2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
3 * Copyright (C) 2015 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 for (AlignmentAnnotation aa : alignPanel.getAlignment()
934 .getAlignmentAnnotation())
936 boolean visible = (aa.sequenceRef == null ? showForAlignment
938 aa.visible = visible;
940 alignPanel.validateAnnotationDimensions(true);
945 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
947 this.annotationSortOrder = order;
951 * Set flags on the viewport that control annotation ordering
953 private void setViewportAnnotationOrder()
955 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
957 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
960 private void setShowAutoCalculatedAbove(boolean showAbove)
962 this.showAutoCalculatedAbove = showAbove;
965 private void mouseOverFlag_stateChanged()
967 viewport.setFollowHighlight(followMouseOverFlag.getState());
968 // TODO: could kick the scrollTo mechanism to reset view for current
972 private void centreColumnLabelFlag_stateChanged()
974 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
975 this.alignPanel.annotationPanel.repaint();
979 public void actionPerformed(ActionEvent evt)
981 viewport.applet.currentAlignFrame = this;
983 Object source = evt.getSource();
985 if (source == inputText)
987 inputText_actionPerformed();
989 else if (source == loadTree)
991 loadTree_actionPerformed();
993 else if (source == loadApplication)
995 launchFullApplication();
997 else if (source == loadAnnotations)
1001 else if (source == outputAnnotations)
1003 outputAnnotations(true);
1005 else if (source == outputFeatures)
1007 outputFeatures(true, "Jalview");
1009 else if (source == closeMenuItem)
1011 closeMenuItem_actionPerformed();
1013 else if (source == copy)
1015 copy_actionPerformed();
1017 else if (source == undoMenuItem)
1019 undoMenuItem_actionPerformed();
1021 else if (source == redoMenuItem)
1023 redoMenuItem_actionPerformed();
1025 else if (source == inputText)
1027 inputText_actionPerformed();
1029 else if (source == closeMenuItem)
1031 closeMenuItem_actionPerformed();
1033 else if (source == undoMenuItem)
1035 undoMenuItem_actionPerformed();
1037 else if (source == redoMenuItem)
1039 redoMenuItem_actionPerformed();
1041 else if (source == copy)
1043 copy_actionPerformed();
1045 else if (source == pasteNew)
1047 pasteNew_actionPerformed();
1049 else if (source == pasteThis)
1051 pasteThis_actionPerformed();
1053 else if (source == cut)
1055 cut_actionPerformed();
1057 else if (source == delete)
1059 delete_actionPerformed();
1061 else if (source == grpsFromSelection)
1063 makeGrpsFromSelection_actionPerformed();
1065 else if (source == deleteGroups)
1067 deleteGroups_actionPerformed();
1069 else if (source == selectAllSequenceMenuItem)
1071 selectAllSequenceMenuItem_actionPerformed();
1073 else if (source == deselectAllSequenceMenuItem)
1075 deselectAllSequenceMenuItem_actionPerformed();
1077 else if (source == invertSequenceMenuItem)
1079 invertSequenceMenuItem_actionPerformed();
1081 else if (source == invertColSel)
1083 viewport.invertColumnSelection();
1084 alignPanel.paintAlignment(true);
1086 else if (source == remove2LeftMenuItem)
1088 trimAlignment(true);
1090 else if (source == remove2RightMenuItem)
1092 trimAlignment(false);
1094 else if (source == removeGappedColumnMenuItem)
1096 removeGappedColumnMenuItem_actionPerformed();
1098 else if (source == removeAllGapsMenuItem)
1100 removeAllGapsMenuItem_actionPerformed();
1102 else if (source == findMenuItem)
1104 findMenuItem_actionPerformed();
1106 else if (source == font)
1108 new FontChooser(alignPanel);
1110 else if (source == newView)
1114 else if (source == showColumns)
1116 viewport.showAllHiddenColumns();
1117 alignPanel.paintAlignment(true);
1119 else if (source == showSeqs)
1121 viewport.showAllHiddenSeqs();
1122 alignPanel.paintAlignment(true);
1124 else if (source == hideColumns)
1126 viewport.hideSelectedColumns();
1127 alignPanel.paintAlignment(true);
1129 else if (source == hideSequences
1130 && viewport.getSelectionGroup() != null)
1132 viewport.hideAllSelectedSeqs();
1133 alignPanel.paintAlignment(true);
1135 else if (source == hideAllButSelection)
