785 else if (source == wrapMenuItem)
787 wrapMenuItem_actionPerformed();
789 else if (source == scaleAbove)
791 viewport.setScaleAboveWrapped(scaleAbove.getState());
793 else if (source == scaleLeft)
795 viewport.setScaleLeftWrapped(scaleLeft.getState());
797 else if (source == scaleRight)
799 viewport.setScaleRightWrapped(scaleRight.getState());
801 else if (source == seqLimits)
803 seqLimits_itemStateChanged();
805 else if (source == viewBoxesMenuItem)
807 viewport.setShowBoxes(viewBoxesMenuItem.getState());
809 else if (source == viewTextMenuItem)
811 viewport.setShowText(viewTextMenuItem.getState());
813 else if (source == renderGapsMenuItem)
815 viewport.setRenderGaps(renderGapsMenuItem.getState());
817 else if (source == annotationPanelMenuItem)
819 boolean showAnnotations = annotationPanelMenuItem.getState();
820 showAlignmentAnnotations.setEnabled(showAnnotations);
821 showSequenceAnnotations.setEnabled(showAnnotations);
822 viewport.setShowAnnotation(showAnnotations);
823 alignPanel.setAnnotationVisible(showAnnotations);
825 else if (source == sequenceFeatures)
827 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
828 alignPanel.seqPanel.seqCanvas.repaint();
830 else if (source == showAlignmentAnnotations)
832 setAnnotationsVisibility();
834 else if (source == showSequenceAnnotations)
836 setAnnotationsVisibility();
838 else if (source == sortAnnBySequence)
840 boolean newState = sortAnnBySequence.getState();
841 sortAnnByLabel.setState(false);
842 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
843 : SequenceAnnotationOrder.NONE);
844 setViewportAnnotationOrder();
846 else if (source == sortAnnByLabel)
848 boolean newState = sortAnnByLabel.getState();
849 sortAnnBySequence.setState(false);
850 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
851 : SequenceAnnotationOrder.NONE);
852 setViewportAnnotationOrder();
854 else if (source == showAutoFirst)
856 showAutoLast.setState(!showAutoFirst.getState());
857 setShowAutoCalculatedAbove(showAutoFirst.getState());
858 setViewportAnnotationOrder();
860 else if (source == showAutoLast)
862 showAutoFirst.setState(!showAutoLast.getState());
863 setShowAutoCalculatedAbove(showAutoFirst.getState());
864 setViewportAnnotationOrder();
866 else if (source == conservationMenuItem)
868 conservationMenuItem_actionPerformed();
870 else if (source == abovePIDThreshold)
872 abovePIDThreshold_actionPerformed();
874 else if (source == applyToAllGroups)
876 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
878 else if (source == autoCalculate)
880 viewport.autoCalculateConsensus = autoCalculate.getState();
882 else if (source == sortByTree)
884 viewport.sortByTree = sortByTree.getState();
886 else if (source == this.centreColumnLabelFlag)
888 centreColumnLabelFlag_stateChanged();
890 else if (source == this.followMouseOverFlag)
892 mouseOverFlag_stateChanged();
894 else if (source == showGroupConsensus)
896 showGroupConsensus_actionPerformed();
898 else if (source == showGroupConservation)
900 showGroupConservation_actionPerformed();
902 else if (source == showSequenceLogo)
904 showSequenceLogo_actionPerformed();
906 else if (source == normSequenceLogo)
908 normSequenceLogo_actionPerformed();
910 else if (source == showConsensusHistogram)
912 showConsensusHistogram_actionPerformed();
914 else if (source == applyAutoAnnotationSettings)
916 applyAutoAnnotationSettings_actionPerformed();
918 alignPanel.paintAlignment(true);
922 * Set the visibility state of sequence-related and/or alignment-related
923 * annotations depending on checkbox selections, and repaint.
927 private void setAnnotationsVisibility()
929 boolean showForAlignment = showAlignmentAnnotations.getState();
930 boolean showForSequences = showSequenceAnnotations.getState();
931 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
933 for (AlignmentAnnotation aa : alignPanel.getAlignment()
934 .getAlignmentAnnotation())
936 boolean visible = (aa.sequenceRef == null ? showForAlignment
938 aa.visible = visible;
941 alignPanel.validateAnnotationDimensions(true);
946 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
948 this.annotationSortOrder = order;
952 * Set flags on the viewport that control annotation ordering
954 private void setViewportAnnotationOrder()
956 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
958 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
961 private void setShowAutoCalculatedAbove(boolean showAbove)
963 this.showAutoCalculatedAbove = showAbove;
966 private void mouseOverFlag_stateChanged()
968 viewport.setFollowHighlight(followMouseOverFlag.getState());
969 // TODO: could kick the scrollTo mechanism to reset view for current
973 private void centreColumnLabelFlag_stateChanged()
975 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
976 this.alignPanel.annotationPanel.repaint();
980 public void actionPerformed(ActionEvent evt)
982 viewport.applet.currentAlignFrame = this;
984 Object source = evt.getSource();
986 if (source == inputText)
988 inputText_actionPerformed();
990 else if (source == loadTree)
992 loadTree_actionPerformed();
994 else if (source == loadApplication)
996 launchFullApplication();
998 else if (source == loadAnnotations)
1002 else if (source == outputAnnotations)
1004 outputAnnotations(true);
1006 else if (source == outputFeatures)
1008 outputFeatures(true, "Jalview");
1010 else if (source == closeMenuItem)
1012 closeMenuItem_actionPerformed();
1014 else if (source == copy)
1016 copy_actionPerformed();
1018 else if (source == undoMenuItem)
1020 undoMenuItem_actionPerformed();
1022 else if (source == redoMenuItem)
1024 redoMenuItem_actionPerformed();
1026 else if (source == inputText)
1028 inputText_actionPerformed();
1030 else if (source == closeMenuItem)
1032 closeMenuItem_actionPerformed();
1034 else if (source == undoMenuItem)
1036 undoMenuItem_actionPerformed();
1038 else if (source == redoMenuItem)
1040 redoMenuItem_actionPerformed();
1042 else if (source == copy)
1044 copy_actionPerformed();
1046 else if (source == pasteNew)
1048 pasteNew_actionPerformed();
1050 else if (source == pasteThis)
1052 pasteThis_actionPerformed();
1054 else if (source == cut)
1056 cut_actionPerformed();
1058 else if (source == delete)
1060 delete_actionPerformed();
1062 else if (source == grpsFromSelection)
1064 makeGrpsFromSelection_actionPerformed();
1066 else if (source == deleteGroups)
1068 deleteGroups_actionPerformed();
1070 else if (source == selectAllSequenceMenuItem)
1072 selectAllSequenceMenuItem_actionPerformed();
1074 else if (source == deselectAllSequenceMenuItem)
1076 deselectAllSequenceMenuItem_actionPerformed();
1078 else if (source == invertSequenceMenuItem)
1080 invertSequenceMenuItem_actionPerformed();
1081 // uncomment to slave sequence selections in split frame
1082 // viewport.sendSelection();
1084 else if (source == invertColSel)
1086 viewport.invertColumnSelection();
1087 alignPanel.paintAlignment(true);
1088 viewport.sendSelection();
1090 else if (source == remove2LeftMenuItem)
1092 trimAlignment(true);
1094 else if (source == remove2RightMenuItem)
1096 trimAlignment(false);
1098 else if (source == removeGappedColumnMenuItem)
1100 removeGappedColumnMenuItem_actionPerformed();
1102 else if (source == removeAllGapsMenuItem)
1104 removeAllGapsMenuItem_actionPerformed();
1106 else if (source == findMenuItem)
1108 findMenuItem_actionPerformed();
1110 else if (source == font)
1112 new FontChooser(alignPanel);
1114 else if (source == newView)
1118 else if (source == showColumns)
1120 viewport.showAllHiddenColumns();
1121 alignPanel.paintAlignment(true);
1122 viewport.sendSelection();
1124 else if (source == showSeqs)
1126 viewport.showAllHiddenSeqs();
1127 alignPanel.paintAlignment(true);
1128 // uncomment if we want to slave sequence selections in split frame
1129 // viewport.sendSelection();
1131 else if (source == hideColumns)
1133 viewport.hideSelectedColumns();
1134 alignPanel.paintAlignment(true);
1135 viewport.sendSelection();
1137 else if (source == hideSequences
1138 && viewport.getSelectionGroup() != null)
1140 viewport.hideAllSelectedSeqs();
1141 alignPanel.paintAlignment(true);
1142 // uncomment if we want to slave sequence selections in split frame
1143 // viewport.sendSelection();
1145 else if (source == hideAllButSelection)
1147 toggleHiddenRegions(false, false);
1148 alignPanel.paintAlignment(true);
1149 viewport.sendSelection();
1151 else if (source == hideAllSelection)
1153 SequenceGroup sg = viewport.getSelectionGroup();
1154 viewport.expandColSelection(sg, false);
1155 viewport.hideAllSelectedSeqs();
1156 viewport.hideSelectedColumns();
1157 alignPanel.paintAlignment(true);
1158 viewport.sendSelection();
1160 else if (source == showAllHidden)
1162 viewport.showAllHiddenColumns();
1163 viewport.showAllHiddenSeqs();
1164 alignPanel.paintAlignment(true);
1165 viewport.sendSelection();
1167 else if (source == showGroupConsensus)
1169 showGroupConsensus_actionPerformed();
1171 else if (source == showGroupConservation)
1173 showGroupConservation_actionPerformed();
1175 else if (source == showSequenceLogo)
1177 showSequenceLogo_actionPerformed();
1179 else if (source == normSequenceLogo)
1181 normSequenceLogo_actionPerformed();
1183 else if (source == showConsensusHistogram)
1185 showConsensusHistogram_actionPerformed();
1187 else if (source == applyAutoAnnotationSettings)
1189 applyAutoAnnotationSettings_actionPerformed();
1191 else if (source == featureSettings)
1193 new FeatureSettings(alignPanel);
1195 else if (source == alProperties)
1197 StringBuffer contents = new jalview.io.AlignmentProperties(
1198 viewport.getAlignment()).formatAsString();
1199 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1200 cap.setText(contents.toString());
1201 Frame frame = new Frame();
1203 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1204 "label.alignment_properties", new String[] { getTitle() }),
1207 else if (source == overviewMenuItem)
1209 overviewMenuItem_actionPerformed();
1211 else if (source == noColourmenuItem)
