2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureRenderer;
29 import jalview.api.FeatureSettingsControllerI;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.JalviewLite;
32 import jalview.commands.CommandI;
33 import jalview.commands.EditCommand;
34 import jalview.commands.EditCommand.Action;
35 import jalview.commands.OrderCommand;
36 import jalview.commands.RemoveGapColCommand;
37 import jalview.commands.RemoveGapsCommand;
38 import jalview.commands.SlideSequencesCommand;
39 import jalview.commands.TrimRegionCommand;
40 import jalview.datamodel.Alignment;
41 import jalview.datamodel.AlignmentAnnotation;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.AlignmentOrder;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.Sequence;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.io.AnnotationFile;
50 import jalview.io.AppletFormatAdapter;
51 import jalview.io.FeaturesFile;
52 import jalview.io.TCoffeeScoreFile;
53 import jalview.schemes.Blosum62ColourScheme;
54 import jalview.schemes.BuriedColourScheme;
55 import jalview.schemes.ClustalxColourScheme;
56 import jalview.schemes.ColourSchemeI;
57 import jalview.schemes.HelixColourScheme;
58 import jalview.schemes.HydrophobicColourScheme;
59 import jalview.schemes.NucleotideColourScheme;
60 import jalview.schemes.PIDColourScheme;
61 import jalview.schemes.PurinePyrimidineColourScheme;
62 import jalview.schemes.RNAHelicesColourChooser;
63 import jalview.schemes.StrandColourScheme;
64 import jalview.schemes.TCoffeeColourScheme;
65 import jalview.schemes.TaylorColourScheme;
66 import jalview.schemes.TurnColourScheme;
67 import jalview.schemes.ZappoColourScheme;
68 import jalview.structure.StructureSelectionManager;
69 import jalview.structures.models.AAStructureBindingModel;
70 import jalview.util.MappingUtils;
71 import jalview.util.MessageManager;
72 import jalview.viewmodel.AlignmentViewport;
74 import java.awt.BorderLayout;
75 import java.awt.Canvas;
76 import java.awt.CheckboxMenuItem;
77 import java.awt.Color;
78 import java.awt.FlowLayout;
80 import java.awt.FontMetrics;
81 import java.awt.Frame;
82 import java.awt.Graphics;
83 import java.awt.Label;
85 import java.awt.MenuBar;
86 import java.awt.MenuItem;
87 import java.awt.Panel;
88 import java.awt.event.ActionEvent;
89 import java.awt.event.ActionListener;
90 import java.awt.event.FocusEvent;
91 import java.awt.event.FocusListener;
92 import java.awt.event.ItemEvent;
93 import java.awt.event.ItemListener;
94 import java.awt.event.KeyEvent;
95 import java.awt.event.KeyListener;
96 import java.awt.event.WindowAdapter;
97 import java.awt.event.WindowEvent;
98 import java.io.IOException;
100 import java.net.URLEncoder;
101 import java.util.Arrays;
102 import java.util.Deque;
103 import java.util.HashMap;
104 import java.util.Hashtable;
105 import java.util.List;
106 import java.util.Map;
107 import java.util.StringTokenizer;
108 import java.util.Vector;
110 import org.jmol.viewer.Viewer;
112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
113 ItemListener, KeyListener, AlignViewControllerGuiI
115 public AlignViewControllerI avc;
117 public AlignmentPanel alignPanel;
119 public AlignViewport viewport;
121 // width and height may be overridden by applet parameters
122 int frameWidth = 700;
124 int frameHeight = 500;
126 String jalviewServletURL;
129 * Flag for showing autocalculated consensus above or below other consensus
132 private boolean showAutoCalculatedAbove;
134 private SequenceAnnotationOrder annotationSortOrder;
137 * Constructor that creates the frame and adds it to the display.
144 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
147 this(al, applet, title, embedded, true);
151 * Constructor that optionally allows the frame to be displayed or only
158 * @param addToDisplay
160 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
161 boolean embedded, boolean addToDisplay)
163 this(al, null, null, applet, title, embedded, addToDisplay);
166 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
167 ColumnSelection columnSelection, JalviewLite applet,
168 String title, boolean embedded)
170 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
173 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
174 ColumnSelection columnSelection, JalviewLite applet,
175 String title, boolean embedded, boolean addToDisplay)
179 jalviewServletURL = applet.getParameter("APPLICATION_URL");
185 } catch (Exception ex)
187 ex.printStackTrace();
189 // need to get window geometry before we calculate alignment layout
195 param = applet.getParameter("windowWidth");
198 int width = Integer.parseInt(param);
201 param = applet.getParameter("windowHeight");
204 int height = Integer.parseInt(param);
205 frameHeight = height;
207 } catch (Exception ex)
211 viewport = new AlignViewport(al, applet);
213 if (hiddenSeqs != null && hiddenSeqs.length > 0)
215 viewport.hideSequence(hiddenSeqs);
217 if (columnSelection != null)
219 viewport.setColumnSelection(columnSelection);
222 alignPanel = new AlignmentPanel(this, viewport);
223 avc = new jalview.controller.AlignViewController(this, viewport,
225 viewport.updateConservation(alignPanel);
226 viewport.updateConsensus(alignPanel);
228 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
229 followMouseOverFlag.setState(viewport.isFollowHighlight());
230 showGroupConsensus.setState(viewport.isShowGroupConsensus());
231 showGroupConservation.setState(viewport.isShowGroupConservation());
232 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
233 showSequenceLogo.setState(viewport.isShowSequenceLogo());
234 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
235 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
236 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
237 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
238 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
239 showAlignmentAnnotations.setState(true);
240 showSequenceAnnotations.setState(false);
242 seqLimits.setState(viewport.getShowJVSuffix());
246 String param = applet.getParameter("sortBy");
249 if (param.equalsIgnoreCase("Id"))
251 sortIDMenuItem_actionPerformed();
253 else if (param.equalsIgnoreCase("Pairwise Identity"))
255 sortPairwiseMenuItem_actionPerformed();
257 else if (param.equalsIgnoreCase("Length"))
259 sortLengthMenuItem_actionPerformed();
263 param = applet.getParameter("wrap");
266 if (param.equalsIgnoreCase("true"))
268 wrapMenuItem.setState(true);
269 wrapMenuItem_actionPerformed();
272 param = applet.getParameter("centrecolumnlabels");
275 centreColumnLabelFlag.setState(true);
276 centreColumnLabelFlag_stateChanged();
280 if (viewport.getAlignment().isNucleotide())
282 viewport.updateStrucConsensus(alignPanel);
283 if (viewport.getAlignment().hasRNAStructure())
285 RNAHelixColour.setEnabled(true);
289 RNAHelixColour.setEnabled(false);
294 RNAHelixColour.setEnabled(false);
295 purinePyrimidineColour.setEnabled(false);
297 // Some JVMS send keyevents to Top frame or lowest panel,
298 // Havent worked out why yet. So add to both this frame and seqCanvas for
300 this.addKeyListener(this);
301 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
302 alignPanel.idPanel.idCanvas.addKeyListener(this);
303 alignPanel.scalePanel.addKeyListener(this);
304 alignPanel.annotationPanel.addKeyListener(this);
305 alignPanel.annotationPanelHolder.addKeyListener(this);
306 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
307 alignPanel.alabels.addKeyListener(this);
309 setAnnotationsVisibility();
313 addToDisplay(embedded);
320 public void addToDisplay(boolean embedded)
322 createAlignFrameWindow(embedded);
324 alignPanel.adjustAnnotationHeight();
325 alignPanel.paintAlignment(true);
328 public AlignViewport getAlignViewport()
333 public SeqCanvas getSeqcanvas()
335 return alignPanel.seqPanel.seqCanvas;
339 * Load a features file onto the alignment
342 * file URL, content, or other resolvable path
344 * is protocol for accessing data referred to by file
347 public boolean parseFeaturesFile(String file, String type)
349 return parseFeaturesFile(file, type, true);
353 * Load a features file onto the alignment
356 * file URL, content, or other resolvable path
358 * is protocol for accessing data referred to by file
359 * @param autoenabledisplay
360 * when true, display features flag will be automatically enabled if
361 * features are loaded
362 * @return true if data parsed as a features file
364 public boolean parseFeaturesFile(String file, String type,
365 boolean autoenabledisplay)
367 // TODO: test if importing a features file onto an alignment which already
368 // has features with links overwrites the original links.
370 Hashtable featureLinks = new Hashtable();
371 boolean featuresFile = false;
374 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
375 .getAlignment(), alignPanel.seqPanel.seqCanvas
376 .getFeatureRenderer().getFeatureColours(), featureLinks,
377 true, viewport.applet.getDefaultParameter("relaxedidmatch",
379 } catch (Exception ex)
381 ex.printStackTrace();
386 if (featureLinks.size() > 0)
388 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
390 if (autoenabledisplay)
392 viewport.setShowSequenceFeatures(true);
393 sequenceFeatures.setState(true);
395 if (alignPanel.seqPanel.seqCanvas.fr != null)
397 // update the min/max ranges where necessary
398 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
400 if (viewport.featureSettings != null)
402 viewport.featureSettings.refreshTable();
404 alignPanel.paintAlignment(true);
405 statusBar.setText(MessageManager
406 .getString("label.successfully_added_features_alignment"));
412 public void keyPressed(KeyEvent evt)
414 if (viewport.cursorMode
415 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
416 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
417 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
418 && Character.isDigit(evt.getKeyChar()))
420 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
423 switch (evt.getKeyCode())
425 case 27: // escape key
426 deselectAllSequenceMenuItem_actionPerformed();
428 alignPanel.alabels.cancelDrag();
431 if (evt.isControlDown() || evt.isMetaDown())
433 cut_actionPerformed();
437 if (viewport.cursorMode && !evt.isControlDown())
439 alignPanel.seqPanel.setCursorColumn();
441 if (evt.isControlDown() || evt.isMetaDown())
443 copy_actionPerformed();
447 if (evt.isControlDown())
449 paste(evt.isShiftDown());
453 if (evt.isControlDown() || evt.isMetaDown())
455 selectAllSequenceMenuItem_actionPerformed();
458 case KeyEvent.VK_DOWN:
459 if (viewport.cursorMode)
461 alignPanel.seqPanel.moveCursor(0, 1);
465 moveSelectedSequences(false);
470 if (viewport.cursorMode)
472 alignPanel.seqPanel.moveCursor(0, -1);
476 moveSelectedSequences(true);
480 case KeyEvent.VK_LEFT:
481 if (evt.isAltDown() || !viewport.cursorMode)
483 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
487 alignPanel.seqPanel.moveCursor(-1, 0);
491 case KeyEvent.VK_RIGHT:
492 if (evt.isAltDown() || !viewport.cursorMode)
494 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
498 alignPanel.seqPanel.moveCursor(1, 0);
502 case KeyEvent.VK_SPACE:
503 if (viewport.cursorMode)
505 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
506 || evt.isShiftDown() || evt.isAltDown());
510 case KeyEvent.VK_DELETE:
511 case KeyEvent.VK_BACK_SPACE:
512 if (viewport.cursorMode)
514 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
515 || evt.isShiftDown() || evt.isAltDown());
519 cut_actionPerformed();
520 alignPanel.seqPanel.seqCanvas.repaint();
525 if (viewport.cursorMode)
527 alignPanel.seqPanel.setCursorRow();
531 if (viewport.cursorMode)
533 alignPanel.seqPanel.setCursorPosition();
537 case KeyEvent.VK_ENTER:
538 case KeyEvent.VK_COMMA:
539 if (viewport.cursorMode)
541 alignPanel.seqPanel.setCursorRowAndColumn();
546 if (viewport.cursorMode)
548 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
552 if (viewport.cursorMode)
554 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
559 viewport.cursorMode = !viewport.cursorMode;
560 statusBar.setText(MessageManager.formatMessage(
561 "label.keyboard_editing_mode",
562 new String[] { (viewport.cursorMode ? "on" : "off") }));
563 if (viewport.cursorMode)
565 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
566 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
571 if (evt.isControlDown())
573 findMenuItem_actionPerformed();
579 boolean toggleSeqs = !evt.isControlDown();
580 boolean toggleCols = !evt.isShiftDown();
581 toggleHiddenRegions(toggleSeqs, toggleCols);
585 case KeyEvent.VK_PAGE_UP:
586 if (viewport.getWrapAlignment())
588 alignPanel.scrollUp(true);
592 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
593 - viewport.endSeq + viewport.startSeq);
597 case KeyEvent.VK_PAGE_DOWN:
598 if (viewport.getWrapAlignment())
600 alignPanel.scrollUp(false);
604 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
605 + viewport.endSeq - viewport.startSeq);
610 if (evt.isControlDown())
612 undoMenuItem_actionPerformed();
617 if (evt.isControlDown())
619 redoMenuItem_actionPerformed();
624 if (evt.isControlDown())
631 if (evt.isControlDown())
633 trimAlignment(false);
638 if (evt.isControlDown())
640 if (evt.isShiftDown())
642 this.removeAllGapsMenuItem_actionPerformed();
646 removeGappedColumnMenuItem_actionPerformed();
651 if (evt.isControlDown())
655 invertColSel_actionPerformed();
659 invertSequenceMenuItem_actionPerformed();
665 if (evt.isControlDown())
667 if (evt.isShiftDown())
669 this.unGroup_actionPerformed();
673 this.createGroup_actionPerformed();
679 if (evt.isControlDown())
681 this.deleteGroups_actionPerformed();
686 if (evt.isControlDown())
693 alignPanel.paintAlignment(true);
697 * called by key handler and the hide all/show all menu items
702 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
704 boolean hide = false;
705 SequenceGroup sg = viewport.getSelectionGroup();
706 if (!toggleSeqs && !toggleCols)
708 // Hide everything by the current selection - this is a hack - we do the
709 // invert and then hide
710 // first check that there will be visible columns after the invert.