1137 toggleHiddenRegions(false, false);
1138 alignPanel.paintAlignment(true);
1140 else if (source == hideAllSelection)
1142 SequenceGroup sg = viewport.getSelectionGroup();
1143 viewport.expandColSelection(sg, false);
1144 viewport.hideAllSelectedSeqs();
1145 viewport.hideSelectedColumns();
1146 alignPanel.paintAlignment(true);
1148 else if (source == showAllHidden)
1150 viewport.showAllHiddenColumns();
1151 viewport.showAllHiddenSeqs();
1152 alignPanel.paintAlignment(true);
1154 else if (source == showGroupConsensus)
1156 showGroupConsensus_actionPerformed();
1158 else if (source == showGroupConservation)
1160 showGroupConservation_actionPerformed();
1162 else if (source == showSequenceLogo)
1164 showSequenceLogo_actionPerformed();
1166 else if (source == normSequenceLogo)
1168 normSequenceLogo_actionPerformed();
1170 else if (source == showConsensusHistogram)
1172 showConsensusHistogram_actionPerformed();
1174 else if (source == applyAutoAnnotationSettings)
1176 applyAutoAnnotationSettings_actionPerformed();
1178 else if (source == featureSettings)
1180 new FeatureSettings(alignPanel);
1182 else if (source == alProperties)
1184 StringBuffer contents = new jalview.io.AlignmentProperties(
1185 viewport.getAlignment()).formatAsString();
1186 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1187 cap.setText(contents.toString());
1188 Frame frame = new Frame();
1190 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1191 "label.alignment_properties", new String[] { getTitle() }),
1194 else if (source == overviewMenuItem)
1196 overviewMenuItem_actionPerformed();
1198 else if (source == noColourmenuItem)
1202 else if (source == clustalColour)
1204 abovePIDThreshold.setState(false);
1205 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1207 else if (source == zappoColour)
1209 changeColour(new ZappoColourScheme());
1211 else if (source == taylorColour)
1213 changeColour(new TaylorColourScheme());
1215 else if (source == hydrophobicityColour)
1217 changeColour(new HydrophobicColourScheme());
1219 else if (source == helixColour)
1221 changeColour(new HelixColourScheme());
1223 else if (source == strandColour)
1225 changeColour(new StrandColourScheme());
1227 else if (source == turnColour)
1229 changeColour(new TurnColourScheme());
1231 else if (source == buriedColour)
1233 changeColour(new BuriedColourScheme());
1235 else if (source == nucleotideColour)
1237 changeColour(new NucleotideColourScheme());
1239 else if (source == purinePyrimidineColour)
1241 changeColour(new PurinePyrimidineColourScheme());
1243 // else if (source == RNAInteractionColour)
1245 // changeColour(new RNAInteractionColourScheme());
1247 else if (source == RNAHelixColour)
1249 new RNAHelicesColourChooser(viewport, alignPanel);
1251 else if (source == modifyPID)
1253 modifyPID_actionPerformed();
1255 else if (source == modifyConservation)
1257 modifyConservation_actionPerformed();
1259 else if (source == userDefinedColour)
1261 new UserDefinedColours(alignPanel, null);
1263 else if (source == PIDColour)
1265 changeColour(new PIDColourScheme());
1267 else if (source == BLOSUM62Colour)
1269 changeColour(new Blosum62ColourScheme());
1271 else if (source == tcoffeeColour)
1273 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1275 else if (source == annotationColour)
1277 new AnnotationColourChooser(viewport, alignPanel);
1279 else if (source == annotationColumnSelection)
1281 new AnnotationColumnChooser(viewport, alignPanel);
1283 else if (source == sortPairwiseMenuItem)
1285 sortPairwiseMenuItem_actionPerformed();
1287 else if (source == sortIDMenuItem)
1289 sortIDMenuItem_actionPerformed();
1291 else if (source == sortLengthMenuItem)
1293 sortLengthMenuItem_actionPerformed();
1295 else if (source == sortGroupMenuItem)
1297 sortGroupMenuItem_actionPerformed();
1299 else if (source == removeRedundancyMenuItem)
1301 removeRedundancyMenuItem_actionPerformed();
1303 else if (source == pairwiseAlignmentMenuItem)
1305 pairwiseAlignmentMenuItem_actionPerformed();
1307 else if (source == PCAMenuItem)
1309 PCAMenuItem_actionPerformed();
1311 else if (source == averageDistanceTreeMenuItem)
1313 averageDistanceTreeMenuItem_actionPerformed();