1215 else if (source == clustalColour)
1217 abovePIDThreshold.setState(false);
1218 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1220 else if (source == zappoColour)
1222 changeColour(new ZappoColourScheme());
1224 else if (source == taylorColour)
1226 changeColour(new TaylorColourScheme());
1228 else if (source == hydrophobicityColour)
1230 changeColour(new HydrophobicColourScheme());
1232 else if (source == helixColour)
1234 changeColour(new HelixColourScheme());
1236 else if (source == strandColour)
1238 changeColour(new StrandColourScheme());
1240 else if (source == turnColour)
1242 changeColour(new TurnColourScheme());
1244 else if (source == buriedColour)
1246 changeColour(new BuriedColourScheme());
1248 else if (source == nucleotideColour)
1250 changeColour(new NucleotideColourScheme());
1252 else if (source == purinePyrimidineColour)
1254 changeColour(new PurinePyrimidineColourScheme());
1256 // else if (source == RNAInteractionColour)
1258 // changeColour(new RNAInteractionColourScheme());
1260 else if (source == RNAHelixColour)
1262 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1263 // new RNAHelicesColourChooser(viewport, alignPanel);
1265 else if (source == modifyPID)
1267 modifyPID_actionPerformed();
1269 else if (source == modifyConservation)
1271 modifyConservation_actionPerformed();
1273 else if (source == userDefinedColour)
1275 new UserDefinedColours(alignPanel, null);
1277 else if (source == PIDColour)
1279 changeColour(new PIDColourScheme());
1281 else if (source == BLOSUM62Colour)
1283 changeColour(new Blosum62ColourScheme());
1285 else if (source == tcoffeeColour)
1287 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1289 else if (source == annotationColour)
1291 new AnnotationColourChooser(viewport, alignPanel);
1293 else if (source == annotationColumnSelection)
1295 new AnnotationColumnChooser(viewport, alignPanel);
1297 else if (source == sortPairwiseMenuItem)
1299 sortPairwiseMenuItem_actionPerformed();
1301 else if (source == sortIDMenuItem)
1303 sortIDMenuItem_actionPerformed();
1305 else if (source == sortLengthMenuItem)
1307 sortLengthMenuItem_actionPerformed();
1309 else if (source == sortGroupMenuItem)
1311 sortGroupMenuItem_actionPerformed();
1313 else if (source == removeRedundancyMenuItem)
1315 removeRedundancyMenuItem_actionPerformed();
1317 else if (source == pairwiseAlignmentMenuItem)
1319 pairwiseAlignmentMenuItem_actionPerformed();
1321 else if (source == PCAMenuItem)
1323 PCAMenuItem_actionPerformed();
1325 else if (source == averageDistanceTreeMenuItem)
1327 averageDistanceTreeMenuItem_actionPerformed();
1329 else if (source == neighbourTreeMenuItem)
1331 neighbourTreeMenuItem_actionPerformed();
1333 else if (source == njTreeBlosumMenuItem)
1335 njTreeBlosumMenuItem_actionPerformed();
1337 else if (source == avDistanceTreeBlosumMenuItem)
1339 avTreeBlosumMenuItem_actionPerformed();
1341 else if (source == documentation)
1343 documentation_actionPerformed();
1345 else if (source == about)
1347 about_actionPerformed();
1352 public void inputText_actionPerformed()
1354 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1355 Frame frame = new Frame();
1357 jalview.bin.JalviewLite.addFrame(frame,
1358 MessageManager.getString("label.input_cut_paste"), 500, 500);
1361 protected void outputText_actionPerformed(ActionEvent e)
1363 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1364 Frame frame = new Frame();
1366 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1367 "label.alignment_output_command",
1368 new Object[] { e.getActionCommand() }), 600, 500);
1370 FileFormatI fileFormat = FileFormats.getInstance().forName(
1371 e.getActionCommand());
1372 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1373 fileFormat, viewport.getAlignment(),
1374 viewport.getShowJVSuffix()));
1377 public void loadAnnotations()
1379 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1380 cap.setText(MessageManager
1381 .getString("label.paste_features_annotations_Tcoffee_here"));
1382 cap.setAnnotationImport();
1383 Frame frame = new Frame();
1385 jalview.bin.JalviewLite.addFrame(frame,
1386 MessageManager.getString("action.paste_annotations"), 400, 300);
1390 public String outputAnnotations(boolean displayTextbox)
1392 String annotation = new AnnotationFile()
1393 .printAnnotationsForView(viewport);
1397 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1398 Frame frame = new Frame();
1400 jalview.bin.JalviewLite.addFrame(frame,
1401 MessageManager.getString("label.annotations"), 600, 500);
1402 cap.setText(annotation);
1408 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1410 if (alignPanel.getFeatureRenderer() != null
1411 && viewport.getFeaturesDisplayed() != null)
1413 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1419 public String outputFeatures(boolean displayTextbox, String format)
1422 FeaturesFile formatter = new FeaturesFile();
1423 if (format.equalsIgnoreCase("Jalview"))
1425 features = formatter.printJalviewFormat(viewport.getAlignment()
1426 .getSequencesArray(), getDisplayedFeatureCols());
1430 features = formatter.printGffFormat(viewport.getAlignment()
1431 .getSequencesArray(), getDisplayedFeatureCols());
1436 boolean frimport = false;
1437 if (features == null || features.equals("No Features Visible"))
1439 features = "# No features visible - paste some and import them here.";
1443 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1446 cap.setAnnotationImport();
1448 Frame frame = new Frame();
1450 jalview.bin.JalviewLite.addFrame(frame,
1451 MessageManager.getString("label.features"), 600, 500);
1452 cap.setText(features);
1456 if (features == null)
1465 void launchFullApplication()
1467 StringBuffer url = new StringBuffer(jalviewServletURL);
1469 // allow servlet parameters to be passed in applet parameter
1470 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1472 url.append(firstSep);
1475 + appendProtocol(viewport.applet.getParameter("file")));
1477 if (viewport.applet.getParameter("features") != null)
1479 url.append("&features=");
1480 url.append(appendProtocol(viewport.applet.getParameter("features")));
1483 if (viewport.applet.getParameter("annotations") != null)
1485 url.append("&annotations=");
1486 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1489 if (viewport.applet.getParameter("jnetfile") != null
1490 || viewport.applet.getParameter("jpredfile") != null)
1492 url.append("&annotations=");
1493 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1494 .getParameter("jnetfile") : viewport.applet
1495 .getParameter("jpredfile")));
1498 if (viewport.applet.getParameter("defaultColour") != null)
1500 url.append("&colour="
1501 + removeWhiteSpace(viewport.applet
1502 .getParameter("defaultColour")));
1505 if (viewport.applet.getParameter("userDefinedColour") != null)
1507 url.append("&colour="
1508 + removeWhiteSpace(viewport.applet
1509 .getParameter("userDefinedColour")));
1511 if (viewport.applet.getParameter("tree") != null)
1514 + appendProtocol(viewport.applet.getParameter("tree")));
1516 if (viewport.applet.getParameter("treeFile") != null)
1519 + appendProtocol(viewport.applet.getParameter("treeFile")));
1522 showURL(url.toString(), "FULL_APP");
1525 String removeWhiteSpace(String colour)
1527 StringBuffer sb = new StringBuffer();
1528 for (int i = 0; i < colour.length(); i++)
1530 if (Character.isWhitespace(colour.charAt(i)))
1536 sb.append(colour.charAt(i));
1540 return sb.toString();
1543 String appendProtocol(String url)
1548 url = URLEncoder.encode(url);
1551 * When we finally deprecate 1.1 compatibility, we can start to use
1552 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1553 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1554 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1555 * ex.printStackTrace(); }
1557 catch (java.net.MalformedURLException ex)
1559 url = viewport.applet.getCodeBase() + url;
1564 public void closeMenuItem_actionPerformed()
1566 PaintRefresher.RemoveComponent(alignPanel);
1567 if (alignPanel.seqPanel != null
1568 && alignPanel.seqPanel.seqCanvas != null)
1570 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1572 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1574 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1577 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1592 void updateEditMenuBar()
1595 if (viewport.getHistoryList().size() > 0)
1597 undoMenuItem.setEnabled(true);
1598 CommandI command = viewport.getHistoryList().peek();
1599 undoMenuItem.setLabel(MessageManager.formatMessage(
1600 "label.undo_command",
1601 new Object[] { command.getDescription() }));
1605 undoMenuItem.setEnabled(false);
1606 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1609 if (viewport.getRedoList().size() > 0)
1611 redoMenuItem.setEnabled(true);
1613 CommandI command = viewport.getRedoList().peek();
1614 redoMenuItem.setLabel(MessageManager.formatMessage(
1615 "label.redo_command",
1616 new Object[] { command.getDescription() }));
1620 redoMenuItem.setEnabled(false);
1621 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1629 public void addHistoryItem(CommandI command)
1631 if (command.getSize() > 0)
1633 viewport.addToHistoryList(command);
1634 viewport.clearRedoList();
1635 updateEditMenuBar();
1636 viewport.updateHiddenColumns();
1641 * TODO: JAL-1104 DOCUMENT ME!
1646 protected void undoMenuItem_actionPerformed()
1648 if (viewport.getHistoryList().isEmpty())
1653 CommandI command = viewport.getHistoryList().pop();
1654 viewport.addToRedoList(command);
1655 command.undoCommand(null);
1657 AlignmentViewport originalSource = getOriginatingSource(command);
1659 if (originalSource != viewport)
1662 .println("Warning: Viewport object mismatch whilst undoing");
1664 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1665 // viewport.getColumnSelection().getHiddenColumns()
1667 updateEditMenuBar();
1668 originalSource.firePropertyChange("alignment", null, originalSource
1669 .getAlignment().getSequences());
1673 * TODO: JAL-1104 DOCUMENT ME!