711 if ((viewport.getColumnSelection() != null
712 && viewport.getColumnSelection().getSelected() != null && viewport
713 .getColumnSelection().getSelected().size() > 0)
714 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
717 // now invert the sequence set, if required - empty selection implies
718 // that no hiding is required.
721 invertSequenceMenuItem_actionPerformed();
722 sg = viewport.getSelectionGroup();
726 viewport.expandColSelection(sg, true);
727 // finally invert the column selection and get the new sequence
728 // selection and indicate it should be hidden.
729 invertColSel_actionPerformed();
736 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
739 viewport.hideAllSelectedSeqs();
741 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
744 viewport.showAllHiddenSeqs();
750 if (viewport.getColumnSelection().getSelected().size() > 0)
752 viewport.hideSelectedColumns();
755 viewport.setSelectionGroup(sg);
760 viewport.showAllHiddenColumns();
766 public void keyReleased(KeyEvent evt)
771 public void keyTyped(KeyEvent evt)
776 public void itemStateChanged(ItemEvent evt)
778 final Object source = evt.getSource();
779 if (source == displayNonconservedMenuItem)
781 displayNonconservedMenuItem_actionPerformed();
783 else if (source == colourTextMenuItem)
785 colourTextMenuItem_actionPerformed();
787 else if (source == wrapMenuItem)
789 wrapMenuItem_actionPerformed();
791 else if (source == scaleAbove)
793 viewport.setScaleAboveWrapped(scaleAbove.getState());
795 else if (source == scaleLeft)
797 viewport.setScaleLeftWrapped(scaleLeft.getState());
799 else if (source == scaleRight)
801 viewport.setScaleRightWrapped(scaleRight.getState());
803 else if (source == seqLimits)
805 seqLimits_itemStateChanged();
807 else if (source == viewBoxesMenuItem)
809 viewport.setShowBoxes(viewBoxesMenuItem.getState());
811 else if (source == viewTextMenuItem)
813 viewport.setShowText(viewTextMenuItem.getState());
815 else if (source == renderGapsMenuItem)
817 viewport.setRenderGaps(renderGapsMenuItem.getState());
819 else if (source == annotationPanelMenuItem)
821 boolean showAnnotations = annotationPanelMenuItem.getState();
822 showAlignmentAnnotations.setEnabled(showAnnotations);
823 showSequenceAnnotations.setEnabled(showAnnotations);
824 viewport.setShowAnnotation(showAnnotations);
825 alignPanel.setAnnotationVisible(showAnnotations);
827 else if (source == sequenceFeatures)
829 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
830 alignPanel.seqPanel.seqCanvas.repaint();
832 else if (source == showAlignmentAnnotations)
834 setAnnotationsVisibility();
836 else if (source == showSequenceAnnotations)
838 setAnnotationsVisibility();
840 else if (source == sortAnnBySequence)
842 boolean newState = sortAnnBySequence.getState();
843 sortAnnByLabel.setState(false);
844 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
845 : SequenceAnnotationOrder.NONE);
846 setViewportAnnotationOrder();
848 else if (source == sortAnnByLabel)
850 boolean newState = sortAnnByLabel.getState();
851 sortAnnBySequence.setState(false);
852 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
853 : SequenceAnnotationOrder.NONE);
854 setViewportAnnotationOrder();
856 else if (source == showAutoFirst)
858 showAutoLast.setState(!showAutoFirst.getState());
859 setShowAutoCalculatedAbove(showAutoFirst.getState());
860 setViewportAnnotationOrder();
862 else if (source == showAutoLast)
864 showAutoFirst.setState(!showAutoLast.getState());
865 setShowAutoCalculatedAbove(showAutoFirst.getState());
866 setViewportAnnotationOrder();
868 else if (source == conservationMenuItem)
870 conservationMenuItem_actionPerformed();
872 else if (source == abovePIDThreshold)
874 abovePIDThreshold_actionPerformed();
876 else if (source == applyToAllGroups)
878 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
880 else if (source == autoCalculate)
882 viewport.autoCalculateConsensus = autoCalculate.getState();
884 else if (source == sortByTree)
886 viewport.sortByTree = sortByTree.getState();
888 else if (source == this.centreColumnLabelFlag)
890 centreColumnLabelFlag_stateChanged();
892 else if (source == this.followMouseOverFlag)
894 mouseOverFlag_stateChanged();
896 else if (source == showGroupConsensus)
898 showGroupConsensus_actionPerformed();
900 else if (source == showGroupConservation)
902 showGroupConservation_actionPerformed();
904 else if (source == showSequenceLogo)
906 showSequenceLogo_actionPerformed();
908 else if (source == normSequenceLogo)
910 normSequenceLogo_actionPerformed();
912 else if (source == showConsensusHistogram)
914 showConsensusHistogram_actionPerformed();
916 else if (source == applyAutoAnnotationSettings)
918 applyAutoAnnotationSettings_actionPerformed();
920 alignPanel.paintAlignment(true);
924 * Set the visibility state of sequence-related and/or alignment-related
925 * annotations depending on checkbox selections, and repaint.
929 private void setAnnotationsVisibility()
931 boolean showForAlignment = showAlignmentAnnotations.getState();
932 boolean showForSequences = showSequenceAnnotations.getState();
933 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
935 for (AlignmentAnnotation aa : alignPanel.getAlignment()
936 .getAlignmentAnnotation())
938 boolean visible = (aa.sequenceRef == null ? showForAlignment
940 aa.visible = visible;
943 alignPanel.validateAnnotationDimensions(true);
948 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
950 this.annotationSortOrder = order;
954 * Set flags on the viewport that control annotation ordering
956 private void setViewportAnnotationOrder()
958 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
960 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
963 private void setShowAutoCalculatedAbove(boolean showAbove)
965 this.showAutoCalculatedAbove = showAbove;
968 private void mouseOverFlag_stateChanged()
970 viewport.setFollowHighlight(followMouseOverFlag.getState());
971 // TODO: could kick the scrollTo mechanism to reset view for current
975 private void centreColumnLabelFlag_stateChanged()
977 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
978 this.alignPanel.annotationPanel.repaint();
982 public void actionPerformed(ActionEvent evt)
984 viewport.applet.currentAlignFrame = this;
986 Object source = evt.getSource();
988 if (source == inputText)
990 inputText_actionPerformed();
992 else if (source == loadTree)
994 loadTree_actionPerformed();
996 else if (source == loadApplication)
998 launchFullApplication();
1000 else if (source == loadAnnotations)
1004 else if (source == outputAnnotations)
1006 outputAnnotations(true);
1008 else if (source == outputFeatures)
1010 outputFeatures(true, "Jalview");
1012 else if (source == closeMenuItem)
1014 closeMenuItem_actionPerformed();
1016 else if (source == copy)
1018 copy_actionPerformed();
1020 else if (source == undoMenuItem)
1022 undoMenuItem_actionPerformed();
1024 else if (source == redoMenuItem)
1026 redoMenuItem_actionPerformed();
1028 else if (source == inputText)
1030 inputText_actionPerformed();
1032 else if (source == closeMenuItem)
1034 closeMenuItem_actionPerformed();
1036 else if (source == undoMenuItem)
1038 undoMenuItem_actionPerformed();
1040 else if (source == redoMenuItem)
1042 redoMenuItem_actionPerformed();
1044 else if (source == copy)
1046 copy_actionPerformed();
1048 else if (source == pasteNew)
1050 pasteNew_actionPerformed();
1052 else if (source == pasteThis)
1054 pasteThis_actionPerformed();
1056 else if (source == cut)
1058 cut_actionPerformed();
1060 else if (source == delete)
1062 delete_actionPerformed();
1064 else if (source == grpsFromSelection)
1066 makeGrpsFromSelection_actionPerformed();
1068 else if (source == deleteGroups)
1070 deleteGroups_actionPerformed();
1072 else if (source == selectAllSequenceMenuItem)
1074 selectAllSequenceMenuItem_actionPerformed();
1076 else if (source == deselectAllSequenceMenuItem)
1078 deselectAllSequenceMenuItem_actionPerformed();
1080 else if (source == invertSequenceMenuItem)
1082 invertSequenceMenuItem_actionPerformed();
1084 else if (source == invertColSel)
1086 viewport.invertColumnSelection();
1087 alignPanel.paintAlignment(true);
1089 else if (source == remove2LeftMenuItem)
1091 trimAlignment(true);
1093 else if (source == remove2RightMenuItem)
1095 trimAlignment(false);
1097 else if (source == removeGappedColumnMenuItem)
1099 removeGappedColumnMenuItem_actionPerformed();
1101 else if (source == removeAllGapsMenuItem)
1103 removeAllGapsMenuItem_actionPerformed();
1105 else if (source == findMenuItem)
1107 findMenuItem_actionPerformed();
1109 else if (source == font)
1111 new FontChooser(alignPanel);
1113 else if (source == newView)
1117 else if (source == showColumns)
1119 viewport.showAllHiddenColumns();
1120 alignPanel.paintAlignment(true);
1122 else if (source == showSeqs)
1124 viewport.showAllHiddenSeqs();
1125 alignPanel.paintAlignment(true);
1127 else if (source == hideColumns)
1129 viewport.hideSelectedColumns();
1130 alignPanel.paintAlignment(true);
1132 else if (source == hideSequences
1133 && viewport.getSelectionGroup() != null)
1135 viewport.hideAllSelectedSeqs();
1136 alignPanel.paintAlignment(true);
1138 else if (source == hideAllButSelection)
1140 toggleHiddenRegions(false, false);
1141 alignPanel.paintAlignment(true);
1143 else if (source == hideAllSelection)
1145 SequenceGroup sg = viewport.getSelectionGroup();
1146 viewport.expandColSelection(sg, false);
1147 viewport.hideAllSelectedSeqs();
1148 viewport.hideSelectedColumns();
1149 alignPanel.paintAlignment(true);
1151 else if (source == showAllHidden)
1153 viewport.showAllHiddenColumns();
1154 viewport.showAllHiddenSeqs();
1155 alignPanel.paintAlignment(true);
1157 else if (source == showGroupConsensus)
1159 showGroupConsensus_actionPerformed();
1161 else if (source == showGroupConservation)
1163 showGroupConservation_actionPerformed();
1165 else if (source == showSequenceLogo)
1167 showSequenceLogo_actionPerformed();
1169 else if (source == normSequenceLogo)
1171 normSequenceLogo_actionPerformed();
1173 else if (source == showConsensusHistogram)
1175 showConsensusHistogram_actionPerformed();
1177 else if (source == applyAutoAnnotationSettings)
1179 applyAutoAnnotationSettings_actionPerformed();
1181 else if (source == featureSettings)