1678 protected void redoMenuItem_actionPerformed()
1680 if (viewport.getRedoList().isEmpty())
1685 CommandI command = viewport.getRedoList().pop();
1686 viewport.addToHistoryList(command);
1687 command.doCommand(null);
1689 AlignmentViewport originalSource = getOriginatingSource(command);
1691 if (originalSource != viewport)
1694 .println("Warning: Viewport object mismatch whilst re-doing");
1696 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1697 // viewport.getColumnSelection().getHiddenColumns()
1700 updateEditMenuBar();
1701 originalSource.firePropertyChange("alignment", null, originalSource
1702 .getAlignment().getSequences());
1705 AlignmentViewport getOriginatingSource(CommandI command)
1707 AlignmentViewport originalSource = null;
1708 // For sequence removal and addition, we need to fire
1709 // the property change event FROM the viewport where the
1710 // original alignment was altered
1711 AlignmentI al = null;
1712 if (command instanceof EditCommand)
1714 EditCommand editCommand = (EditCommand) command;
1715 al = editCommand.getAlignment();
1716 Vector comps = (Vector) PaintRefresher.components.get(viewport
1717 .getSequenceSetId());
1718 for (int i = 0; i < comps.size(); i++)
1720 if (comps.elementAt(i) instanceof AlignmentPanel)
1722 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1724 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1731 if (originalSource == null)
1733 // The original view is closed, we must validate
1734 // the current view against the closed view first
1737 PaintRefresher.validateSequences(al, viewport.getAlignment());
1740 originalSource = viewport;
1743 return originalSource;
1747 * Move the currently selected sequences up or down one position in the
1752 public void moveSelectedSequences(boolean up)
1754 SequenceGroup sg = viewport.getSelectionGroup();
1759 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1760 up ? null : viewport.getHiddenRepSequences(), up);
1761 alignPanel.paintAlignment(true);
1764 * Also move cDNA/protein complement sequences
1766 AlignViewportI complement = viewport.getCodingComplement();
1767 if (complement != null)
1769 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1770 viewport, complement);
1771 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1772 up ? null : complement.getHiddenRepSequences(), up);
1773 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1777 synchronized void slideSequences(boolean right, int size)
1779 List<SequenceI> sg = new Vector<SequenceI>();
1780 if (viewport.cursorMode)
1782 sg.add(viewport.getAlignment().getSequenceAt(
1783 alignPanel.seqPanel.seqCanvas.cursorY));
1785 else if (viewport.getSelectionGroup() != null
1786 && viewport.getSelectionGroup().getSize() != viewport
1787 .getAlignment().getHeight())
1789 sg = viewport.getSelectionGroup().getSequences(
1790 viewport.getHiddenRepSequences());
1798 Vector<SequenceI> invertGroup = new Vector();
1800 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1802 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1804 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1808 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1810 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1812 for (int i = 0; i < invertGroup.size(); i++)
1814 seqs2[i] = invertGroup.elementAt(i);
1817 SlideSequencesCommand ssc;
1820 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1821 size, viewport.getGapCharacter());
1825 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1826 size, viewport.getGapCharacter());
1829 int groupAdjustment = 0;
1830 if (ssc.getGapsInsertedBegin() && right)
1832 if (viewport.cursorMode)
1834 alignPanel.seqPanel.moveCursor(size, 0);
1838 groupAdjustment = size;
1841 else if (!ssc.getGapsInsertedBegin() && !right)
1843 if (viewport.cursorMode)
1845 alignPanel.seqPanel.moveCursor(-size, 0);
1849 groupAdjustment = -size;
1853 if (groupAdjustment != 0)
1855 viewport.getSelectionGroup().setStartRes(
1856 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1857 viewport.getSelectionGroup().setEndRes(
1858 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1861 boolean appendHistoryItem = false;
1862 Deque<CommandI> historyList = viewport.getHistoryList();
1863 if (historyList != null && historyList.size() > 0
1864 && historyList.peek() instanceof SlideSequencesCommand)
1866 appendHistoryItem = ssc
1867 .appendSlideCommand((SlideSequencesCommand) historyList
1871 if (!appendHistoryItem)
1873 addHistoryItem(ssc);
1879 static StringBuffer copiedSequences;
1881 static Vector copiedHiddenColumns;
1883 protected void copy_actionPerformed()
1885 if (viewport.getSelectionGroup() == null)
1890 SequenceGroup sg = viewport.getSelectionGroup();
1891 copiedSequences = new StringBuffer();
1892 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1893 for (int i = 0; i < sg.getSize(); i++)
1895 SequenceI seq = sg.getSequenceAt(i);
1896 int index = viewport.getAlignment().findIndex(seq);
1897 orderedSeqs.put(index, seq);
1900 int index = 0, startRes, endRes;
1903 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1905 copiedHiddenColumns = new Vector();
1906 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1907 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1909 copiedHiddenColumns.addElement(new int[] {
1910 region[0] - hiddenOffset, region[1] - hiddenOffset });
1915 copiedHiddenColumns = null;
1918 for (int i = 0; i < sg.getSize(); i++)
1920 SequenceI seq = null;
1924 if (orderedSeqs.containsKey(index))
1926 seq = orderedSeqs.get(index);
1937 // Returns residue following index if gap
1938 startRes = seq.findPosition(sg.getStartRes());
1941 // Need to find the residue preceeding index if gap
1944 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1946 ch = seq.getCharAt(j);
1947 if (!jalview.util.Comparison.isGap((ch)))
1955 endRes += seq.getStart() - 1;
1958 copiedSequences.append(seq.getName()
1964 + seq.getSequenceAsString(sg.getStartRes(),
1965 sg.getEndRes() + 1) + "\n");
1970 protected void pasteNew_actionPerformed()
1975 protected void pasteThis_actionPerformed()
1980 void paste(boolean newAlignment)
1985 if (copiedSequences == null)
1990 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1991 Vector seqs = new Vector();
1992 while (st.hasMoreElements())
1994 String name = st.nextToken();
1995 int start = Integer.parseInt(st.nextToken());
1996 int end = Integer.parseInt(st.nextToken());
1997 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1999 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2000 for (int i = 0; i < seqs.size(); i++)
2002 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2007 String newtitle = MessageManager
2008 .getString("label.copied_sequences");
2009 if (getTitle().startsWith(
2010 MessageManager.getString("label.copied_sequences")))
2012 newtitle = getTitle();
2016 newtitle = newtitle.concat(MessageManager.formatMessage(
2017 "label.from_msname", new String[] { getTitle() }));
2019 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2020 viewport.applet, newtitle, false);
2021 if (copiedHiddenColumns != null)
2023 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2025 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2026 af.viewport.hideColumns(region[0], region[1]);
2030 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2035 addSequences(newSeqs);
2038 } catch (Exception ex)
2040 } // could be anything being pasted in here
2044 void addSequences(SequenceI[] seqs)
2046 for (int i = 0; i < seqs.length; i++)
2048 viewport.getAlignment().addSequence(seqs[i]);
2052 addHistoryItem(new EditCommand(
2053 MessageManager.getString("label.add_sequences"), Action.PASTE,
2054 seqs, 0, viewport.getAlignment().getWidth(),
2055 viewport.getAlignment()));
2057 viewport.setEndSeq(viewport.getAlignment().getHeight());
2058 viewport.getAlignment().getWidth();
2059 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2064 protected void cut_actionPerformed()
2066 copy_actionPerformed();
2067 delete_actionPerformed();
2070 protected void delete_actionPerformed()
2073 SequenceGroup sg = viewport.getSelectionGroup();
2079 Vector seqs = new Vector();
2081 for (int i = 0; i < sg.getSize(); i++)
2083 seq = sg.getSequenceAt(i);
2084 seqs.addElement(seq);
2088 * If the cut affects all sequences, warn, remove highlighted columns
2090 if (sg.getSize() == viewport.getAlignment().getHeight())
2092 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2093 .getAlignment().getWidth()) ? true : false;
2094 if (isEntireAlignWidth)
2096 String title = MessageManager.getString("label.delete_all");
2097 Panel infoPanel = new Panel();
2098 infoPanel.setLayout(new FlowLayout());
2100 .add(new Label(MessageManager.getString("warn.delete_all")));
2102 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2103 dialog.setMainPanel(infoPanel);
2104 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2105 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2106 dialog.setVisible(true);
2113 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2114 sg.getEndRes() + 1);
2117 SequenceI[] cut = new SequenceI[seqs.size()];
2118 for (int i = 0; i < seqs.size(); i++)
2120 cut[i] = (SequenceI) seqs.elementAt(i);
2124 * //ADD HISTORY ITEM
2126 addHistoryItem(new EditCommand(
2127 MessageManager.getString("label.cut_sequences"), Action.CUT,
2128 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2129 viewport.getAlignment()));
2131 viewport.setSelectionGroup(null);
2132 viewport.getAlignment().deleteGroup(sg);
2134 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2137 if (viewport.getAlignment().getHeight() < 1)
2139 this.setVisible(false);
2141 viewport.sendSelection();
2145 * group consensus toggled
2148 protected void showGroupConsensus_actionPerformed()
2150 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2151 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2156 * group conservation toggled.
2158 protected void showGroupConservation_actionPerformed()
2160 viewport.setShowGroupConservation(showGroupConservation.getState());
2161 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2168 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2169 * .event.ActionEvent)
2171 protected void showConsensusHistogram_actionPerformed()
2173 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2174 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2182 * .event.ActionEvent)
2184 protected void showSequenceLogo_actionPerformed()
2186 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2187 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190 protected void normSequenceLogo_actionPerformed()
2192 showSequenceLogo.setState(true);
2193 viewport.setShowSequenceLogo(true);
2194 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2195 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2198 protected void applyAutoAnnotationSettings_actionPerformed()
2200 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2203 protected void makeGrpsFromSelection_actionPerformed()
2205 if (avc.makeGroupsFromSelection())
2207 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2208 alignPanel.updateAnnotation();
2209 alignPanel.paintAlignment(true);
2213 protected void createGroup_actionPerformed()
2218 protected void unGroup_actionPerformed()
2222 alignPanel.alignmentChanged();
2226 protected void deleteGroups_actionPerformed()
2228 if (avc.deleteGroups())
2230 alignPanel.alignmentChanged();
2234 public void selectAllSequenceMenuItem_actionPerformed()
2236 SequenceGroup sg = new SequenceGroup();
2237 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2239 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2241 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2242 viewport.setSelectionGroup(sg);
2243 // JAL-2034 - should delegate to
2244 // alignPanel to decide if overview needs
2246 alignPanel.paintAlignment(false);
2247 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2248 viewport.sendSelection();
2251 public void deselectAllSequenceMenuItem_actionPerformed()
2253 if (viewport.cursorMode)
2255 alignPanel.seqPanel.keyboardNo1 = null;
2256 alignPanel.seqPanel.keyboardNo2 = null;
2258 viewport.setSelectionGroup(null);
2259 viewport.getColumnSelection().clear();
2260 viewport.setSelectionGroup(null);
2261 alignPanel.idPanel.idCanvas.searchResults = null;
2262 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2263 // JAL-2034 - should delegate to
2264 // alignPanel to decide if overview needs
2266 alignPanel.paintAlignment(false);
2267 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2268 viewport.sendSelection();
2271 public void invertSequenceMenuItem_actionPerformed()
2273 SequenceGroup sg = viewport.getSelectionGroup();
2274 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2276 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2279 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2280 viewport.sendSelection();
2283 public void invertColSel_actionPerformed()
2285 viewport.invertColumnSelection();
2286 alignPanel.paintAlignment(true);
2287 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2288 viewport.sendSelection();
2291 void trimAlignment(boolean trimLeft)
2293 ColumnSelection colSel = viewport.getColumnSelection();
2296 if (!colSel.isEmpty())
2300 column = colSel.getMin();
2304 column = colSel.getMax();
2308 if (viewport.getSelectionGroup() != null)
2310 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2311 viewport.getHiddenRepSequences());
2315 seqs = viewport.getAlignment().getSequencesArray();
2318 TrimRegionCommand trimRegion;
2321 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2322 column, viewport.getAlignment());
2323 viewport.setStartRes(0);
2327 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2328 column, viewport.getAlignment());
2331 statusBar.setText(MessageManager.formatMessage(
2332 "label.removed_columns",
2333 new String[] { Integer.valueOf(trimRegion.getSize())
2335 addHistoryItem(trimRegion);
2337 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2339 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2340 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2342 viewport.getAlignment().deleteGroup(sg);
2346 viewport.firePropertyChange("alignment", null, viewport
2347 .getAlignment().getSequences());
2351 public void removeGappedColumnMenuItem_actionPerformed()
2353 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2356 if (viewport.getSelectionGroup() != null)
2358 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2359 viewport.getHiddenRepSequences());
2360 start = viewport.getSelectionGroup().getStartRes();
2361 end = viewport.getSelectionGroup().getEndRes();
2365 seqs = viewport.getAlignment().getSequencesArray();
2368 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2369 "Remove Gapped Columns", seqs, start, end,
2370 viewport.getAlignment());
2372 addHistoryItem(removeGapCols);
2374 statusBar.setText(MessageManager.formatMessage(
2375 "label.removed_empty_columns",
2376 new String[] { Integer.valueOf(removeGapCols.getSize())
2379 // This is to maintain viewport position on first residue
2380 // of first sequence
2381 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2382 int startRes = seq.findPosition(viewport.startRes);
2383 // ShiftList shifts;
2384 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2385 // edit.alColumnChanges=shifts.getInverse();
2386 // if (viewport.hasHiddenColumns)
2387 // viewport.getColumnSelection().compensateForEdits(shifts);
2388 viewport.setStartRes(seq.findIndex(startRes) - 1);
2389 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2394 public void removeAllGapsMenuItem_actionPerformed()
2396 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2399 if (viewport.getSelectionGroup() != null)
2401 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2402 viewport.getHiddenRepSequences());
2403 start = viewport.getSelectionGroup().getStartRes();
2404 end = viewport.getSelectionGroup().getEndRes();
2408 seqs = viewport.getAlignment().getSequencesArray();
2411 // This is to maintain viewport position on first residue
2412 // of first sequence
2413 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2414 int startRes = seq.findPosition(viewport.startRes);
2416 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2417 viewport.getAlignment()));
2419 viewport.setStartRes(seq.findIndex(startRes) - 1);
2421 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2426 public void findMenuItem_actionPerformed()
2428 new Finder(alignPanel);
2432 * create a new view derived from the current view
2435 * @return frame for the new view
2437 public AlignFrame newView(String viewtitle)
2440 if (viewport.hasHiddenRows())
2442 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2443 .getFullAlignment().getSequencesArray());
2447 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2450 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2452 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2454 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2456 newal.addAnnotation(viewport.getAlignment()
2457 .getAlignmentAnnotation()[i]);
2462 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2464 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2465 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2466 PaintRefresher.Register(newaf.alignPanel,
2467 newaf.alignPanel.av.getSequenceSetId());
2469 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2470 newaf.alignPanel.av.getSequenceSetId());
2471 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2472 newaf.alignPanel.av.getSequenceSetId());
2474 Vector comps = (Vector) PaintRefresher.components.get(viewport
2475 .getSequenceSetId());
2477 for (int i = 0; i < comps.size(); i++)
2479 if (comps.elementAt(i) instanceof AlignmentPanel)
2485 String title = new String(this.getTitle());
2486 if (viewtitle != null)
2488 title = viewtitle + " ( " + title + ")";
2492 if (title.indexOf("(View") > -1)
2494 title = title.substring(0, title.indexOf("(View"));
2496 title += "(View " + viewSize + ")";
2499 newaf.setTitle(title.toString());
2501 newaf.viewport.setHistoryList(viewport.getHistoryList());
2502 newaf.viewport.setRedoList(viewport.getRedoList());
2508 * @return list of feature groups on the view
2510 public String[] getFeatureGroups()
2512 FeatureRenderer fr = null;
2513 if (alignPanel != null
2514 && (fr = alignPanel.getFeatureRenderer()) != null)
2516 List<String> gps = fr.getFeatureGroups();
2517 String[] _gps = gps.toArray(new String[gps.size()]);
2524 * get sequence feature groups that are hidden or shown
2530 public String[] getFeatureGroupsOfState(boolean visible)
2532 FeatureRenderer fr = null;
2533 if (alignPanel != null
2534 && (fr = alignPanel.getFeatureRenderer()) != null)
2536 List<String> gps = fr.getGroups(visible);
2537 String[] _gps = gps.toArray(new String[gps.size()]);
2544 * Change the display state for the given feature groups
2547 * list of group strings
2549 * visible or invisible
2551 public void setFeatureGroupState(String[] groups, boolean state)
2553 FeatureRenderer fr = null;
2554 this.sequenceFeatures.setState(true);
2555 viewport.setShowSequenceFeatures(true);
2556 if (alignPanel != null
2557 && (fr = alignPanel.getFeatureRenderer()) != null)
2560 fr.setGroupVisibility(Arrays.asList(groups), state);
2561 alignPanel.seqPanel.seqCanvas.repaint();
2562 if (alignPanel.overviewPanel != null)
2564 alignPanel.overviewPanel.updateOverviewImage();
2569 public void seqLimits_itemStateChanged()
2571 viewport.setShowJVSuffix(seqLimits.getState());
2572 alignPanel.fontChanged();
2573 alignPanel.paintAlignment(true);
2576 protected void colourTextMenuItem_actionPerformed()
2578 viewport.setColourText(colourTextMenuItem.getState());
2579 alignPanel.paintAlignment(true);
2582 protected void displayNonconservedMenuItem_actionPerformed()
2584 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2585 alignPanel.paintAlignment(true);
2588 protected void wrapMenuItem_actionPerformed()
2590 viewport.setWrapAlignment(wrapMenuItem.getState());
2591 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2592 scaleAbove.setEnabled(wrapMenuItem.getState());
2593 scaleLeft.setEnabled(wrapMenuItem.getState());
2594 scaleRight.setEnabled(wrapMenuItem.getState());
2595 alignPanel.paintAlignment(true);
2598 public void overviewMenuItem_actionPerformed()
2600 if (alignPanel.overviewPanel != null)
2605 Frame frame = new Frame();
2606 OverviewPanel overview = new OverviewPanel(alignPanel);
2607 frame.add(overview);
2608 // +50 must allow for applet frame window
2609 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2610 "label.overview_params", new String[] { this.getTitle() }),
2611 overview.getPreferredSize().width,
2612 overview.getPreferredSize().height + 50);
2615 final AlignmentPanel ap = alignPanel;
2616 frame.addWindowListener(new WindowAdapter()
2619 public void windowClosing(WindowEvent e)
2623 ap.setOverviewPanel(null);
2628 alignPanel.setOverviewPanel(overview);
2633 public void changeColour(ColourSchemeI cs)
2638 if (viewport.getAbovePIDThreshold())
2640 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2644 if (viewport.getConservationSelected())
2646 cs.setConservationApplied(true);
2647 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2652 cs.setConservationApplied(false);
2655 viewport.setGlobalColourScheme(cs);
2657 alignPanel.paintAlignment(true);
2660 protected void modifyPID_actionPerformed()
2662 if (viewport.getAbovePIDThreshold()
2663 && viewport.getGlobalColourScheme() != null)
2665 SliderPanel.setPIDSliderSource(alignPanel,
2666 viewport.getGlobalColourScheme(), "Background");
2667 SliderPanel.showPIDSlider();
2671 protected void modifyConservation_actionPerformed()
2673 if (viewport.getConservationSelected()
2674 && viewport.getGlobalColourScheme() != null)
2676 SliderPanel.setConservationSlider(alignPanel,
2677 viewport.getGlobalColourScheme(), "Background");
2678 SliderPanel.showConservationSlider();
2682 protected void conservationMenuItem_actionPerformed()
2684 viewport.setConservationSelected(conservationMenuItem.getState());
2686 viewport.setAbovePIDThreshold(false);
2687 abovePIDThreshold.setState(false);
2689 changeColour(viewport.getGlobalColourScheme());
2691 modifyConservation_actionPerformed();
2694 public void abovePIDThreshold_actionPerformed()
2696 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2698 conservationMenuItem.setState(false);
2699 viewport.setConservationSelected(false);
2701 changeColour(viewport.getGlobalColourScheme());
2703 modifyPID_actionPerformed();
2706 public void sortPairwiseMenuItem_actionPerformed()
2708 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2709 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2710 .getAlignment().getSequenceAt(0), null);
2712 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2713 viewport.getAlignment()));
2714 alignPanel.paintAlignment(true);
2717 public void sortIDMenuItem_actionPerformed()
2719 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2720 AlignmentSorter.sortByID(viewport.getAlignment());
2721 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2722 viewport.getAlignment()));
2723 alignPanel.paintAlignment(true);
2726 public void sortLengthMenuItem_actionPerformed()
2728 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2729 AlignmentSorter.sortByLength(viewport.getAlignment());
2730 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2731 viewport.getAlignment()));
2732 alignPanel.paintAlignment(true);
2735 public void sortGroupMenuItem_actionPerformed()
2737 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2738 AlignmentSorter.sortByGroup(viewport.getAlignment());
2739 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2740 viewport.getAlignment()));
2741 alignPanel.paintAlignment(true);
2745 public void removeRedundancyMenuItem_actionPerformed()
2747 new RedundancyPanel(alignPanel);
2750 public void pairwiseAlignmentMenuItem_actionPerformed()
2752 if (viewport.getSelectionGroup() != null
2753 && viewport.getSelectionGroup().getSize() > 1)
2755 Frame frame = new Frame();
2756 frame.add(new PairwiseAlignPanel(alignPanel));
2757 jalview.bin.JalviewLite.addFrame(frame,
2758 MessageManager.getString("action.pairwise_alignment"), 600,
2763 public void PCAMenuItem_actionPerformed()
2765 // are the sequences aligned?
2766 if (!viewport.getAlignment().isAligned(false))
2769 int Width = viewport.getAlignment().getWidth();
2771 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2773 current = viewport.getAlignment().getSequenceAt(i);
2775 if (current.getLength() < Width)
2777 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2780 alignPanel.paintAlignment(true);
2783 if ((viewport.getSelectionGroup() != null
2784 && viewport.getSelectionGroup().getSize() < 4 && viewport
2785 .getSelectionGroup().getSize() > 0)
2786 || viewport.getAlignment().getHeight() < 4)
2793 new PCAPanel(viewport);
2794 } catch (java.lang.OutOfMemoryError ex)
2800 public void averageDistanceTreeMenuItem_actionPerformed()
2802 NewTreePanel("AV", "PID", "Average distance tree using PID");
2805 public void neighbourTreeMenuItem_actionPerformed()
2807 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2810 protected void njTreeBlosumMenuItem_actionPerformed()
2812 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2815 protected void avTreeBlosumMenuItem_actionPerformed()
2817 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2820 void NewTreePanel(String type, String pwType, String title)
2822 // are the sequences aligned?