1183 new FeatureSettings(alignPanel);
1185 else if (source == alProperties)
1187 StringBuffer contents = new jalview.io.AlignmentProperties(
1188 viewport.getAlignment()).formatAsString();
1189 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1190 cap.setText(contents.toString());
1191 Frame frame = new Frame();
1193 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1194 "label.alignment_properties", new String[] { getTitle() }),
1197 else if (source == overviewMenuItem)
1199 overviewMenuItem_actionPerformed();
1201 else if (source == noColourmenuItem)
1205 else if (source == clustalColour)
1207 abovePIDThreshold.setState(false);
1208 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1210 else if (source == zappoColour)
1212 changeColour(new ZappoColourScheme());
1214 else if (source == taylorColour)
1216 changeColour(new TaylorColourScheme());
1218 else if (source == hydrophobicityColour)
1220 changeColour(new HydrophobicColourScheme());
1222 else if (source == helixColour)
1224 changeColour(new HelixColourScheme());
1226 else if (source == strandColour)
1228 changeColour(new StrandColourScheme());
1230 else if (source == turnColour)
1232 changeColour(new TurnColourScheme());
1234 else if (source == buriedColour)
1236 changeColour(new BuriedColourScheme());
1238 else if (source == nucleotideColour)
1240 changeColour(new NucleotideColourScheme());
1242 else if (source == purinePyrimidineColour)
1244 changeColour(new PurinePyrimidineColourScheme());
1246 // else if (source == RNAInteractionColour)
1248 // changeColour(new RNAInteractionColourScheme());
1250 else if (source == RNAHelixColour)
1252 new RNAHelicesColourChooser(viewport, alignPanel);
1254 else if (source == modifyPID)
1256 modifyPID_actionPerformed();
1258 else if (source == modifyConservation)
1260 modifyConservation_actionPerformed();
1262 else if (source == userDefinedColour)
1264 new UserDefinedColours(alignPanel, null);
1266 else if (source == PIDColour)
1268 changeColour(new PIDColourScheme());
1270 else if (source == BLOSUM62Colour)
1272 changeColour(new Blosum62ColourScheme());
1274 else if (source == tcoffeeColour)
1276 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1278 else if (source == annotationColour)
1280 new AnnotationColourChooser(viewport, alignPanel);
1282 else if (source == annotationColumnSelection)
1284 new AnnotationColumnChooser(viewport, alignPanel);
1286 else if (source == sortPairwiseMenuItem)
1288 sortPairwiseMenuItem_actionPerformed();
1290 else if (source == sortIDMenuItem)
1292 sortIDMenuItem_actionPerformed();
1294 else if (source == sortLengthMenuItem)
1296 sortLengthMenuItem_actionPerformed();
1298 else if (source == sortGroupMenuItem)
1300 sortGroupMenuItem_actionPerformed();
1302 else if (source == removeRedundancyMenuItem)
1304 removeRedundancyMenuItem_actionPerformed();
1306 else if (source == pairwiseAlignmentMenuItem)
1308 pairwiseAlignmentMenuItem_actionPerformed();
1310 else if (source == PCAMenuItem)
1312 PCAMenuItem_actionPerformed();
1314 else if (source == averageDistanceTreeMenuItem)
1316 averageDistanceTreeMenuItem_actionPerformed();
1318 else if (source == neighbourTreeMenuItem)
1320 neighbourTreeMenuItem_actionPerformed();
1322 else if (source == njTreeBlosumMenuItem)
1324 njTreeBlosumMenuItem_actionPerformed();
1326 else if (source == avDistanceTreeBlosumMenuItem)
1328 avTreeBlosumMenuItem_actionPerformed();
1330 else if (source == documentation)
1332 documentation_actionPerformed();
1334 else if (source == about)
1336 about_actionPerformed();
1341 public void inputText_actionPerformed()
1343 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1344 Frame frame = new Frame();
1346 jalview.bin.JalviewLite.addFrame(frame,
1347 MessageManager.getString("label.input_cut_paste"), 500, 500);
1350 protected void outputText_actionPerformed(ActionEvent e)
1352 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1353 Frame frame = new Frame();
1355 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1356 "label.alignment_output_command",
1357 new Object[] { e.getActionCommand() }), 600, 500);
1359 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1360 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1361 e.getActionCommand(), viewport.getAlignment(),
1362 viewport.getShowJVSuffix()));
1365 public void loadAnnotations()
1367 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1368 cap.setText(MessageManager
1369 .getString("label.paste_features_annotations_Tcoffee_here"));
1370 cap.setAnnotationImport();
1371 Frame frame = new Frame();
1373 jalview.bin.JalviewLite.addFrame(frame,
1374 MessageManager.getString("action.paste_annotations"), 400, 300);
1378 public String outputAnnotations(boolean displayTextbox)
1380 String annotation = new AnnotationFile()
1381 .printAnnotationsForView(viewport);
1385 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1386 Frame frame = new Frame();
1388 jalview.bin.JalviewLite.addFrame(frame,
1389 MessageManager.getString("label.annotations"), 600, 500);
1390 cap.setText(annotation);
1396 private Map<String, Object> getDisplayedFeatureCols()
1398 if (alignPanel.getFeatureRenderer() != null
1399 && viewport.getFeaturesDisplayed() != null)
1401 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1407 public String outputFeatures(boolean displayTextbox, String format)
1410 if (format.equalsIgnoreCase("Jalview"))
1412 features = new FeaturesFile().printJalviewFormat(viewport
1413 .getAlignment().getSequencesArray(),
1414 getDisplayedFeatureCols());
1418 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1419 .getSequencesArray(), getDisplayedFeatureCols());
1424 boolean frimport = false;
1425 if (features == null || features.equals("No Features Visible"))
1427 features = "# No features visible - paste some and import them here.";
1431 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1434 cap.setAnnotationImport();
1436 Frame frame = new Frame();
1438 jalview.bin.JalviewLite.addFrame(frame,
1439 MessageManager.getString("label.features"), 600, 500);
1440 cap.setText(features);
1444 if (features == null)
1453 void launchFullApplication()
1455 StringBuffer url = new StringBuffer(jalviewServletURL);
1457 // allow servlet parameters to be passed in applet parameter
1458 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1460 url.append(firstSep);
1463 + appendProtocol(viewport.applet.getParameter("file")));
1465 if (viewport.applet.getParameter("features") != null)
1467 url.append("&features=");
1468 url.append(appendProtocol(viewport.applet.getParameter("features")));
1471 if (viewport.applet.getParameter("annotations") != null)
1473 url.append("&annotations=");
1474 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1477 if (viewport.applet.getParameter("jnetfile") != null)
1479 url.append("&annotations=");
1480 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1483 if (viewport.applet.getParameter("defaultColour") != null)
1485 url.append("&colour="
1486 + removeWhiteSpace(viewport.applet
1487 .getParameter("defaultColour")));
1490 if (viewport.applet.getParameter("userDefinedColour") != null)
1492 url.append("&colour="
1493 + removeWhiteSpace(viewport.applet
1494 .getParameter("userDefinedColour")));
1496 if (viewport.applet.getParameter("tree") != null)
1499 + appendProtocol(viewport.applet.getParameter("tree")));
1501 if (viewport.applet.getParameter("treeFile") != null)
1504 + appendProtocol(viewport.applet.getParameter("treeFile")));
1507 showURL(url.toString(), "FULL_APP");
1510 String removeWhiteSpace(String colour)
1512 StringBuffer sb = new StringBuffer();
1513 for (int i = 0; i < colour.length(); i++)
1515 if (Character.isWhitespace(colour.charAt(i)))
1521 sb.append(colour.charAt(i));
1525 return sb.toString();
1528 String appendProtocol(String url)
1533 url = URLEncoder.encode(url);
1536 * When we finally deprecate 1.1 compatibility, we can start to use
1537 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1538 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1539 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1540 * ex.printStackTrace(); }
1542 catch (java.net.MalformedURLException ex)
1544 url = viewport.applet.getCodeBase() + url;
1549 public void closeMenuItem_actionPerformed()
1551 PaintRefresher.RemoveComponent(alignPanel);
1552 if (alignPanel.seqPanel != null
1553 && alignPanel.seqPanel.seqCanvas != null)
1555 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1557 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1559 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1562 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1577 void updateEditMenuBar()
1580 if (viewport.getHistoryList().size() > 0)
1582 undoMenuItem.setEnabled(true);
1583 CommandI command = viewport.getHistoryList().peek();
1584 undoMenuItem.setLabel(MessageManager.formatMessage(
1585 "label.undo_command",
1586 new Object[] { command.getDescription() }));
1590 undoMenuItem.setEnabled(false);
1591 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1594 if (viewport.getRedoList().size() > 0)
1596 redoMenuItem.setEnabled(true);
1598 CommandI command = viewport.getRedoList().peek();
1599 redoMenuItem.setLabel(MessageManager.formatMessage(
1600 "label.redo_command",
1601 new Object[] { command.getDescription() }));
1605 redoMenuItem.setEnabled(false);
1606 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1614 public void addHistoryItem(CommandI command)
1616 if (command.getSize() > 0)
1618 viewport.addToHistoryList(command);
1619 viewport.clearRedoList();
1620 updateEditMenuBar();
1621 viewport.updateHiddenColumns();
1626 * TODO: JAL-1104 DOCUMENT ME!
1631 protected void undoMenuItem_actionPerformed()
1633 if (viewport.getHistoryList().isEmpty())
1638 CommandI command = viewport.getHistoryList().pop();
1639 viewport.addToRedoList(command);
1640 command.undoCommand(null);
1642 AlignmentViewport originalSource = getOriginatingSource(command);
1644 if (originalSource != viewport)
1647 .println("Warning: Viewport object mismatch whilst undoing");
1649 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1650 // viewport.getColumnSelection().getHiddenColumns()
1652 updateEditMenuBar();
1653 originalSource.firePropertyChange("alignment", null, originalSource
1654 .getAlignment().getSequences());
1658 * TODO: JAL-1104 DOCUMENT ME!