2823 if (!viewport.getAlignment().isAligned(false))
2826 int Width = viewport.getAlignment().getWidth();
2828 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2830 current = viewport.getAlignment().getSequenceAt(i);
2832 if (current.getLength() < Width)
2834 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2837 alignPanel.paintAlignment(true);
2841 if ((viewport.getSelectionGroup() != null && viewport
2842 .getSelectionGroup().getSize() > 1)
2843 || (viewport.getAlignment().getHeight() > 1))
2845 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2847 addTreeMenuItem(tp, title);
2849 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2853 void loadTree_actionPerformed()
2855 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2856 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2857 cap.setTreeImport();
2858 Frame frame = new Frame();
2860 jalview.bin.JalviewLite.addFrame(frame,
2861 MessageManager.getString("label.paste_newick_file"), 400, 300);
2864 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2866 TreePanel tp = new TreePanel(alignPanel, treeFile,
2867 MessageManager.getString("label.load_tree_from_file"), tree);
2868 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2869 addTreeMenuItem(tp, treeFile);
2873 * sort the alignment using the given treePanel
2876 * tree used to sort view
2878 * string used for undo event name
2880 public void sortByTree(TreePanel treePanel, String title)
2882 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2884 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2885 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2886 // HistoryItem.SORT));
2887 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2888 "label.order_by_params", new String[] { title }), oldOrder,
2889 viewport.getAlignment()));
2890 alignPanel.paintAlignment(true);
2894 * Do any automatic reordering of the alignment and add the necessary bits to
2895 * the menu structure for the new tree
2900 protected void addTreeMenuItem(final TreePanel treePanel,
2903 final MenuItem item = new MenuItem(title);
2904 sortByTreeMenu.add(item);
2905 item.addActionListener(new java.awt.event.ActionListener()
2908 public void actionPerformed(ActionEvent evt)
2910 sortByTree(treePanel, title); // treePanel.getTitle());
2914 treePanel.addWindowListener(new WindowAdapter()
2917 public void windowOpened(WindowEvent e)
2919 if (viewport.sortByTree)
2921 sortByTree(treePanel, title);
2923 super.windowOpened(e);
2927 public void windowClosing(WindowEvent e)
2929 sortByTreeMenu.remove(item);
2934 public boolean sortBy(AlignmentOrder alorder, String undoname)
2936 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2937 if (viewport.applet.debug)
2939 System.err.println("Sorting " + alorder.getOrder().size()
2940 + " in alignment '" + getTitle() + "'");
2942 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2943 if (undoname != null)
2945 addHistoryItem(new OrderCommand(undoname, oldOrder,
2946 viewport.getAlignment()));
2948 alignPanel.paintAlignment(true);
2952 protected void documentation_actionPerformed()
2954 alignPanel.av.applet.openJalviewHelpUrl();
2957 protected void about_actionPerformed()
2960 class AboutPanel extends Canvas
2966 public AboutPanel(String version, String builddate)
2968 this.version = version;
2969 this.builddate = builddate;
2973 public void paint(Graphics g)
2975 g.setColor(Color.white);
2976 g.fillRect(0, 0, getSize().width, getSize().height);
2977 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2978 FontMetrics fm = g.getFontMetrics();
2979 int fh = fm.getHeight();
2981 g.setColor(Color.black);
2982 // TODO: update this text for each release or centrally store it for
2983 // lite and application
2984 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2985 g.drawString(MessageManager.formatMessage(
2986 "label.jalviewLite_release", new String[] { version }), x,
2988 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2989 g.drawString(MessageManager.formatMessage(
2990 "label.jaview_build_date", new String[] { builddate }), x,
2992 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2993 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2995 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2996 x + 50, y += fh + 8);
2998 MessageManager.getString("label.jalview_dev_managers"), x,
3000 g.drawString(MessageManager
3001 .getString("label.jalview_distribution_lists"), x, y += fh);
3002 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3005 MessageManager.getString("label.jalview_cite_1_authors"),
3008 MessageManager.getString("label.jalview_cite_1_title"), x,
3010 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3015 Frame frame = new Frame();
3016 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3018 jalview.bin.JalviewLite.addFrame(frame,
3019 MessageManager.getString("label.jalview"), 580, 220);
3023 public void showURL(String url, String target)
3025 if (viewport.applet == null)
3027 System.out.println("Not running as applet - no browser available.");
3031 viewport.applet.showURL(url, target);
3035 // ////////////////////////////////////////////////////////////////////////////////
3036 // JBuilder Graphics here
3038 MenuBar alignFrameMenuBar = new MenuBar();
3040 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3042 MenuItem loadApplication = new MenuItem(
3043 MessageManager.getString("label.view_full_application"));
3045 MenuItem loadTree = new MenuItem(
3046 MessageManager.getString("label.load_associated_tree"));
3048 MenuItem loadAnnotations = new MenuItem(
3049 MessageManager.getString("label.load_features_annotations"));
3051 MenuItem outputFeatures = new MenuItem(
3052 MessageManager.getString("label.export_features"));
3054 MenuItem outputAnnotations = new MenuItem(
3055 MessageManager.getString("label.export_annotations"));
3057 MenuItem closeMenuItem = new MenuItem(
3058 MessageManager.getString("action.close"));
3060 MenuItem selectAllSequenceMenuItem = new MenuItem(
3061 MessageManager.getString("action.select_all"));
3063 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3064 MessageManager.getString("action.deselect_all"));
3066 MenuItem invertSequenceMenuItem = new MenuItem(
3067 MessageManager.getString("action.invert_selection"));
3069 MenuItem remove2LeftMenuItem = new MenuItem();
3071 MenuItem remove2RightMenuItem = new MenuItem();
3073 MenuItem removeGappedColumnMenuItem = new MenuItem();
3075 MenuItem removeAllGapsMenuItem = new MenuItem();
3077 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3079 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3081 MenuItem sortPairwiseMenuItem = new MenuItem();
3083 MenuItem sortIDMenuItem = new MenuItem();
3085 MenuItem sortLengthMenuItem = new MenuItem();
3087 MenuItem sortGroupMenuItem = new MenuItem();
3089 MenuItem removeRedundancyMenuItem = new MenuItem();
3091 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3093 MenuItem PCAMenuItem = new MenuItem();
3095 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3097 MenuItem neighbourTreeMenuItem = new MenuItem();
3099 BorderLayout borderLayout1 = new BorderLayout();
3101 public Label statusBar = new Label();
3103 MenuItem clustalColour = new MenuItem();
3105 MenuItem zappoColour = new MenuItem();
3107 MenuItem taylorColour = new MenuItem();
3109 MenuItem hydrophobicityColour = new MenuItem();
3111 MenuItem helixColour = new MenuItem();
3113 MenuItem strandColour = new MenuItem();
3115 MenuItem turnColour = new MenuItem();
3117 MenuItem buriedColour = new MenuItem();
3119 MenuItem purinePyrimidineColour = new MenuItem();
3121 // MenuItem RNAInteractionColour = new MenuItem();
3123 MenuItem RNAHelixColour = new MenuItem();
3125 MenuItem userDefinedColour = new MenuItem();
3127 MenuItem PIDColour = new MenuItem();
3129 MenuItem BLOSUM62Colour = new MenuItem();
3131 MenuItem tcoffeeColour = new MenuItem();
3133 MenuItem njTreeBlosumMenuItem = new MenuItem();
3135 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3137 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3139 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3141 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3143 MenuItem alProperties = new MenuItem(
3144 MessageManager.getString("label.alignment_props"));
3146 MenuItem overviewMenuItem = new MenuItem();
3148 MenuItem undoMenuItem = new MenuItem();
3150 MenuItem redoMenuItem = new MenuItem();
3152 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3154 MenuItem noColourmenuItem = new MenuItem();
3156 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3158 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3160 MenuItem findMenuItem = new MenuItem();
3162 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3164 MenuItem nucleotideColour = new MenuItem();
3166 MenuItem deleteGroups = new MenuItem();
3168 MenuItem grpsFromSelection = new MenuItem();
3170 MenuItem createGroup = new MenuItem();
3172 MenuItem unGroup = new MenuItem();
3174 MenuItem delete = new MenuItem();
3176 MenuItem copy = new MenuItem();
3178 MenuItem cut = new MenuItem();
3180 Menu pasteMenu = new Menu();
3182 MenuItem pasteNew = new MenuItem();
3184 MenuItem pasteThis = new MenuItem();
3186 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3188 MenuItem font = new MenuItem();
3190 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3192 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3194 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3196 MenuItem modifyPID = new MenuItem();
3198 MenuItem modifyConservation = new MenuItem();
3200 CheckboxMenuItem autoCalculate = null;
3202 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3203 "Sort Alignment With New Tree", true);
3205 Menu sortByTreeMenu = new Menu();
3207 MenuItem inputText = new MenuItem();
3209 MenuItem documentation = new MenuItem();
3211 MenuItem about = new MenuItem();
3213 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3215 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3217 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3219 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3221 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3223 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3225 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3227 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3229 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3232 * Initialise menus and other items
3236 private void jbInit() throws Exception
3238 setMenuBar(alignFrameMenuBar);
3241 * Configure File menu items and actions
3244 .setLabel(MessageManager.getString("label.input_from_textbox"));
3245 inputText.addActionListener(this);
3246 Menu outputTextboxMenu = new Menu(
3247 MessageManager.getString("label.out_to_textbox"));
3248 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3250 MenuItem item = new MenuItem(ff);
3252 item.addActionListener(new java.awt.event.ActionListener()
3255 public void actionPerformed(ActionEvent e)
3257 outputText_actionPerformed(e);