1663 protected void redoMenuItem_actionPerformed()
1665 if (viewport.getRedoList().isEmpty())
1670 CommandI command = viewport.getRedoList().pop();
1671 viewport.addToHistoryList(command);
1672 command.doCommand(null);
1674 AlignmentViewport originalSource = getOriginatingSource(command);
1676 if (originalSource != viewport)
1679 .println("Warning: Viewport object mismatch whilst re-doing");
1681 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1682 // viewport.getColumnSelection().getHiddenColumns()
1685 updateEditMenuBar();
1686 originalSource.firePropertyChange("alignment", null, originalSource
1687 .getAlignment().getSequences());
1690 AlignmentViewport getOriginatingSource(CommandI command)
1692 AlignmentViewport originalSource = null;
1693 // For sequence removal and addition, we need to fire
1694 // the property change event FROM the viewport where the
1695 // original alignment was altered
1696 AlignmentI al = null;
1697 if (command instanceof EditCommand)
1699 EditCommand editCommand = (EditCommand) command;
1700 al = editCommand.getAlignment();
1701 Vector comps = (Vector) PaintRefresher.components.get(viewport
1702 .getSequenceSetId());
1703 for (int i = 0; i < comps.size(); i++)
1705 if (comps.elementAt(i) instanceof AlignmentPanel)
1707 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1709 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1716 if (originalSource == null)
1718 // The original view is closed, we must validate
1719 // the current view against the closed view first
1722 PaintRefresher.validateSequences(al, viewport.getAlignment());
1725 originalSource = viewport;
1728 return originalSource;
1732 * Move the currently selected sequences up or down one position in the
1737 public void moveSelectedSequences(boolean up)
1739 SequenceGroup sg = viewport.getSelectionGroup();
1744 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1745 up ? null : viewport.getHiddenRepSequences(), up);
1746 alignPanel.paintAlignment(true);
1749 * Also move cDNA/protein complement sequences
1751 AlignViewportI complement = viewport.getCodingComplement();
1752 if (complement != null)
1754 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1755 viewport, complement);
1756 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1757 up ? null : complement.getHiddenRepSequences(), up);
1758 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1762 synchronized void slideSequences(boolean right, int size)
1764 List<SequenceI> sg = new Vector<SequenceI>();
1765 if (viewport.cursorMode)
1767 sg.add(viewport.getAlignment().getSequenceAt(
1768 alignPanel.seqPanel.seqCanvas.cursorY));
1770 else if (viewport.getSelectionGroup() != null
1771 && viewport.getSelectionGroup().getSize() != viewport
1772 .getAlignment().getHeight())
1774 sg = viewport.getSelectionGroup().getSequences(
1775 viewport.getHiddenRepSequences());
1783 Vector<SequenceI> invertGroup = new Vector();
1785 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1787 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1789 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1793 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1795 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1797 for (int i = 0; i < invertGroup.size(); i++)
1799 seqs2[i] = invertGroup.elementAt(i);
1802 SlideSequencesCommand ssc;
1805 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1806 size, viewport.getGapCharacter());
1810 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1811 size, viewport.getGapCharacter());
1814 int groupAdjustment = 0;
1815 if (ssc.getGapsInsertedBegin() && right)
1817 if (viewport.cursorMode)
1819 alignPanel.seqPanel.moveCursor(size, 0);
1823 groupAdjustment = size;
1826 else if (!ssc.getGapsInsertedBegin() && !right)
1828 if (viewport.cursorMode)
1830 alignPanel.seqPanel.moveCursor(-size, 0);
1834 groupAdjustment = -size;
1838 if (groupAdjustment != 0)
1840 viewport.getSelectionGroup().setStartRes(
1841 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1842 viewport.getSelectionGroup().setEndRes(
1843 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1846 boolean appendHistoryItem = false;
1847 Deque<CommandI> historyList = viewport.getHistoryList();
1848 if (historyList != null && historyList.size() > 0
1849 && historyList.peek() instanceof SlideSequencesCommand)
1851 appendHistoryItem = ssc
1852 .appendSlideCommand((SlideSequencesCommand) historyList
1856 if (!appendHistoryItem)
1858 addHistoryItem(ssc);
1864 static StringBuffer copiedSequences;
1866 static Vector copiedHiddenColumns;
1868 protected void copy_actionPerformed()
1870 if (viewport.getSelectionGroup() == null)
1875 SequenceGroup sg = viewport.getSelectionGroup();
1876 copiedSequences = new StringBuffer();
1877 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1878 for (int i = 0; i < sg.getSize(); i++)
1880 SequenceI seq = sg.getSequenceAt(i);
1881 int index = viewport.getAlignment().findIndex(seq);
1882 orderedSeqs.put(index, seq);
1885 int index = 0, startRes, endRes;
1888 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1890 copiedHiddenColumns = new Vector();
1891 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1892 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1894 copiedHiddenColumns.addElement(new int[] {
1895 region[0] - hiddenOffset, region[1] - hiddenOffset });
1900 copiedHiddenColumns = null;
1903 for (int i = 0; i < sg.getSize(); i++)
1905 SequenceI seq = null;
1909 if (orderedSeqs.containsKey(index))
1911 seq = orderedSeqs.get(index);
1922 // Returns residue following index if gap
1923 startRes = seq.findPosition(sg.getStartRes());
1926 // Need to find the residue preceeding index if gap
1929 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1931 ch = seq.getCharAt(j);
1932 if (!jalview.util.Comparison.isGap((ch)))
1940 endRes += seq.getStart() - 1;
1943 copiedSequences.append(seq.getName()
1949 + seq.getSequenceAsString(sg.getStartRes(),
1950 sg.getEndRes() + 1) + "\n");
1955 protected void pasteNew_actionPerformed()
1960 protected void pasteThis_actionPerformed()
1965 void paste(boolean newAlignment)
1970 if (copiedSequences == null)
1975 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1976 Vector seqs = new Vector();
1977 while (st.hasMoreElements())
1979 String name = st.nextToken();
1980 int start = Integer.parseInt(st.nextToken());
1981 int end = Integer.parseInt(st.nextToken());
1982 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1984 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1985 for (int i = 0; i < seqs.size(); i++)
1987 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1992 String newtitle = MessageManager
1993 .getString("label.copied_sequences");
1994 if (getTitle().startsWith(
1995 MessageManager.getString("label.copied_sequences")))
1997 newtitle = getTitle();
2001 newtitle = newtitle.concat(MessageManager.formatMessage(
2002 "label.from_msname", new String[] { getTitle() }));
2004 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2005 viewport.applet, newtitle, false);
2006 if (copiedHiddenColumns != null)
2008 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2010 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2011 af.viewport.hideColumns(region[0], region[1]);
2015 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2020 addSequences(newSeqs);
2023 } catch (Exception ex)
2025 } // could be anything being pasted in here
2029 void addSequences(SequenceI[] seqs)
2031 for (int i = 0; i < seqs.length; i++)
2033 viewport.getAlignment().addSequence(seqs[i]);
2037 addHistoryItem(new EditCommand(
2038 MessageManager.getString("label.add_sequences"), Action.PASTE,
2039 seqs, 0, viewport.getAlignment().getWidth(),
2040 viewport.getAlignment()));
2042 viewport.setEndSeq(viewport.getAlignment().getHeight());
2043 viewport.getAlignment().getWidth();
2044 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2049 protected void cut_actionPerformed()
2051 copy_actionPerformed();
2052 delete_actionPerformed();
2055 protected void delete_actionPerformed()
2058 SequenceGroup sg = viewport.getSelectionGroup();
2064 Vector seqs = new Vector();
2066 for (int i = 0; i < sg.getSize(); i++)
2068 seq = sg.getSequenceAt(i);
2069 seqs.addElement(seq);
2073 * If the cut affects all sequences, warn, remove highlighted columns
2075 if (sg.getSize() == viewport.getAlignment().getHeight())
2077 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2078 .getAlignment().getWidth()) ? true : false;
2079 if (isEntireAlignWidth)
2081 String title = MessageManager.getString("label.delete_all");
2082 Panel infoPanel = new Panel();
2083 infoPanel.setLayout(new FlowLayout());
2085 .add(new Label(MessageManager.getString("warn.delete_all")));
2087 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2088 dialog.setMainPanel(infoPanel);
2089 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2090 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2091 dialog.setVisible(true);
2098 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2099 sg.getEndRes() + 1);
2102 SequenceI[] cut = new SequenceI[seqs.size()];
2103 for (int i = 0; i < seqs.size(); i++)
2105 cut[i] = (SequenceI) seqs.elementAt(i);
2109 * //ADD HISTORY ITEM
2111 addHistoryItem(new EditCommand(
2112 MessageManager.getString("label.cut_sequences"), Action.CUT,
2113 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2114 viewport.getAlignment()));
2116 viewport.setSelectionGroup(null);
2117 viewport.getAlignment().deleteGroup(sg);
2119 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2122 if (viewport.getAlignment().getHeight() < 1)
2124 this.setVisible(false);
2126 viewport.sendSelection();
2130 * group consensus toggled
2133 protected void showGroupConsensus_actionPerformed()
2135 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2136 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2141 * group conservation toggled.
2143 protected void showGroupConservation_actionPerformed()
2145 viewport.setShowGroupConservation(showGroupConservation.getState());
2146 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2153 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2154 * .event.ActionEvent)
2156 protected void showConsensusHistogram_actionPerformed()
2158 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2159 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2166 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2167 * .event.ActionEvent)
2169 protected void showSequenceLogo_actionPerformed()
2171 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2172 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175 protected void normSequenceLogo_actionPerformed()
2177 showSequenceLogo.setState(true);
2178 viewport.setShowSequenceLogo(true);
2179 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2180 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183 protected void applyAutoAnnotationSettings_actionPerformed()
2185 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188 protected void makeGrpsFromSelection_actionPerformed()
2190 if (avc.makeGroupsFromSelection())
2192 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2193 alignPanel.updateAnnotation();
2194 alignPanel.paintAlignment(true);
2198 protected void createGroup_actionPerformed()
2203 protected void unGroup_actionPerformed()
2207 alignPanel.alignmentChanged();
2211 protected void deleteGroups_actionPerformed()
2213 if (avc.deleteGroups())
2215 alignPanel.alignmentChanged();
2219 public void selectAllSequenceMenuItem_actionPerformed()
2221 SequenceGroup sg = new SequenceGroup();
2222 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2224 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2226 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2227 viewport.setSelectionGroup(sg);
2228 alignPanel.paintAlignment(true);
2229 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2230 viewport.sendSelection();
2233 public void deselectAllSequenceMenuItem_actionPerformed()
2235 if (viewport.cursorMode)
2237 alignPanel.seqPanel.keyboardNo1 = null;
2238 alignPanel.seqPanel.keyboardNo2 = null;
2240 viewport.setSelectionGroup(null);
2241 viewport.getColumnSelection().clear();
2242 viewport.setSelectionGroup(null);
2243 alignPanel.idPanel.idCanvas.searchResults = null;
2244 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2245 alignPanel.paintAlignment(true);
2246 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2247 viewport.sendSelection();
2250 public void invertSequenceMenuItem_actionPerformed()
2252 SequenceGroup sg = viewport.getSelectionGroup();
2253 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2255 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2258 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2259 viewport.sendSelection();
2262 public void invertColSel_actionPerformed()
2264 viewport.invertColumnSelection();
2265 alignPanel.paintAlignment(true);
2266 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2267 viewport.sendSelection();
2270 void trimAlignment(boolean trimLeft)
2272 ColumnSelection colSel = viewport.getColumnSelection();
2275 if (!colSel.isEmpty())
2279 column = colSel.getMin();
2283 column = colSel.getMax();
2287 if (viewport.getSelectionGroup() != null)
2289 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2290 viewport.getHiddenRepSequences());
2294 seqs = viewport.getAlignment().getSequencesArray();
2297 TrimRegionCommand trimRegion;
2300 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2301 column, viewport.getAlignment());
2302 viewport.setStartRes(0);
2306 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2307 column, viewport.getAlignment());
2310 statusBar.setText(MessageManager.formatMessage(
2311 "label.removed_columns",
2312 new String[] { Integer.valueOf(trimRegion.getSize())
2314 addHistoryItem(trimRegion);
2316 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2318 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2319 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2321 viewport.getAlignment().deleteGroup(sg);
2325 viewport.firePropertyChange("alignment", null, viewport
2326 .getAlignment().getSequences());
2330 public void removeGappedColumnMenuItem_actionPerformed()
2332 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2335 if (viewport.getSelectionGroup() != null)
2337 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2338 viewport.getHiddenRepSequences());
2339 start = viewport.getSelectionGroup().getStartRes();
2340 end = viewport.getSelectionGroup().getEndRes();
2344 seqs = viewport.getAlignment().getSequencesArray();
2347 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2348 "Remove Gapped Columns", seqs, start, end,
2349 viewport.getAlignment());
2351 addHistoryItem(removeGapCols);
2353 statusBar.setText(MessageManager.formatMessage(
2354 "label.removed_empty_columns",
2355 new String[] { Integer.valueOf(removeGapCols.getSize())
2358 // This is to maintain viewport position on first residue
2359 // of first sequence
2360 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2361 int startRes = seq.findPosition(viewport.startRes);
2362 // ShiftList shifts;
2363 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2364 // edit.alColumnChanges=shifts.getInverse();
2365 // if (viewport.hasHiddenColumns)
2366 // viewport.getColumnSelection().compensateForEdits(shifts);
2367 viewport.setStartRes(seq.findIndex(startRes) - 1);
2368 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2373 public void removeAllGapsMenuItem_actionPerformed()
2375 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2378 if (viewport.getSelectionGroup() != null)
2380 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2381 viewport.getHiddenRepSequences());
2382 start = viewport.getSelectionGroup().getStartRes();
2383 end = viewport.getSelectionGroup().getEndRes();
2387 seqs = viewport.getAlignment().getSequencesArray();
2390 // This is to maintain viewport position on first residue
2391 // of first sequence
2392 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2393 int startRes = seq.findPosition(viewport.startRes);
2395 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2396 viewport.getAlignment()));
2398 viewport.setStartRes(seq.findIndex(startRes) - 1);
2400 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2405 public void findMenuItem_actionPerformed()
2407 new Finder(alignPanel);
2411 * create a new view derived from the current view
2414 * @return frame for the new view
2416 public AlignFrame newView(String viewtitle)
2419 if (viewport.hasHiddenRows())
2421 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2422 .getFullAlignment().getSequencesArray());
2426 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2429 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2431 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2433 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2435 newal.addAnnotation(viewport.getAlignment()
2436 .getAlignmentAnnotation()[i]);
2441 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2443 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2444 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2445 PaintRefresher.Register(newaf.alignPanel,
2446 newaf.alignPanel.av.getSequenceSetId());
2448 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2449 newaf.alignPanel.av.getSequenceSetId());
2450 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2451 newaf.alignPanel.av.getSequenceSetId());
2453 Vector comps = (Vector) PaintRefresher.components.get(viewport
2454 .getSequenceSetId());
2456 for (int i = 0; i < comps.size(); i++)
2458 if (comps.elementAt(i) instanceof AlignmentPanel)
2464 String title = new String(this.getTitle());
2465 if (viewtitle != null)
2467 title = viewtitle + " ( " + title + ")";
2471 if (title.indexOf("(View") > -1)
2473 title = title.substring(0, title.indexOf("(View"));
2475 title += "(View " + viewSize + ")";
2478 newaf.setTitle(title.toString());
2480 newaf.viewport.setHistoryList(viewport.getHistoryList());
2481 newaf.viewport.setRedoList(viewport.getRedoList());
2487 * @return list of feature groups on the view
2489 public String[] getFeatureGroups()
2491 FeatureRenderer fr = null;
2492 if (alignPanel != null
2493 && (fr = alignPanel.getFeatureRenderer()) != null)
2495 List<String> gps = fr.getFeatureGroups();
2496 String[] _gps = gps.toArray(new String[gps.size()]);
2503 * get sequence feature groups that are hidden or shown
2509 public String[] getFeatureGroupsOfState(boolean visible)
2511 FeatureRenderer fr = null;
2512 if (alignPanel != null
2513 && (fr = alignPanel.getFeatureRenderer()) != null)
2515 List<String> gps = fr.getGroups(visible);
2516 String[] _gps = gps.toArray(new String[gps.size()]);
2523 * Change the display state for the given feature groups
2526 * list of group strings
2528 * visible or invisible
2530 public void setFeatureGroupState(String[] groups, boolean state)
2532 FeatureRenderer fr = null;
2533 this.sequenceFeatures.setState(true);
2534 viewport.setShowSequenceFeatures(true);
2535 if (alignPanel != null
2536 && (fr = alignPanel.getFeatureRenderer()) != null)
2539 fr.setGroupVisibility(Arrays.asList(groups), state);
2540 alignPanel.seqPanel.seqCanvas.repaint();
2541 if (alignPanel.overviewPanel != null)
2543 alignPanel.overviewPanel.updateOverviewImage();
2548 public void seqLimits_itemStateChanged()
2550 viewport.setShowJVSuffix(seqLimits.getState());
2551 alignPanel.fontChanged();
2552 alignPanel.paintAlignment(true);
2555 protected void colourTextMenuItem_actionPerformed()
2557 viewport.setColourText(colourTextMenuItem.getState());
2558 alignPanel.paintAlignment(true);
2561 protected void displayNonconservedMenuItem_actionPerformed()
2563 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2564 alignPanel.paintAlignment(true);
2567 protected void wrapMenuItem_actionPerformed()
2569 viewport.setWrapAlignment(wrapMenuItem.getState());
2570 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2571 scaleAbove.setEnabled(wrapMenuItem.getState());
2572 scaleLeft.setEnabled(wrapMenuItem.getState());
2573 scaleRight.setEnabled(wrapMenuItem.getState());
2574 alignPanel.paintAlignment(true);
2577 public void overviewMenuItem_actionPerformed()
2579 if (alignPanel.overviewPanel != null)
2584 Frame frame = new Frame();
2585 OverviewPanel overview = new OverviewPanel(alignPanel);
2586 frame.add(overview);
2587 // +50 must allow for applet frame window
2588 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2589 "label.overview_params", new String[] { this.getTitle() }),
2590 overview.getPreferredSize().width,
2591 overview.getPreferredSize().height + 50);
2594 final AlignmentPanel ap = alignPanel;
2595 frame.addWindowListener(new WindowAdapter()
2598 public void windowClosing(WindowEvent e)
2602 ap.setOverviewPanel(null);
2607 alignPanel.setOverviewPanel(overview);
2612 public void changeColour(ColourSchemeI cs)
2617 if (viewport.getAbovePIDThreshold())
2619 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2623 if (viewport.getConservationSelected())
2625 cs.setConservationApplied(true);
2626 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2631 cs.setConservationApplied(false);
2634 viewport.setGlobalColourScheme(cs);
2636 alignPanel.paintAlignment(true);
2639 protected void modifyPID_actionPerformed()
2641 if (viewport.getAbovePIDThreshold()
2642 && viewport.getGlobalColourScheme() != null)
2644 SliderPanel.setPIDSliderSource(alignPanel,
2645 viewport.getGlobalColourScheme(), "Background");
2646 SliderPanel.showPIDSlider();
2650 protected void modifyConservation_actionPerformed()
2652 if (viewport.getConservationSelected()
2653 && viewport.getGlobalColourScheme() != null)
2655 SliderPanel.setConservationSlider(alignPanel,
2656 viewport.getGlobalColourScheme(), "Background");
2657 SliderPanel.showConservationSlider();
2661 protected void conservationMenuItem_actionPerformed()
2663 viewport.setConservationSelected(conservationMenuItem.getState());
2665 viewport.setAbovePIDThreshold(false);
2666 abovePIDThreshold.setState(false);
2668 changeColour(viewport.getGlobalColourScheme());
2670 modifyConservation_actionPerformed();
2673 public void abovePIDThreshold_actionPerformed()
2675 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2677 conservationMenuItem.setState(false);
2678 viewport.setConservationSelected(false);
2680 changeColour(viewport.getGlobalColourScheme());
2682 modifyPID_actionPerformed();
2685 public void sortPairwiseMenuItem_actionPerformed()
2687 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2688 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2689 .getAlignment().getSequenceAt(0), null);
2691 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2692 viewport.getAlignment()));
2693 alignPanel.paintAlignment(true);
2696 public void sortIDMenuItem_actionPerformed()
2698 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2699 AlignmentSorter.sortByID(viewport.getAlignment());
2700 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2701 viewport.getAlignment()));
2702 alignPanel.paintAlignment(true);
2705 public void sortLengthMenuItem_actionPerformed()
2707 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2708 AlignmentSorter.sortByLength(viewport.getAlignment());
2709 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2710 viewport.getAlignment()));
2711 alignPanel.paintAlignment(true);
2714 public void sortGroupMenuItem_actionPerformed()
2716 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2717 AlignmentSorter.sortByGroup(viewport.getAlignment());
2718 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2719 viewport.getAlignment()));
2720 alignPanel.paintAlignment(true);
2724 public void removeRedundancyMenuItem_actionPerformed()
2726 new RedundancyPanel(alignPanel);
2729 public void pairwiseAlignmentMenuItem_actionPerformed()
2731 if (viewport.getSelectionGroup() != null
2732 && viewport.getSelectionGroup().getSize() > 1)
2734 Frame frame = new Frame();
2735 frame.add(new PairwiseAlignPanel(alignPanel));
2736 jalview.bin.JalviewLite.addFrame(frame,
2737 MessageManager.getString("action.pairwise_alignment"), 600,
2742 public void PCAMenuItem_actionPerformed()
2744 // are the sequences aligned?
2745 if (!viewport.getAlignment().isAligned(false))
2748 int Width = viewport.getAlignment().getWidth();
2750 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2752 current = viewport.getAlignment().getSequenceAt(i);
2754 if (current.getLength() < Width)
2756 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2759 alignPanel.paintAlignment(true);
2762 if ((viewport.getSelectionGroup() != null
2763 && viewport.getSelectionGroup().getSize() < 4 && viewport
2764 .getSelectionGroup().getSize() > 0)
2765 || viewport.getAlignment().getHeight() < 4)
2772 new PCAPanel(viewport);
2773 } catch (java.lang.OutOfMemoryError ex)
2779 public void averageDistanceTreeMenuItem_actionPerformed()
2781 NewTreePanel("AV", "PID", "Average distance tree using PID");
2784 public void neighbourTreeMenuItem_actionPerformed()
2786 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2789 protected void njTreeBlosumMenuItem_actionPerformed()
2791 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2794 protected void avTreeBlosumMenuItem_actionPerformed()
2796 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2799 void NewTreePanel(String type, String pwType, String title)
2801 // are the sequences aligned?
2802 if (!viewport.getAlignment().isAligned(false))
2805 int Width = viewport.getAlignment().getWidth();
2807 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2809 current = viewport.getAlignment().getSequenceAt(i);
2811 if (current.getLength() < Width)
2813 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2816 alignPanel.paintAlignment(true);
2820 if ((viewport.getSelectionGroup() != null && viewport
2821 .getSelectionGroup().getSize() > 1)
2822 || (viewport.getAlignment().getHeight() > 1))
2824 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2826 addTreeMenuItem(tp, title);
2828 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2832 void loadTree_actionPerformed()
2834 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2835 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2836 cap.setTreeImport();
2837 Frame frame = new Frame();
2839 jalview.bin.JalviewLite.addFrame(frame,
2840 MessageManager.getString("label.paste_newick_file"), 400, 300);
2843 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2845 TreePanel tp = new TreePanel(alignPanel, treeFile,
2846 MessageManager.getString("label.load_tree_from_file"), tree);
2847 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2848 addTreeMenuItem(tp, treeFile);
2852 * sort the alignment using the given treePanel
2855 * tree used to sort view
2857 * string used for undo event name
2859 public void sortByTree(TreePanel treePanel, String title)
2861 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2863 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2864 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2865 // HistoryItem.SORT));
2866 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2867 "label.order_by_params", new String[] { title }), oldOrder,
2868 viewport.getAlignment()));
2869 alignPanel.paintAlignment(true);
2873 * Do any automatic reordering of the alignment and add the necessary bits to
2874 * the menu structure for the new tree
2879 protected void addTreeMenuItem(final TreePanel treePanel,
2882 final MenuItem item = new MenuItem(title);
2883 sortByTreeMenu.add(item);
2884 item.addActionListener(new java.awt.event.ActionListener()
2887 public void actionPerformed(ActionEvent evt)
2889 sortByTree(treePanel, title); // treePanel.getTitle());
2893 treePanel.addWindowListener(new WindowAdapter()
2896 public void windowOpened(WindowEvent e)
2898 if (viewport.sortByTree)
2900 sortByTree(treePanel, title);
2902 super.windowOpened(e);
2906 public void windowClosing(WindowEvent e)
2908 sortByTreeMenu.remove(item);
2913 public boolean sortBy(AlignmentOrder alorder, String undoname)
2915 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2916 if (viewport.applet.debug)
2918 System.err.println("Sorting " + alorder.getOrder().size()
2919 + " in alignment '" + getTitle() + "'");
2921 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2922 if (undoname != null)
2924 addHistoryItem(new OrderCommand(undoname, oldOrder,
2925 viewport.getAlignment()));
2927 alignPanel.paintAlignment(true);
2931 protected void documentation_actionPerformed()
2933 alignPanel.av.applet.openJalviewHelpUrl();
2936 protected void about_actionPerformed()
2939 class AboutPanel extends Canvas
2945 public AboutPanel(String version, String builddate)
2947 this.version = version;
2948 this.builddate = builddate;
2952 public void paint(Graphics g)
2954 g.setColor(Color.white);
2955 g.fillRect(0, 0, getSize().width, getSize().height);
2956 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2957 FontMetrics fm = g.getFontMetrics();
2958 int fh = fm.getHeight();
2960 g.setColor(Color.black);