3261 outputTextboxMenu.add(item);
3263 closeMenuItem.addActionListener(this);
3264 loadApplication.addActionListener(this);
3265 loadTree.addActionListener(this);
3266 loadAnnotations.addActionListener(this);
3267 outputFeatures.addActionListener(this);
3268 outputAnnotations.addActionListener(this);
3271 * Configure Edit menu items and actions
3273 undoMenuItem.setEnabled(false);
3274 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3275 undoMenuItem.addActionListener(this);
3276 redoMenuItem.setEnabled(false);
3277 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3278 redoMenuItem.addActionListener(this);
3279 copy.setLabel(MessageManager.getString("action.copy"));
3280 copy.addActionListener(this);
3281 cut.setLabel(MessageManager.getString("action.cut"));
3282 cut.addActionListener(this);
3283 delete.setLabel(MessageManager.getString("action.delete"));
3284 delete.addActionListener(this);
3285 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3286 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3287 pasteNew.addActionListener(this);
3288 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3289 pasteThis.addActionListener(this);
3290 remove2LeftMenuItem.setLabel(MessageManager
3291 .getString("action.remove_left"));
3292 remove2LeftMenuItem.addActionListener(this);
3293 remove2RightMenuItem.setLabel(MessageManager
3294 .getString("action.remove_right"));
3295 remove2RightMenuItem.addActionListener(this);
3296 removeGappedColumnMenuItem.setLabel(MessageManager
3297 .getString("action.remove_empty_columns"));
3298 removeGappedColumnMenuItem.addActionListener(this);
3299 removeAllGapsMenuItem.setLabel(MessageManager
3300 .getString("action.remove_all_gaps"));
3301 removeAllGapsMenuItem.addActionListener(this);
3302 removeRedundancyMenuItem.setLabel(MessageManager
3303 .getString("action.remove_redundancy"));
3304 removeRedundancyMenuItem.addActionListener(this);
3307 * Configure Select menu items and actions
3309 findMenuItem.setLabel(MessageManager.getString("action.find"));
3310 findMenuItem.addActionListener(this);
3311 selectAllSequenceMenuItem.addActionListener(this);
3312 deselectAllSequenceMenuItem.addActionListener(this);
3313 invertSequenceMenuItem.setLabel(MessageManager
3314 .getString("action.invert_sequence_selection"));
3315 invertSequenceMenuItem.addActionListener(this);
3316 invertColSel.setLabel(MessageManager
3317 .getString("action.invert_column_selection"));
3318 invertColSel.addActionListener(this);
3319 deleteGroups.setLabel(MessageManager
3320 .getString("action.undefine_groups"));
3321 deleteGroups.addActionListener(this);
3322 grpsFromSelection.setLabel(MessageManager
3323 .getString("action.make_groups_selection"));
3324 grpsFromSelection.addActionListener(this);
3325 createGroup.setLabel(MessageManager.getString("action.create_group"));
3326 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3327 annotationColumnSelection.setLabel(MessageManager
3328 .getString("action.select_by_annotation"));
3329 annotationColumnSelection.addActionListener(this);
3332 * Configure View menu items and actions
3334 newView.setLabel(MessageManager.getString("action.new_view"));
3335 newView.addActionListener(this);
3336 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3337 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3338 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3339 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3341 .setLabel(MessageManager.getString("label.selected_columns"));
3342 hideSequences.setLabel(MessageManager
3343 .getString("label.selected_sequences"));
3344 hideAllButSelection.setLabel(MessageManager
3345 .getString("label.all_but_selected_region"));
3346 hideAllSelection.setLabel(MessageManager
3347 .getString("label.selected_region"));
3348 showAllHidden.setLabel(MessageManager
3349 .getString("label.all_sequences_columns"));
3350 showColumns.addActionListener(this);
3351 showSeqs.addActionListener(this);
3352 hideColumns.addActionListener(this);
3353 hideSequences.addActionListener(this);
3354 hideAllButSelection.addActionListener(this);
3355 hideAllSelection.addActionListener(this);
3356 showAllHidden.addActionListener(this);
3357 featureSettings.setLabel(MessageManager
3358 .getString("action.feature_settings"));
3359 featureSettings.addActionListener(this);
3360 sequenceFeatures.setLabel(MessageManager
3361 .getString("label.show_sequence_features"));
3362 sequenceFeatures.addItemListener(this);
3363 sequenceFeatures.setState(false);
3364 followMouseOverFlag.setLabel(MessageManager
3365 .getString("label.automatic_scrolling"));
3366 followMouseOverFlag.addItemListener(this);
3367 alProperties.addActionListener(this);
3368 overviewMenuItem.setLabel(MessageManager
3369 .getString("label.overview_window"));
3370 overviewMenuItem.addActionListener(this);
3373 * Configure Annotations menu items and actions
3375 annotationPanelMenuItem.setLabel(MessageManager
3376 .getString("label.show_annotations"));
3377 annotationPanelMenuItem.addItemListener(this);
3378 showGroupConsensus.setLabel(MessageManager
3379 .getString("label.group_consensus"));
3380 showGroupConservation.setLabel(MessageManager
3381 .getString("label.group_conservation"));
3382 showConsensusHistogram.setLabel(MessageManager
3383 .getString("label.show_consensus_histogram"));
3384 showSequenceLogo.setLabel(MessageManager
3385 .getString("label.show_consensus_logo"));
3386 normSequenceLogo.setLabel(MessageManager
3387 .getString("label.norm_consensus_logo"));
3388 applyAutoAnnotationSettings.setLabel(MessageManager
3389 .getString("label.apply_all_groups"));
3390 applyAutoAnnotationSettings.setState(true);
3391 Menu autoAnnMenu = new Menu(
3392 MessageManager.getString("label.autocalculated_annotation"));
3393 showGroupConsensus.addItemListener(this);
3394 showGroupConservation.addItemListener(this);
3395 showConsensusHistogram.addItemListener(this);
3396 showSequenceLogo.addItemListener(this);
3397 normSequenceLogo.addItemListener(this);
3398 applyAutoAnnotationSettings.addItemListener(this);
3399 showAlignmentAnnotations = new CheckboxMenuItem(
3400 MessageManager.getString("label.show_all_al_annotations"));
3401 showSequenceAnnotations = new CheckboxMenuItem(
3402 MessageManager.getString("label.show_all_seq_annotations"));
3403 sortAnnBySequence = new CheckboxMenuItem(
3404 MessageManager.getString("label.sort_annotations_by_sequence"));
3405 sortAnnByLabel = new CheckboxMenuItem(
3406 MessageManager.getString("label.sort_annotations_by_label"));
3407 showAutoFirst = new CheckboxMenuItem(
3408 MessageManager.getString("label.show_first"));
3409 showAutoFirst.setState(false); // pending applet parameter
3410 setShowAutoCalculatedAbove(showAutoFirst.getState());
3411 showAutoLast = new CheckboxMenuItem(
3412 MessageManager.getString("label.show_last"));
3413 showAutoLast.setState(!showAutoFirst.getState());
3414 showAlignmentAnnotations.addItemListener(this);
3415 showSequenceAnnotations.addItemListener(this);
3416 sortAnnBySequence.addItemListener(this);
3417 sortAnnByLabel.addItemListener(this);
3418 showAutoFirst.addItemListener(this);
3419 showAutoLast.addItemListener(this);
3422 * Configure Format menu items and actions
3424 font.setLabel(MessageManager.getString("action.font"));
3425 font.addActionListener(this);
3426 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3427 scaleAbove.setState(true);
3428 scaleAbove.setEnabled(false);
3429 scaleAbove.addItemListener(this);
3430 scaleLeft.setEnabled(false);
3431 scaleLeft.setState(true);
3432 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3433 scaleLeft.addItemListener(this);
3434 scaleRight.setEnabled(false);
3435 scaleRight.setState(true);
3436 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3437 scaleRight.addItemListener(this);
3438 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3439 viewBoxesMenuItem.setState(true);
3440 viewBoxesMenuItem.addItemListener(this);
3441 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3442 viewTextMenuItem.setState(true);
3443 viewTextMenuItem.addItemListener(this);
3444 colourTextMenuItem.setLabel(MessageManager
3445 .getString("label.colour_text"));
3446 colourTextMenuItem.addItemListener(this);
3447 displayNonconservedMenuItem.setLabel(MessageManager
3448 .getString("label.show_non_conserved"));
3449 displayNonconservedMenuItem.addItemListener(this);
3450 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3451 wrapMenuItem.addItemListener(this);
3452 renderGapsMenuItem.setLabel(MessageManager
3453 .getString("action.show_gaps"));
3454 renderGapsMenuItem.setState(true);
3455 renderGapsMenuItem.addItemListener(this);
3456 centreColumnLabelFlag.setLabel(MessageManager
3457 .getString("label.centre_column_labels"));
3458 centreColumnLabelFlag.addItemListener(this);
3459 seqLimits.setState(true);
3460 seqLimits.setLabel(MessageManager
3461 .getString("label.show_sequence_limits"));
3462 seqLimits.addItemListener(this);
3465 * Configure Colour menu items and actions
3467 applyToAllGroups.setLabel(MessageManager
3468 .getString("label.apply_colour_to_all_groups"));
3469 applyToAllGroups.setState(true);
3470 applyToAllGroups.addItemListener(this);
3471 clustalColour.setLabel(MessageManager
3472 .getString("label.colourScheme_clustal"));
3473 clustalColour.addActionListener(this);
3474 zappoColour.setLabel(MessageManager
3475 .getString("label.colourScheme_zappo"));
3476 zappoColour.addActionListener(this);
3477 taylorColour.setLabel(MessageManager
3478 .getString("label.colourScheme_taylor"));
3479 taylorColour.addActionListener(this);
3480 hydrophobicityColour.setLabel(MessageManager
3481 .getString("label.colourScheme_hydrophobic"));
3482 hydrophobicityColour.addActionListener(this);
3483 helixColour.setLabel(MessageManager
3484 .getString("label.colourScheme_helix_propensity"));
3485 helixColour.addActionListener(this);
3486 strandColour.setLabel(MessageManager
3487 .getString("label.colourScheme_strand_propensity"));
3488 strandColour.addActionListener(this);
3489 turnColour.setLabel(MessageManager
3490 .getString("label.colourScheme_turn_propensity"));
3491 turnColour.addActionListener(this);
3492 buriedColour.setLabel(MessageManager
3493 .getString("label.colourScheme_buried_index"));
3494 buriedColour.addActionListener(this);
3495 purinePyrimidineColour.setLabel(MessageManager
3496 .getString("label.colourScheme_purine/pyrimidine"));
3497 purinePyrimidineColour.addActionListener(this);
3498 // RNAInteractionColour.setLabel(MessageManager
3499 // .getString("label.rna_interaction"));
3500 // RNAInteractionColour.addActionListener(this);
3501 RNAHelixColour.setLabel(MessageManager
3502 .getString("label.colourScheme_rna_helices"));
3503 RNAHelixColour.addActionListener(this);
3504 userDefinedColour.setLabel(MessageManager
3505 .getString("action.user_defined"));
3506 userDefinedColour.addActionListener(this);
3507 PIDColour.setLabel(MessageManager
3508 .getString("label.colourScheme_%_identity"));