2961 // TODO: update this text for each release or centrally store it for
2962 // lite and application
2963 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2964 g.drawString(MessageManager.formatMessage(
2965 "label.jalviewLite_release", new String[] { version }), x,
2967 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2968 g.drawString(MessageManager.formatMessage(
2969 "label.jaview_build_date", new String[] { builddate }), x,
2971 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2974 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2975 x + 50, y += fh + 8);
2977 MessageManager.getString("label.jalview_dev_managers"), x,
2979 g.drawString(MessageManager
2980 .getString("label.jalview_distribution_lists"), x, y += fh);
2981 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2984 MessageManager.getString("label.jalview_cite_1_authors"),
2987 MessageManager.getString("label.jalview_cite_1_title"), x,
2989 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2994 Frame frame = new Frame();
2995 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2997 jalview.bin.JalviewLite.addFrame(frame,
2998 MessageManager.getString("label.jalview"), 580, 220);
3002 public void showURL(String url, String target)
3004 if (viewport.applet == null)
3006 System.out.println("Not running as applet - no browser available.");
3010 viewport.applet.showURL(url, target);
3014 // ////////////////////////////////////////////////////////////////////////////////
3015 // JBuilder Graphics here
3017 MenuBar alignFrameMenuBar = new MenuBar();
3019 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3021 MenuItem loadApplication = new MenuItem(
3022 MessageManager.getString("label.view_full_application"));
3024 MenuItem loadTree = new MenuItem(
3025 MessageManager.getString("label.load_associated_tree"));
3027 MenuItem loadAnnotations = new MenuItem(
3028 MessageManager.getString("label.load_features_annotations"));
3030 MenuItem outputFeatures = new MenuItem(
3031 MessageManager.getString("label.export_features"));
3033 MenuItem outputAnnotations = new MenuItem(
3034 MessageManager.getString("label.export_annotations"));
3036 MenuItem closeMenuItem = new MenuItem(
3037 MessageManager.getString("action.close"));
3039 MenuItem selectAllSequenceMenuItem = new MenuItem(
3040 MessageManager.getString("action.select_all"));
3042 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3043 MessageManager.getString("action.deselect_all"));
3045 MenuItem invertSequenceMenuItem = new MenuItem(
3046 MessageManager.getString("action.invert_selection"));
3048 MenuItem remove2LeftMenuItem = new MenuItem();
3050 MenuItem remove2RightMenuItem = new MenuItem();
3052 MenuItem removeGappedColumnMenuItem = new MenuItem();
3054 MenuItem removeAllGapsMenuItem = new MenuItem();
3056 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3058 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3060 MenuItem sortPairwiseMenuItem = new MenuItem();
3062 MenuItem sortIDMenuItem = new MenuItem();
3064 MenuItem sortLengthMenuItem = new MenuItem();
3066 MenuItem sortGroupMenuItem = new MenuItem();
3068 MenuItem removeRedundancyMenuItem = new MenuItem();
3070 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3072 MenuItem PCAMenuItem = new MenuItem();
3074 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3076 MenuItem neighbourTreeMenuItem = new MenuItem();
3078 BorderLayout borderLayout1 = new BorderLayout();
3080 public Label statusBar = new Label();
3082 MenuItem clustalColour = new MenuItem();
3084 MenuItem zappoColour = new MenuItem();
3086 MenuItem taylorColour = new MenuItem();
3088 MenuItem hydrophobicityColour = new MenuItem();
3090 MenuItem helixColour = new MenuItem();
3092 MenuItem strandColour = new MenuItem();
3094 MenuItem turnColour = new MenuItem();
3096 MenuItem buriedColour = new MenuItem();
3098 MenuItem purinePyrimidineColour = new MenuItem();
3100 // MenuItem RNAInteractionColour = new MenuItem();
3102 MenuItem RNAHelixColour = new MenuItem();
3104 MenuItem userDefinedColour = new MenuItem();
3106 MenuItem PIDColour = new MenuItem();
3108 MenuItem BLOSUM62Colour = new MenuItem();
3110 MenuItem tcoffeeColour = new MenuItem();
3112 MenuItem njTreeBlosumMenuItem = new MenuItem();
3114 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3116 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3118 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3120 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3122 MenuItem alProperties = new MenuItem(
3123 MessageManager.getString("label.alignment_props"));
3125 MenuItem overviewMenuItem = new MenuItem();
3127 MenuItem undoMenuItem = new MenuItem();
3129 MenuItem redoMenuItem = new MenuItem();
3131 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3133 MenuItem noColourmenuItem = new MenuItem();
3135 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3137 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3139 MenuItem findMenuItem = new MenuItem();
3141 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3143 MenuItem nucleotideColour = new MenuItem();
3145 MenuItem deleteGroups = new MenuItem();
3147 MenuItem grpsFromSelection = new MenuItem();
3149 MenuItem createGroup = new MenuItem();
3151 MenuItem unGroup = new MenuItem();
3153 MenuItem delete = new MenuItem();
3155 MenuItem copy = new MenuItem();
3157 MenuItem cut = new MenuItem();
3159 Menu pasteMenu = new Menu();
3161 MenuItem pasteNew = new MenuItem();
3163 MenuItem pasteThis = new MenuItem();
3165 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3167 MenuItem font = new MenuItem();
3169 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3171 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3173 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3175 MenuItem modifyPID = new MenuItem();
3177 MenuItem modifyConservation = new MenuItem();
3179 CheckboxMenuItem autoCalculate = null;
3181 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3182 "Sort Alignment With New Tree", true);
3184 Menu sortByTreeMenu = new Menu();
3186 MenuItem inputText = new MenuItem();
3188 MenuItem documentation = new MenuItem();
3190 MenuItem about = new MenuItem();
3192 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3194 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3196 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3198 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3200 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3202 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3204 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3206 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3208 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3211 * Initialise menus and other items
3215 private void jbInit() throws Exception
3217 setMenuBar(alignFrameMenuBar);
3220 * Configure File menu items and actions
3223 .setLabel(MessageManager.getString("label.input_from_textbox"));
3224 inputText.addActionListener(this);
3225 Menu outputTextboxMenu = new Menu(
3226 MessageManager.getString("label.out_to_textbox"));
3227 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3230 MenuItem item = new MenuItem(
3231 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3233 item.addActionListener(new java.awt.event.ActionListener()
3236 public void actionPerformed(ActionEvent e)
3238 outputText_actionPerformed(e);
3242 outputTextboxMenu.add(item);
3244 closeMenuItem.addActionListener(this);
3245 loadApplication.addActionListener(this);
3246 loadTree.addActionListener(this);
3247 loadAnnotations.addActionListener(this);
3248 outputFeatures.addActionListener(this);
3249 outputAnnotations.addActionListener(this);
3252 * Configure Edit menu items and actions
3254 undoMenuItem.setEnabled(false);
3255 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3256 undoMenuItem.addActionListener(this);
3257 redoMenuItem.setEnabled(false);
3258 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3259 redoMenuItem.addActionListener(this);
3260 copy.setLabel(MessageManager.getString("action.copy"));
3261 copy.addActionListener(this);
3262 cut.setLabel(MessageManager.getString("action.cut"));
3263 cut.addActionListener(this);
3264 delete.setLabel(MessageManager.getString("action.delete"));
3265 delete.addActionListener(this);
3266 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3267 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3268 pasteNew.addActionListener(this);
3269 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3270 pasteThis.addActionListener(this);
3271 remove2LeftMenuItem.setLabel(MessageManager
3272 .getString("action.remove_left"));
3273 remove2LeftMenuItem.addActionListener(this);
3274 remove2RightMenuItem.setLabel(MessageManager
3275 .getString("action.remove_right"));
3276 remove2RightMenuItem.addActionListener(this);
3277 removeGappedColumnMenuItem.setLabel(MessageManager
3278 .getString("action.remove_empty_columns"));
3279 removeGappedColumnMenuItem.addActionListener(this);
3280 removeAllGapsMenuItem.setLabel(MessageManager
3281 .getString("action.remove_all_gaps"));
3282 removeAllGapsMenuItem.addActionListener(this);
3283 removeRedundancyMenuItem.setLabel(MessageManager
3284 .getString("action.remove_redundancy"));
3285 removeRedundancyMenuItem.addActionListener(this);
3288 * Configure Select menu items and actions
3290 findMenuItem.setLabel(MessageManager.getString("action.find"));
3291 findMenuItem.addActionListener(this);
3292 selectAllSequenceMenuItem.addActionListener(this);
3293 deselectAllSequenceMenuItem.addActionListener(this);
3294 invertSequenceMenuItem.setLabel(MessageManager
3295 .getString("action.invert_sequence_selection"));
3296 invertSequenceMenuItem.addActionListener(this);
3297 invertColSel.setLabel(MessageManager
3298 .getString("action.invert_column_selection"));
3299 invertColSel.addActionListener(this);
3300 deleteGroups.setLabel(MessageManager
3301 .getString("action.undefine_groups"));
3302 deleteGroups.addActionListener(this);
3303 grpsFromSelection.setLabel(MessageManager
3304 .getString("action.make_groups_selection"));
3305 grpsFromSelection.addActionListener(this);
3306 createGroup.setLabel(MessageManager.getString("action.create_group"));
3307 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3308 annotationColumnSelection.setLabel(MessageManager
3309 .getString("action.select_by_annotation"));
3310 annotationColumnSelection.addActionListener(this);
3313 * Configure View menu items and actions
3315 newView.setLabel(MessageManager.getString("action.new_view"));
3316 newView.addActionListener(this);
3317 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3318 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3319 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3320 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3322 .setLabel(MessageManager.getString("label.selected_columns"));
3323 hideSequences.setLabel(MessageManager
3324 .getString("label.selected_sequences"));
3325 hideAllButSelection.setLabel(MessageManager
3326 .getString("label.all_but_selected_region"));
3327 hideAllSelection.setLabel(MessageManager
3328 .getString("label.selected_region"));
3329 showAllHidden.setLabel(MessageManager
3330 .getString("label.all_sequences_columns"));
3331 showColumns.addActionListener(this);
3332 showSeqs.addActionListener(this);
3333 hideColumns.addActionListener(this);
3334 hideSequences.addActionListener(this);
3335 hideAllButSelection.addActionListener(this);
3336 hideAllSelection.addActionListener(this);
3337 showAllHidden.addActionListener(this);
3338 featureSettings.setLabel(MessageManager
3339 .getString("action.feature_settings"));
3340 featureSettings.addActionListener(this);
3341 sequenceFeatures.setLabel(MessageManager
3342 .getString("label.show_sequence_features"));
3343 sequenceFeatures.addItemListener(this);
3344 sequenceFeatures.setState(false);
3345 followMouseOverFlag.setLabel(MessageManager
3346 .getString("label.automatic_scrolling"));
3347 followMouseOverFlag.addItemListener(this);
3348 alProperties.addActionListener(this);
3349 overviewMenuItem.setLabel(MessageManager
3350 .getString("label.overview_window"));
3351 overviewMenuItem.addActionListener(this);
3354 * Configure Annotations menu items and actions
3356 annotationPanelMenuItem.setLabel(MessageManager
3357 .getString("label.show_annotations"));
3358 annotationPanelMenuItem.addItemListener(this);
3359 showGroupConsensus.setLabel(MessageManager
3360 .getString("label.group_consensus"));
3361 showGroupConservation.setLabel(MessageManager
3362 .getString("label.group_conservation"));
3363 showConsensusHistogram.setLabel(MessageManager
3364 .getString("label.show_consensus_histogram"));
3365 showSequenceLogo.setLabel(MessageManager
3366 .getString("label.show_consensus_logo"));
3367 normSequenceLogo.setLabel(MessageManager
3368 .getString("label.norm_consensus_logo"));
3369 applyAutoAnnotationSettings.setLabel(MessageManager
3370 .getString("label.apply_all_groups"));
3371 applyAutoAnnotationSettings.setState(true);
3372 Menu autoAnnMenu = new Menu(
3373 MessageManager.getString("label.autocalculated_annotation"));
3374 showGroupConsensus.addItemListener(this);
3375 showGroupConservation.addItemListener(this);
3376 showConsensusHistogram.addItemListener(this);
3377 showSequenceLogo.addItemListener(this);
3378 normSequenceLogo.addItemListener(this);
3379 applyAutoAnnotationSettings.addItemListener(this);
3380 showAlignmentAnnotations = new CheckboxMenuItem(
3381 MessageManager.getString("label.show_all_al_annotations"));
3382 showSequenceAnnotations = new CheckboxMenuItem(
3383 MessageManager.getString("label.show_all_seq_annotations"));
3384 sortAnnBySequence = new CheckboxMenuItem(
3385 MessageManager.getString("label.sort_annotations_by_sequence"));
3386 sortAnnByLabel = new CheckboxMenuItem(
3387 MessageManager.getString("label.sort_annotations_by_label"));
3388 showAutoFirst = new CheckboxMenuItem(
3389 MessageManager.getString("label.show_first"));
3390 showAutoFirst.setState(false); // pending applet parameter
3391 setShowAutoCalculatedAbove(showAutoFirst.getState());
3392 showAutoLast = new CheckboxMenuItem(
3393 MessageManager.getString("label.show_last"));
3394 showAutoLast.setState(!showAutoFirst.getState());
3395 showAlignmentAnnotations.addItemListener(this);
3396 showSequenceAnnotations.addItemListener(this);
3397 sortAnnBySequence.addItemListener(this);
3398 sortAnnByLabel.addItemListener(this);
3399 showAutoFirst.addItemListener(this);
3400 showAutoLast.addItemListener(this);
3403 * Configure Format menu items and actions
3405 font.setLabel(MessageManager.getString("action.font"));
3406 font.addActionListener(this);
3407 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3408 scaleAbove.setState(true);
3409 scaleAbove.setEnabled(false);
3410 scaleAbove.addItemListener(this);
3411 scaleLeft.setEnabled(false);
3412 scaleLeft.setState(true);
3413 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3414 scaleLeft.addItemListener(this);
3415 scaleRight.setEnabled(false);
3416 scaleRight.setState(true);
3417 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3418 scaleRight.addItemListener(this);
3419 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3420 viewBoxesMenuItem.setState(true);
3421 viewBoxesMenuItem.addItemListener(this);
3422 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3423 viewTextMenuItem.setState(true);
3424 viewTextMenuItem.addItemListener(this);
3425 colourTextMenuItem.setLabel(MessageManager
3426 .getString("label.colour_text"));
3427 colourTextMenuItem.addItemListener(this);
3428 displayNonconservedMenuItem.setLabel(MessageManager
3429 .getString("label.show_non_conversed"));
3430 displayNonconservedMenuItem.addItemListener(this);
3431 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3432 wrapMenuItem.addItemListener(this);
3433 renderGapsMenuItem.setLabel(MessageManager
3434 .getString("action.show_gaps"));
3435 renderGapsMenuItem.setState(true);
3436 renderGapsMenuItem.addItemListener(this);
3437 centreColumnLabelFlag.setLabel(MessageManager
3438 .getString("label.centre_column_labels"));
3439 centreColumnLabelFlag.addItemListener(this);
3440 seqLimits.setState(true);
3441 seqLimits.setLabel(MessageManager
3442 .getString("label.show_sequence_limits"));
3443 seqLimits.addItemListener(this);
3446 * Configure Colour menu items and actions
3448 applyToAllGroups.setLabel(MessageManager
3449 .getString("label.apply_colour_to_all_groups"));
3450 applyToAllGroups.setState(true);
3451 applyToAllGroups.addItemListener(this);
3452 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3453 clustalColour.addActionListener(this);
3454 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3455 zappoColour.addActionListener(this);
3456 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3457 taylorColour.addActionListener(this);
3458 hydrophobicityColour.setLabel(MessageManager
3459 .getString("label.hydrophobicity"));
3460 hydrophobicityColour.addActionListener(this);
3462 .setLabel(MessageManager.getString("label.helix_propensity"));
3463 helixColour.addActionListener(this);
3464 strandColour.setLabel(MessageManager
3465 .getString("label.strand_propensity"));
3466 strandColour.addActionListener(this);
3467 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3468 turnColour.addActionListener(this);
3469 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3470 buriedColour.addActionListener(this);
3471 purinePyrimidineColour.setLabel(MessageManager
3472 .getString("label.purine_pyrimidine"));
3473 purinePyrimidineColour.addActionListener(this);
3474 // RNAInteractionColour.setLabel(MessageManager
3475 // .getString("label.rna_interaction"));
3476 // RNAInteractionColour.addActionListener(this);
3477 RNAHelixColour.setLabel(MessageManager
3478 .getString("action.by_rna_helixes"));
3479 RNAHelixColour.addActionListener(this);
3480 userDefinedColour.setLabel(MessageManager
3481 .getString("action.user_defined"));
3482 userDefinedColour.addActionListener(this);
3483 PIDColour.setLabel(MessageManager
3484 .getString("label.percentage_identity"));
3485 PIDColour.addActionListener(this);
3486 BLOSUM62Colour.setLabel(MessageManager
3487 .getString("label.blosum62_score"));
3488 BLOSUM62Colour.addActionListener(this);
3490 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3491 // it will be enabled only if a score file is provided
3492 tcoffeeColour.setEnabled(false);
3493 tcoffeeColour.addActionListener(this);
3494 conservationMenuItem.setLabel(MessageManager
3495 .getString("action.by_conservation"));
3496 conservationMenuItem.addItemListener(this);
3497 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3498 noColourmenuItem.addActionListener(this);
3499 abovePIDThreshold.setLabel(MessageManager
3500 .getString("label.above_identity_threshold"));
3501 abovePIDThreshold.addItemListener(this);
3502 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3503 nucleotideColour.addActionListener(this);
3504 modifyPID.setLabel(MessageManager
3505 .getString("label.modify_identity_thereshold"));
3506 modifyPID.addActionListener(this);
3507 modifyConservation.setLabel(MessageManager
3508 .getString("label.modify_conservation_thereshold"));
3509 modifyConservation.addActionListener(this);
3510 annotationColour.setLabel(MessageManager
3511 .getString("action.by_annotation"));
3512 annotationColour.addActionListener(this);
3515 * Configure Calculate menu items and actions
3517 sortPairwiseMenuItem.setLabel(MessageManager
3518 .getString("action.by_pairwise_id"));
3519 sortPairwiseMenuItem.addActionListener(this);
3520 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3521 sortIDMenuItem.addActionListener(this);
3522 sortLengthMenuItem.setLabel(MessageManager
3523 .getString("action.by_length"));
3524 sortLengthMenuItem.addActionListener(this);
3525 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3526 sortGroupMenuItem.addActionListener(this);
3527 pairwiseAlignmentMenuItem.setLabel(MessageManager
3528 .getString("action.pairwise_alignment"));
3529 pairwiseAlignmentMenuItem.addActionListener(this);
3530 PCAMenuItem.setLabel(MessageManager
3531 .getString("label.principal_component_analysis"));
3532 PCAMenuItem.addActionListener(this);
3533 autoCalculate = new CheckboxMenuItem(
3534 MessageManager.getString("label.autocalculate_consensus"), true);
3535 averageDistanceTreeMenuItem.setLabel(MessageManager
3536 .getString("label.average_distance_identity"));
3537 averageDistanceTreeMenuItem.addActionListener(this);
3538 neighbourTreeMenuItem.setLabel(MessageManager
3539 .getString("label.neighbour_joining_identity"));
3540 neighbourTreeMenuItem.addActionListener(this);
3541 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3542 .getString("label.average_distance_bloslum62"));
3543 avDistanceTreeBlosumMenuItem.addActionListener(this);
3544 njTreeBlosumMenuItem.setLabel(MessageManager
3545 .getString("label.neighbour_blosum62"));
3546 njTreeBlosumMenuItem.addActionListener(this);
3547 sortByTreeMenu.setLabel(MessageManager
3548 .getString("action.by_tree_order"));
3549 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3550 Menu calculateTreeMenu = new Menu(
3551 MessageManager.getString("action.calculate_tree"));
3552 autoCalculate.addItemListener(this);
3553 sortByTree.addItemListener(this);
3556 * Configure Help menu items and actions
3558 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3559 documentation.setLabel(MessageManager.getString("label.documentation"));
3560 documentation.addActionListener(this);
3561 about.setLabel(MessageManager.getString("label.about"));
3562 about.addActionListener(this);
3565 * Add top level menus to frame
3567 alignFrameMenuBar.add(fileMenu);
3568 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3569 alignFrameMenuBar.add(editMenu);
3570 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3571 alignFrameMenuBar.add(selectMenu);
3572 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3573 alignFrameMenuBar.add(viewMenu);
3574 Menu annotationsMenu = new Menu(
3575 MessageManager.getString("action.annotations"));
3576 alignFrameMenuBar.add(annotationsMenu);
3577 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3578 alignFrameMenuBar.add(formatMenu);
3579 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3580 alignFrameMenuBar.add(colourMenu);
3581 Menu calculateMenu = new Menu(
3582 MessageManager.getString("action.calculate"));
3583 alignFrameMenuBar.add(calculateMenu);
3584 alignFrameMenuBar.add(helpMenu);
3589 fileMenu.add(inputText);
3590 fileMenu.add(loadTree);
3591 fileMenu.add(loadAnnotations);
3592 fileMenu.addSeparator();
3593 fileMenu.add(outputTextboxMenu);
3594 fileMenu.add(outputFeatures);
3595 fileMenu.add(outputAnnotations);
3596 if (jalviewServletURL != null)
3598 fileMenu.add(loadApplication);
3600 fileMenu.addSeparator();
3601 fileMenu.add(closeMenuItem);
3606 editMenu.add(undoMenuItem);
3607 editMenu.add(redoMenuItem);
3610 pasteMenu.add(pasteNew);
3611 pasteMenu.add(pasteThis);
3612 editMenu.add(pasteMenu);
3613 editMenu.add(delete);
3614 editMenu.addSeparator();
3615 editMenu.add(remove2LeftMenuItem);
3616 editMenu.add(remove2RightMenuItem);
3617 editMenu.add(removeGappedColumnMenuItem);
3618 editMenu.add(removeAllGapsMenuItem);
3619 editMenu.add(removeRedundancyMenuItem);
3624 selectMenu.add(findMenuItem);
3625 selectMenu.addSeparator();
3626 selectMenu.add(selectAllSequenceMenuItem);
3627 selectMenu.add(deselectAllSequenceMenuItem);
3628 selectMenu.add(invertSequenceMenuItem);
3629 selectMenu.add(invertColSel);
3630 selectMenu.add(createGroup);
3631 selectMenu.add(unGroup);
3632 selectMenu.add(grpsFromSelection);
3633 selectMenu.add(deleteGroups);
3634 selectMenu.add(annotationColumnSelection);
3639 viewMenu.add(newView);
3640 viewMenu.addSeparator();
3641 showMenu.add(showColumns);
3642 showMenu.add(showSeqs);
3643 showMenu.add(showAllHidden);
3644 viewMenu.add(showMenu);
3645 hideMenu.add(hideColumns);
3646 hideMenu.add(hideSequences);
3647 hideMenu.add(hideAllSelection);
3648 hideMenu.add(hideAllButSelection);
3649 viewMenu.add(hideMenu);
3650 viewMenu.addSeparator();
3651 viewMenu.add(followMouseOverFlag);
3652 viewMenu.addSeparator();
3653 viewMenu.add(sequenceFeatures);
3654 viewMenu.add(featureSettings);
3655 viewMenu.addSeparator();
3656 viewMenu.add(alProperties);
3657 viewMenu.addSeparator();
3658 viewMenu.add(overviewMenuItem);
3663 annotationsMenu.add(annotationPanelMenuItem);
3664 annotationsMenu.addSeparator();
3665 annotationsMenu.add(showAlignmentAnnotations);
3666 annotationsMenu.add(showSequenceAnnotations);
3667 annotationsMenu.add(sortAnnBySequence);
3668 annotationsMenu.add(sortAnnByLabel);
3669 annotationsMenu.addSeparator();
3670 autoAnnMenu.add(showAutoFirst);
3671 autoAnnMenu.add(showAutoLast);
3672 autoAnnMenu.addSeparator();
3673 autoAnnMenu.add(applyAutoAnnotationSettings);
3674 autoAnnMenu.add(showConsensusHistogram);
3675 autoAnnMenu.add(showSequenceLogo);
3676 autoAnnMenu.add(normSequenceLogo);
3677 autoAnnMenu.addSeparator();
3678 autoAnnMenu.add(showGroupConservation);
3679 autoAnnMenu.add(showGroupConsensus);
3680 annotationsMenu.add(autoAnnMenu);
3685 formatMenu.add(font);
3686 formatMenu.add(seqLimits);
3687 formatMenu.add(wrapMenuItem);
3688 formatMenu.add(scaleAbove);
3689 formatMenu.add(scaleLeft);
3690 formatMenu.add(scaleRight);
3691 formatMenu.add(viewBoxesMenuItem);
3692 formatMenu.add(viewTextMenuItem);
3693 formatMenu.add(colourTextMenuItem);
3694 formatMenu.add(displayNonconservedMenuItem);
3695 formatMenu.add(renderGapsMenuItem);
3696 formatMenu.add(centreColumnLabelFlag);
3701 colourMenu.add(applyToAllGroups);
3702 colourMenu.addSeparator();
3703 colourMenu.add(noColourmenuItem);
3704 colourMenu.add(clustalColour);
3705 colourMenu.add(BLOSUM62Colour);
3706 colourMenu.add(PIDColour);
3707 colourMenu.add(zappoColour);
3708 colourMenu.add(taylorColour);
3709 colourMenu.add(hydrophobicityColour);
3710 colourMenu.add(helixColour);
3711 colourMenu.add(strandColour);
3712 colourMenu.add(turnColour);
3713 colourMenu.add(buriedColour);
3714 colourMenu.add(nucleotideColour);
3715 colourMenu.add(purinePyrimidineColour);
3716 // colourMenu.add(RNAInteractionColour);
3717 colourMenu.add(tcoffeeColour);
3718 colourMenu.add(userDefinedColour);
3719 colourMenu.addSeparator();
3720 colourMenu.add(conservationMenuItem);
3721 colourMenu.add(modifyConservation);
3722 colourMenu.add(abovePIDThreshold);
3723 colourMenu.add(modifyPID);
3724 colourMenu.add(annotationColour);
3725 colourMenu.add(RNAHelixColour);
3730 sortMenu.add(sortIDMenuItem);
3731 sortMenu.add(sortLengthMenuItem);
3732 sortMenu.add(sortByTreeMenu);
3733 sortMenu.add(sortGroupMenuItem);
3734 sortMenu.add(sortPairwiseMenuItem);
3735 calculateMenu.add(sortMenu);
3736 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3737 calculateTreeMenu.add(neighbourTreeMenuItem);
3738 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3739 calculateTreeMenu.add(njTreeBlosumMenuItem);
3740 calculateMenu.add(calculateTreeMenu);
3741 calculateMenu.addSeparator();
3742 calculateMenu.add(pairwiseAlignmentMenuItem);
3743 calculateMenu.add(PCAMenuItem);
3744 calculateMenu.add(autoCalculate);
3745 calculateMenu.add(sortByTree);
3750 helpMenu.add(documentation);
3751 helpMenu.add(about);
3756 statusBar.setBackground(Color.white);
3757 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3758 statusBar.setText(MessageManager.getString("label.status_bar"));
3759 this.add(statusBar, BorderLayout.SOUTH);
3763 public void setStatus(String string)
3765 statusBar.setText(string);
3768 MenuItem featureSettings = new MenuItem();
3770 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3772 MenuItem annotationColour = new MenuItem();
3774 MenuItem annotationColumnSelection = new MenuItem();
3776 MenuItem invertColSel = new MenuItem();
3778 MenuItem showColumns = new MenuItem();
3780 MenuItem showSeqs = new MenuItem();
3782 MenuItem hideColumns = new MenuItem();
3784 MenuItem hideSequences = new MenuItem();
3786 MenuItem hideAllButSelection = new MenuItem();
3788 MenuItem hideAllSelection = new MenuItem();
3790 MenuItem showAllHidden = new MenuItem();
3792 MenuItem newView = new MenuItem();
3794 private CheckboxMenuItem showAlignmentAnnotations;
3796 private CheckboxMenuItem showSequenceAnnotations;
3798 private CheckboxMenuItem sortAnnBySequence;
3800 private CheckboxMenuItem sortAnnByLabel;
3802 private CheckboxMenuItem showAutoFirst;
3804 private CheckboxMenuItem showAutoLast;
3806 private SplitFrame splitFrame;
3809 * Attach the alignFrame panels after embedding menus, if necessary. This used
3810 * to be called setEmbedded, but is now creates the dropdown menus in a
3811 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3813 * @param reallyEmbedded
3814 * true to attach the view to the applet area on the page rather than
3817 public void createAlignFrameWindow(boolean reallyEmbedded)
3821 embedAlignFrameInApplet(viewport.applet);
3826 // test and embed menu bar if necessary.