3509 PIDColour.addActionListener(this);
3510 BLOSUM62Colour.setLabel(MessageManager
3511 .getString("label.colourScheme_blosum62"));
3512 BLOSUM62Colour.addActionListener(this);
3513 tcoffeeColour.setLabel(MessageManager
3514 .getString("label.colourScheme_t-coffee_scores"));
3515 // it will be enabled only if a score file is provided
3516 tcoffeeColour.setEnabled(false);
3517 tcoffeeColour.addActionListener(this);
3518 conservationMenuItem.setLabel(MessageManager
3519 .getString("action.by_conservation"));
3520 conservationMenuItem.addItemListener(this);
3521 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3522 noColourmenuItem.addActionListener(this);
3523 abovePIDThreshold.setLabel(MessageManager
3524 .getString("label.above_identity_threshold"));
3525 abovePIDThreshold.addItemListener(this);
3526 nucleotideColour.setLabel(MessageManager
3527 .getString("label.colourScheme_nucleotide"));
3528 nucleotideColour.addActionListener(this);
3529 modifyPID.setLabel(MessageManager
3530 .getString("label.modify_identity_threshold"));
3531 modifyPID.addActionListener(this);
3532 modifyConservation.setLabel(MessageManager
3533 .getString("label.modify_conservation_threshold"));
3534 modifyConservation.addActionListener(this);
3535 annotationColour.setLabel(MessageManager
3536 .getString("action.by_annotation"));
3537 annotationColour.addActionListener(this);
3540 * Configure Calculate menu items and actions
3542 sortPairwiseMenuItem.setLabel(MessageManager
3543 .getString("action.by_pairwise_id"));
3544 sortPairwiseMenuItem.addActionListener(this);
3545 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3546 sortIDMenuItem.addActionListener(this);
3547 sortLengthMenuItem.setLabel(MessageManager
3548 .getString("action.by_length"));
3549 sortLengthMenuItem.addActionListener(this);
3550 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3551 sortGroupMenuItem.addActionListener(this);
3552 pairwiseAlignmentMenuItem.setLabel(MessageManager
3553 .getString("action.pairwise_alignment"));
3554 pairwiseAlignmentMenuItem.addActionListener(this);
3555 PCAMenuItem.setLabel(MessageManager
3556 .getString("label.principal_component_analysis"));
3557 PCAMenuItem.addActionListener(this);
3558 autoCalculate = new CheckboxMenuItem(
3559 MessageManager.getString("label.autocalculate_consensus"), true);
3560 averageDistanceTreeMenuItem.setLabel(MessageManager
3561 .getString("label.average_distance_identity"));
3562 averageDistanceTreeMenuItem.addActionListener(this);
3563 neighbourTreeMenuItem.setLabel(MessageManager
3564 .getString("label.neighbour_joining_identity"));
3565 neighbourTreeMenuItem.addActionListener(this);
3566 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3567 .getString("label.average_distance_blosum62"));
3568 avDistanceTreeBlosumMenuItem.addActionListener(this);
3569 njTreeBlosumMenuItem.setLabel(MessageManager
3570 .getString("label.neighbour_blosum62"));
3571 njTreeBlosumMenuItem.addActionListener(this);
3572 sortByTreeMenu.setLabel(MessageManager
3573 .getString("action.by_tree_order"));
3574 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3575 Menu calculateTreeMenu = new Menu(
3576 MessageManager.getString("action.calculate_tree"));
3577 autoCalculate.addItemListener(this);
3578 sortByTree.addItemListener(this);
3581 * Configure Help menu items and actions
3583 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3584 documentation.setLabel(MessageManager.getString("label.documentation"));
3585 documentation.addActionListener(this);
3586 about.setLabel(MessageManager.getString("label.about"));
3587 about.addActionListener(this);
3590 * Add top level menus to frame
3592 alignFrameMenuBar.add(fileMenu);
3593 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3594 alignFrameMenuBar.add(editMenu);
3595 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3596 alignFrameMenuBar.add(selectMenu);
3597 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3598 alignFrameMenuBar.add(viewMenu);
3599 Menu annotationsMenu = new Menu(
3600 MessageManager.getString("action.annotations"));
3601 alignFrameMenuBar.add(annotationsMenu);
3602 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3603 alignFrameMenuBar.add(formatMenu);
3604 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3605 alignFrameMenuBar.add(colourMenu);
3606 Menu calculateMenu = new Menu(
3607 MessageManager.getString("action.calculate"));
3608 alignFrameMenuBar.add(calculateMenu);
3609 alignFrameMenuBar.add(helpMenu);
3614 fileMenu.add(inputText);
3615 fileMenu.add(loadTree);
3616 fileMenu.add(loadAnnotations);
3617 fileMenu.addSeparator();
3618 fileMenu.add(outputTextboxMenu);
3619 fileMenu.add(outputFeatures);
3620 fileMenu.add(outputAnnotations);
3621 if (jalviewServletURL != null)
3623 fileMenu.add(loadApplication);
3625 fileMenu.addSeparator();
3626 fileMenu.add(closeMenuItem);
3631 editMenu.add(undoMenuItem);
3632 editMenu.add(redoMenuItem);
3635 pasteMenu.add(pasteNew);
3636 pasteMenu.add(pasteThis);
3637 editMenu.add(pasteMenu);
3638 editMenu.add(delete);
3639 editMenu.addSeparator();
3640 editMenu.add(remove2LeftMenuItem);
3641 editMenu.add(remove2RightMenuItem);
3642 editMenu.add(removeGappedColumnMenuItem);
3643 editMenu.add(removeAllGapsMenuItem);
3644 editMenu.add(removeRedundancyMenuItem);
3649 selectMenu.add(findMenuItem);
3650 selectMenu.addSeparator();
3651 selectMenu.add(selectAllSequenceMenuItem);
3652 selectMenu.add(deselectAllSequenceMenuItem);
3653 selectMenu.add(invertSequenceMenuItem);
3654 selectMenu.add(invertColSel);
3655 selectMenu.add(createGroup);
3656 selectMenu.add(unGroup);
3657 selectMenu.add(grpsFromSelection);
3658 selectMenu.add(deleteGroups);
3659 selectMenu.add(annotationColumnSelection);
3664 viewMenu.add(newView);
3665 viewMenu.addSeparator();
3666 showMenu.add(showColumns);
3667 showMenu.add(showSeqs);
3668 showMenu.add(showAllHidden);
3669 viewMenu.add(showMenu);
3670 hideMenu.add(hideColumns);
3671 hideMenu.add(hideSequences);
3672 hideMenu.add(hideAllSelection);
3673 hideMenu.add(hideAllButSelection);
3674 viewMenu.add(hideMenu);
3675 viewMenu.addSeparator();
3676 viewMenu.add(followMouseOverFlag);
3677 viewMenu.addSeparator();
3678 viewMenu.add(sequenceFeatures);
3679 viewMenu.add(featureSettings);
3680 viewMenu.addSeparator();
3681 viewMenu.add(alProperties);
3682 viewMenu.addSeparator();
3683 viewMenu.add(overviewMenuItem);
3688 annotationsMenu.add(annotationPanelMenuItem);
3689 annotationsMenu.addSeparator();
3690 annotationsMenu.add(showAlignmentAnnotations);
3691 annotationsMenu.add(showSequenceAnnotations);
3692 annotationsMenu.add(sortAnnBySequence);
3693 annotationsMenu.add(sortAnnByLabel);
3694 annotationsMenu.addSeparator();
3695 autoAnnMenu.add(showAutoFirst);
3696 autoAnnMenu.add(showAutoLast);
3697 autoAnnMenu.addSeparator();
3698 autoAnnMenu.add(applyAutoAnnotationSettings);
3699 autoAnnMenu.add(showConsensusHistogram);
3700 autoAnnMenu.add(showSequenceLogo);
3701 autoAnnMenu.add(normSequenceLogo);
3702 autoAnnMenu.addSeparator();
3703 autoAnnMenu.add(showGroupConservation);
3704 autoAnnMenu.add(showGroupConsensus);
3705 annotationsMenu.add(autoAnnMenu);
3710 formatMenu.add(font);
3711 formatMenu.add(seqLimits);
3712 formatMenu.add(wrapMenuItem);
3713 formatMenu.add(scaleAbove);
3714 formatMenu.add(scaleLeft);
3715 formatMenu.add(scaleRight);
3716 formatMenu.add(viewBoxesMenuItem);
3717 formatMenu.add(viewTextMenuItem);
3718 formatMenu.add(colourTextMenuItem);
3719 formatMenu.add(displayNonconservedMenuItem);
3720 formatMenu.add(renderGapsMenuItem);
3721 formatMenu.add(centreColumnLabelFlag);
3726 colourMenu.add(applyToAllGroups);
3727 colourMenu.addSeparator();
3728 colourMenu.add(noColourmenuItem);
3729 colourMenu.add(clustalColour);
3730 colourMenu.add(BLOSUM62Colour);
3731 colourMenu.add(PIDColour);
3732 colourMenu.add(zappoColour);
3733 colourMenu.add(taylorColour);
3734 colourMenu.add(hydrophobicityColour);
3735 colourMenu.add(helixColour);
3736 colourMenu.add(strandColour);
3737 colourMenu.add(turnColour);
3738 colourMenu.add(buriedColour);
3739 colourMenu.add(nucleotideColour);
3740 colourMenu.add(purinePyrimidineColour);
3741 // colourMenu.add(RNAInteractionColour);
3742 colourMenu.add(tcoffeeColour);
3743 colourMenu.add(userDefinedColour);
3744 colourMenu.addSeparator();
3745 colourMenu.add(conservationMenuItem);
3746 colourMenu.add(modifyConservation);
3747 colourMenu.add(abovePIDThreshold);
3748 colourMenu.add(modifyPID);
3749 colourMenu.add(annotationColour);
3750 colourMenu.add(RNAHelixColour);
3755 sortMenu.add(sortIDMenuItem);
3756 sortMenu.add(sortLengthMenuItem);
3757 sortMenu.add(sortByTreeMenu);
3758 sortMenu.add(sortGroupMenuItem);
3759 sortMenu.add(sortPairwiseMenuItem);
3760 calculateMenu.add(sortMenu);
3761 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3762 calculateTreeMenu.add(neighbourTreeMenuItem);
3763 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3764 calculateTreeMenu.add(njTreeBlosumMenuItem);
3765 calculateMenu.add(calculateTreeMenu);
3766 calculateMenu.addSeparator();
3767 calculateMenu.add(pairwiseAlignmentMenuItem);
3768 calculateMenu.add(PCAMenuItem);
3769 calculateMenu.add(autoCalculate);
3770 calculateMenu.add(sortByTree);
3775 helpMenu.add(documentation);
3776 helpMenu.add(about);
3781 statusBar.setBackground(Color.white);
3782 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3783 statusBar.setText(MessageManager.getString("label.status_bar"));
3784 this.add(statusBar, BorderLayout.SOUTH);
3788 public void setStatus(String string)
3790 statusBar.setText(string);
3793 MenuItem featureSettings = new MenuItem();
3795 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3797 MenuItem annotationColour = new MenuItem();
3799 MenuItem annotationColumnSelection = new MenuItem();
3801 MenuItem invertColSel = new MenuItem();
3803 MenuItem showColumns = new MenuItem();
3805 MenuItem showSeqs = new MenuItem();
3807 MenuItem hideColumns = new MenuItem();
3809 MenuItem hideSequences = new MenuItem();
3811 MenuItem hideAllButSelection = new MenuItem();
3813 MenuItem hideAllSelection = new MenuItem();
3815 MenuItem showAllHidden = new MenuItem();
3817 MenuItem newView = new MenuItem();
3819 private CheckboxMenuItem showAlignmentAnnotations;
3821 private CheckboxMenuItem showSequenceAnnotations;
3823 private CheckboxMenuItem sortAnnBySequence;
3825 private CheckboxMenuItem sortAnnByLabel;
3827 private CheckboxMenuItem showAutoFirst;
3829 private CheckboxMenuItem showAutoLast;
3831 private SplitFrame splitFrame;
3834 * Attach the alignFrame panels after embedding menus, if necessary. This used
3835 * to be called setEmbedded, but is now creates the dropdown menus in a
3836 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3838 * @param reallyEmbedded
3839 * true to attach the view to the applet area on the page rather than
3842 public void createAlignFrameWindow(boolean reallyEmbedded)
3846 embedAlignFrameInApplet(viewport.applet);
3851 // test and embed menu bar if necessary.
3853 if (embedMenuIfNeeded(alignPanel))
3856 * adjust for status bar height too. ? pointless as overridden by layout
3859 alignPanel.setSize(getSize().width,
3860 getSize().height - statusBar.getHeight());
3862 add(statusBar, BorderLayout.SOUTH);
3863 add(alignPanel, BorderLayout.CENTER);
3864 // and register with the applet so it can pass external API calls to us
3865 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3871 * Add the components of this AlignFrame to the applet container.
3875 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3878 // Explicitly build the embedded menu panel for the on-page applet
3880 // view cannot be closed if its actually on the page
3881 fileMenu.remove(closeMenuItem);
3882 fileMenu.remove(3); // Remove Separator
3883 // construct embedded menu, using default font
3884 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3885 // and actually add the components to the applet area
3886 theApplet.setLayout(new BorderLayout());
3887 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3888 theApplet.add(statusBar, BorderLayout.SOUTH);
3889 // TODO should size be left to the layout manager?
3890 alignPanel.setSize(theApplet.getSize().width,
3891 theApplet.getSize().height - embeddedMenu.getHeight()
3892 - statusBar.getHeight());
3893 theApplet.add(alignPanel, BorderLayout.CENTER);
3894 final AlignFrame me = this;
3895 theApplet.addFocusListener(new FocusListener()
3899 public void focusLost(FocusEvent e)
3901 if (theApplet.currentAlignFrame == me)
3903 theApplet.currentAlignFrame = null;
3908 public void focusGained(FocusEvent e)
3910 theApplet.currentAlignFrame = me;
3913 theApplet.validate();
3917 * create a new binding between structures in an existing jmol viewer instance
3918 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3919 * this does not open a new Jmol window, or modify the display of the
3920 * structures in the original jmol window. Note This method doesn't work
3921 * without an additional javascript library to exchange messages between the
3922 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3925 * JmolViewer instance
3926 * @param sequenceIds
3927 * - sequence Ids to search for associations
3929 public SequenceStructureBinding addStructureViewInstance(
3930 Object jmolviewer, String[] sequenceIds)
3932 Viewer viewer = null;
3935 viewer = (Viewer) jmolviewer;
3936 } catch (ClassCastException ex)
3938 System.err.println("Unsupported viewer object :"
3939 + jmolviewer.getClass());
3943 System.err.println("Can't use this object as a structure viewer:"
3944 + jmolviewer.getClass());
3947 SequenceI[] seqs = null;
3948 if (sequenceIds == null || sequenceIds.length == 0)
3950 seqs = viewport.getAlignment().getSequencesArray();
3954 Vector sqi = new Vector();
3955 AlignmentI al = viewport.getAlignment();
3956 for (int sid = 0; sid < sequenceIds.length; sid++)
3958 SequenceI sq = al.findName(sequenceIds[sid]);
3966 seqs = new SequenceI[sqi.size()];
3967 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3969 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3977 AAStructureBindingModel jmv = null;
3978 // TODO: search for a jmv that involves viewer
3980 { // create a new viewer/jalview binding.
3981 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3988 * bind a pdb file to a sequence in the current view
3991 * - sequenceId within the dataset.
3992 * @param pdbEntryString
3993 * - the short name for the PDB file
3995 * - pdb file - either a URL or a valid PDB file.
3996 * @return true if binding was as success TODO: consider making an exception
3997 * structure for indicating when PDB parsing or sequenceId location
4000 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4003 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4004 boolean needtoadd = false;
4005 if (toaddpdb != null)
4007 Vector pdbe = toaddpdb.getAllPDBEntries();
4008 PDBEntry pdbentry = null;
4009 if (pdbe != null && pdbe.size() > 0)
4011 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4013 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4014 if (!pdbentry.getId().equals(pdbEntryString)
4015 && !pdbentry.getFile().equals(pdbFile))
4025 if (pdbentry == null)
4027 pdbentry = new PDBEntry();
4028 pdbentry.setId(pdbEntryString);
4029 pdbentry.setFile(pdbFile);
4030 needtoadd = true; // add this new entry to sequence.
4032 // resolve data source
4033 // TODO: this code should be a refactored to an io package
4034 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4035 pdbFile, FileFormat.PDB);
4036 if (protocol == null)
4042 pdbentry.setProperty("protocol", protocol);
4043 toaddpdb.addPDBId(pdbentry);
4044 alignPanel.getStructureSelectionManager()
4045 .registerPDBEntry(pdbentry);
4051 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4055 Vector sequences = new Vector();
4056 for (int i = 0; i < seqs.length; i++)
4058 if (seqs[i] != null)
4060 sequences.addElement(new Object[] { seqs[i],
4061 (chains != null) ? chains[i] : null });
4064 seqs = new SequenceI[sequences.size()];
4065 chains = new String[sequences.size()];
4066 for (int i = 0, isize = sequences.size(); i < isize; i++)
4068 Object[] oj = (Object[]) sequences.elementAt(i);
4070 seqs[i] = (SequenceI) oj[0];
4071 chains[i] = (String) oj[1];
4074 return new Object[] { seqs, chains };
4078 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4079 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4081 // Scrub any null sequences from the array
4082 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4083 seqs = (SequenceI[]) sqch[0];
4084 chains = (String[]) sqch[1];
4085 if (seqs == null || seqs.length == 0)
4088 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4090 if (protocol == null)
4092 String sourceType = (String) pdb.getProperty("protocol");
4095 protocol = DataSourceType.valueOf(sourceType);
4096 } catch (IllegalArgumentException e)
4100 if (protocol == null)
4102 System.err.println("Couldn't work out protocol to open structure: "
4107 if (applet.useXtrnalSviewer)
4109 // register the association(s) and quit, don't create any windows.
4110 if (StructureSelectionManager.getStructureSelectionManager(applet)
4111 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4113 System.err.println("Failed to map " + pdb.getFile() + " ("
4114 + protocol + ") to any sequences");
4118 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4120 // can only do alignments with Jmol
4121 // find the last jmol window assigned to this alignment
4122 AppletJmol ajm = null, tajm;
4123 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4124 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4126 tajm = (AppletJmol) jmols.elementAt(i);
4127 if (tajm.ap.alignFrame == this)
4136 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4137 // try and add the pdb structure
4142 // otherwise, create a new window
4143 if (applet.jmolAvailable)
4145 new AppletJmol(pdb, seqs, chains, alignPanel,
4147 applet.lastFrameX += 40;
4148 applet.lastFrameY += 40;
4152 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4157 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4158 SequenceI[][] seqs, String[][] chains, String[] protocols)
4160 // TODO Auto-generated method stub
4161 System.err.println("Aligned Structure View: Not yet implemented.");
4165 * modify the current selection, providing the user has not made a selection
4169 * - sequences from this alignment
4171 * - columns to be selected on the alignment
4173 public void select(SequenceGroup sel, ColumnSelection csel)
4175 alignPanel.seqPanel.selection(sel, csel, null);
4178 public void scrollTo(int row, int column)
4180 alignPanel.seqPanel.scrollTo(row, column);
4183 public void scrollToRow(int row)
4185 alignPanel.seqPanel.scrollToRow(row);
4188 public void scrollToColumn(int column)
4190 alignPanel.seqPanel.scrollToColumn(column);
4194 * @return the alignments unique ID.
4196 public String getSequenceSetId()
4198 return viewport.getSequenceSetId();
4202 * Load the (T-Coffee) score file from the specified url
4205 * File/URL/T-COFFEE score file contents
4206 * @throws IOException
4207 * @return true if alignment was annotated with data from source
4209 public boolean loadScoreFile(String source) throws IOException
4212 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4213 AppletFormatAdapter.checkProtocol(source));
4214 if (!file.isValid())
4216 // TODO: raise dialog for gui
4217 System.err.println("Problems parsing T-Coffee scores: "
4218 + file.getWarningMessage());
4219 System.err.println("Origin was:\n" + source);
4224 * check that the score matrix matches the alignment dimensions
4227 if ((aln = viewport.getAlignment()) != null
4228 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4231 // TODO: raise a dialog box here rather than bomb out.
4233 .println("The scores matrix does not match the alignment dimensions");
4237 // TODO add parameter to indicate if matching should be done
4238 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4240 alignPanel.fontChanged();
4241 tcoffeeColour.setEnabled(true);
4242 // switch to this color
4243 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4248 System.err.println("Problems resolving T-Coffee scores:");
4249 if (file.getWarningMessage() != null)
4251 System.err.println(file.getWarningMessage());
4257 public SplitFrame getSplitFrame()
4259 return this.splitFrame;
4262 public void setSplitFrame(SplitFrame sf)
4264 this.splitFrame = sf;
4267 // may not need this
4269 public void setShowSeqFeatures(boolean b)
4271 // showSeqFeatures.setSelected(b);
4272 viewport.setShowSequenceFeatures(b);
4277 public void setMenusForViewport()
4279 // setMenusFromViewport(viewport);
4284 public void refreshFeatureUI(boolean enableIfNecessary)
4286 if (enableIfNecessary)
4288 sequenceFeatures.setState(true);
4289 alignPanel.av.setShowSequenceFeatures(true);
4294 public FeatureSettingsControllerI getFeatureSettingsUI()
4296 return alignPanel.av.featureSettings;