3828 if (embedMenuIfNeeded(alignPanel))
3831 * adjust for status bar height too. ? pointless as overridden by layout
3834 alignPanel.setSize(getSize().width,
3835 getSize().height - statusBar.getHeight());
3837 add(statusBar, BorderLayout.SOUTH);
3838 add(alignPanel, BorderLayout.CENTER);
3839 // and register with the applet so it can pass external API calls to us
3840 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3846 * Add the components of this AlignFrame to the applet container.
3850 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3853 // Explicitly build the embedded menu panel for the on-page applet
3855 // view cannot be closed if its actually on the page
3856 fileMenu.remove(closeMenuItem);
3857 fileMenu.remove(3); // Remove Separator
3858 // construct embedded menu, using default font
3859 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3860 // and actually add the components to the applet area
3861 theApplet.setLayout(new BorderLayout());
3862 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3863 theApplet.add(statusBar, BorderLayout.SOUTH);
3864 // TODO should size be left to the layout manager?
3865 alignPanel.setSize(theApplet.getSize().width,
3866 theApplet.getSize().height - embeddedMenu.getHeight()
3867 - statusBar.getHeight());
3868 theApplet.add(alignPanel, BorderLayout.CENTER);
3869 final AlignFrame me = this;
3870 theApplet.addFocusListener(new FocusListener()
3874 public void focusLost(FocusEvent e)
3876 if (theApplet.currentAlignFrame == me)
3878 theApplet.currentAlignFrame = null;
3883 public void focusGained(FocusEvent e)
3885 theApplet.currentAlignFrame = me;
3888 theApplet.validate();
3892 * create a new binding between structures in an existing jmol viewer instance
3893 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3894 * this does not open a new Jmol window, or modify the display of the
3895 * structures in the original jmol window. Note This method doesn't work
3896 * without an additional javascript library to exchange messages between the
3897 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3900 * JmolViewer instance
3901 * @param sequenceIds
3902 * - sequence Ids to search for associations
3904 public SequenceStructureBinding addStructureViewInstance(
3905 Object jmolviewer, String[] sequenceIds)
3907 Viewer viewer = null;
3910 viewer = (Viewer) jmolviewer;
3911 } catch (ClassCastException ex)
3913 System.err.println("Unsupported viewer object :"
3914 + jmolviewer.getClass());
3918 System.err.println("Can't use this object as a structure viewer:"
3919 + jmolviewer.getClass());
3922 SequenceI[] seqs = null;
3923 if (sequenceIds == null || sequenceIds.length == 0)
3925 seqs = viewport.getAlignment().getSequencesArray();
3929 Vector sqi = new Vector();
3930 AlignmentI al = viewport.getAlignment();
3931 for (int sid = 0; sid < sequenceIds.length; sid++)
3933 SequenceI sq = al.findName(sequenceIds[sid]);
3941 seqs = new SequenceI[sqi.size()];
3942 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3944 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3952 AAStructureBindingModel jmv = null;
3953 // TODO: search for a jmv that involves viewer
3955 { // create a new viewer/jalview binding.
3956 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3963 * bind a pdb file to a sequence in the current view
3966 * - sequenceId within the dataset.
3967 * @param pdbEntryString
3968 * - the short name for the PDB file
3970 * - pdb file - either a URL or a valid PDB file.
3971 * @return true if binding was as success TODO: consider making an exception
3972 * structure for indicating when PDB parsing or sequenceId location
3975 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3978 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3979 boolean needtoadd = false;
3980 if (toaddpdb != null)
3982 Vector pdbe = toaddpdb.getAllPDBEntries();
3983 PDBEntry pdbentry = null;
3984 if (pdbe != null && pdbe.size() > 0)
3986 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3988 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3989 if (!pdbentry.getId().equals(pdbEntryString)
3990 && !pdbentry.getFile().equals(pdbFile))
4000 if (pdbentry == null)
4002 pdbentry = new PDBEntry();
4003 pdbentry.setId(pdbEntryString);
4004 pdbentry.setFile(pdbFile);
4005 needtoadd = true; // add this new entry to sequence.
4007 // resolve data source
4008 // TODO: this code should be a refactored to an io package
4009 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4010 if (protocol == null)
4016 // make a note of the access mode and add
4017 if (pdbentry.getProperty() == null)
4019 pdbentry.setProperty(new Hashtable());
4021 pdbentry.getProperty().put("protocol", protocol);
4022 toaddpdb.addPDBId(pdbentry);
4023 alignPanel.getStructureSelectionManager()
4024 .registerPDBEntry(pdbentry);
4030 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4034 Vector sequences = new Vector();
4035 for (int i = 0; i < seqs.length; i++)
4037 if (seqs[i] != null)
4039 sequences.addElement(new Object[] { seqs[i],
4040 (chains != null) ? chains[i] : null });
4043 seqs = new SequenceI[sequences.size()];
4044 chains = new String[sequences.size()];
4045 for (int i = 0, isize = sequences.size(); i < isize; i++)
4047 Object[] oj = (Object[]) sequences.elementAt(i);
4049 seqs[i] = (SequenceI) oj[0];
4050 chains[i] = (String) oj[1];
4053 return new Object[] { seqs, chains };
4057 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4058 SequenceI[] seqs, String[] chains, String protocol)
4060 // Scrub any null sequences from the array
4061 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4062 seqs = (SequenceI[]) sqch[0];
4063 chains = (String[]) sqch[1];
4064 if (seqs == null || seqs.length == 0)
4067 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4069 if (protocol == null || protocol.trim().length() == 0
4070 || protocol.equals("null"))
4072 protocol = (String) pdb.getProperty().get("protocol");
4073 if (protocol == null)
4075 System.err.println("Couldn't work out protocol to open structure: "
4080 if (applet.useXtrnalSviewer)
4082 // register the association(s) and quit, don't create any windows.
4083 if (StructureSelectionManager.getStructureSelectionManager(applet)
4084 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4086 System.err.println("Failed to map " + pdb.getFile() + " ("
4087 + protocol + ") to any sequences");
4091 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4093 // can only do alignments with Jmol
4094 // find the last jmol window assigned to this alignment
4095 jalview.appletgui.AppletJmol ajm = null, tajm;
4096 Vector jmols = applet
4097 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4098 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4100 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4101 if (tajm.ap.alignFrame == this)
4110 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4111 // try and add the pdb structure
4116 // otherwise, create a new window
4117 if (applet.jmolAvailable)
4119 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4121 applet.lastFrameX += 40;
4122 applet.lastFrameY += 40;
4126 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4131 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4132 SequenceI[][] seqs, String[][] chains, String[] protocols)
4134 // TODO Auto-generated method stub
4135 System.err.println("Aligned Structure View: Not yet implemented.");
4139 * modify the current selection, providing the user has not made a selection
4143 * - sequences from this alignment
4145 * - columns to be selected on the alignment
4147 public void select(SequenceGroup sel, ColumnSelection csel)
4149 alignPanel.seqPanel.selection(sel, csel, null);
4152 public void scrollTo(int row, int column)
4154 alignPanel.seqPanel.scrollTo(row, column);
4157 public void scrollToRow(int row)
4159 alignPanel.seqPanel.scrollToRow(row);
4162 public void scrollToColumn(int column)
4164 alignPanel.seqPanel.scrollToColumn(column);
4168 * @return the alignments unique ID.
4170 public String getSequenceSetId()
4172 return viewport.getSequenceSetId();
4176 * Load the (T-Coffee) score file from the specified url
4179 * File/URL/T-COFFEE score file contents
4180 * @throws IOException
4181 * @return true if alignment was annotated with data from source
4183 public boolean loadScoreFile(String source) throws IOException
4186 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4187 AppletFormatAdapter.checkProtocol(source));
4188 if (!file.isValid())
4190 // TODO: raise dialog for gui
4191 System.err.println("Problems parsing T-Coffee scores: "
4192 + file.getWarningMessage());
4193 System.err.println("Origin was:\n" + source);
4198 * check that the score matrix matches the alignment dimensions
4201 if ((aln = viewport.getAlignment()) != null
4202 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4205 // TODO: raise a dialog box here rather than bomb out.
4207 .println("The scores matrix does not match the alignment dimensions");
4211 // TODO add parameter to indicate if matching should be done
4212 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4214 alignPanel.fontChanged();
4215 tcoffeeColour.setEnabled(true);
4216 // switch to this color
4217 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4222 System.err.println("Problems resolving T-Coffee scores:");
4223 if (file.getWarningMessage() != null)
4225 System.err.println(file.getWarningMessage());
4231 public SplitFrame getSplitFrame()
4233 return this.splitFrame;
4236 public void setSplitFrame(SplitFrame sf)
4238 this.splitFrame = sf;
4241 // may not need this
4243 public void setShowSeqFeatures(boolean b)
4245 // showSeqFeatures.setSelected(b);
4246 viewport.setShowSequenceFeatures(b);
4251 public void setMenusForViewport()
4253 // setMenusFromViewport(viewport);
4258 public void refreshFeatureUI(boolean enableIfNecessary)
4260 if (enableIfNecessary)
4262 sequenceFeatures.setState(true);
4263 alignPanel.av.setShowSequenceFeatures(true);
4268 public FeatureSettingsControllerI getFeatureSettingsUI()
4270 return alignPanel.av.featureSettings;