1315 else if (source == neighbourTreeMenuItem)
1317 neighbourTreeMenuItem_actionPerformed();
1319 else if (source == njTreeBlosumMenuItem)
1321 njTreeBlosumMenuItem_actionPerformed();
1323 else if (source == avDistanceTreeBlosumMenuItem)
1325 avTreeBlosumMenuItem_actionPerformed();
1327 else if (source == documentation)
1329 documentation_actionPerformed();
1331 else if (source == about)
1333 about_actionPerformed();
1338 public void inputText_actionPerformed()
1340 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1341 Frame frame = new Frame();
1343 jalview.bin.JalviewLite.addFrame(frame,
1344 MessageManager.getString("label.input_cut_paste"), 500, 500);
1347 protected void outputText_actionPerformed(ActionEvent e)
1349 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1350 Frame frame = new Frame();
1352 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1353 "label.alignment_output_command",
1354 new Object[] { e.getActionCommand() }), 600, 500);
1356 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1357 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1358 e.getActionCommand(), viewport.getAlignment(),
1359 viewport.getShowJVSuffix()));
1362 public void loadAnnotations()
1364 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1365 cap.setText(MessageManager
1366 .getString("label.paste_features_annotations_Tcoffee_here"));
1367 cap.setAnnotationImport();
1368 Frame frame = new Frame();
1370 jalview.bin.JalviewLite.addFrame(frame,
1371 MessageManager.getString("action.paste_annotations"), 400, 300);
1375 public String outputAnnotations(boolean displayTextbox)
1377 String annotation = new AnnotationFile()
1378 .printAnnotationsForView(viewport);
1382 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1383 Frame frame = new Frame();
1385 jalview.bin.JalviewLite.addFrame(frame,
1386 MessageManager.getString("label.annotations"), 600, 500);
1387 cap.setText(annotation);
1393 private Map<String, Object> getDisplayedFeatureCols()
1395 if (alignPanel.getFeatureRenderer() != null
1396 && viewport.getFeaturesDisplayed() != null)
1398 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1404 public String outputFeatures(boolean displayTextbox, String format)
1407 if (format.equalsIgnoreCase("Jalview"))
1409 features = new FeaturesFile().printJalviewFormat(viewport
1410 .getAlignment().getSequencesArray(),
1411 getDisplayedFeatureCols());
1415 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1416 .getSequencesArray(), getDisplayedFeatureCols());
1421 boolean frimport = false;
1422 if (features == null || features.equals("No Features Visible"))
1424 features = "# No features visible - paste some and import them here.";
1428 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1431 cap.setAnnotationImport();
1433 Frame frame = new Frame();
1435 jalview.bin.JalviewLite.addFrame(frame,
1436 MessageManager.getString("label.features"), 600, 500);
1437 cap.setText(features);
1441 if (features == null)
1450 void launchFullApplication()
1452 StringBuffer url = new StringBuffer(jalviewServletURL);
1454 // allow servlet parameters to be passed in applet parameter
1455 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1457 url.append(firstSep);
1460 + appendProtocol(viewport.applet.getParameter("file")));
1462 if (viewport.applet.getParameter("features") != null)
1464 url.append("&features=");
1465 url.append(appendProtocol(viewport.applet.getParameter("features")));
1468 if (viewport.applet.getParameter("annotations") != null)
1470 url.append("&annotations=");
1471 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1474 if (viewport.applet.getParameter("jnetfile") != null)
1476 url.append("&annotations=");
1477 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1480 if (viewport.applet.getParameter("defaultColour") != null)
1482 url.append("&colour="
1483 + removeWhiteSpace(viewport.applet
1484 .getParameter("defaultColour")));
1487 if (viewport.applet.getParameter("userDefinedColour") != null)
1489 url.append("&colour="
1490 + removeWhiteSpace(viewport.applet
1491 .getParameter("userDefinedColour")));
1493 if (viewport.applet.getParameter("tree") != null)
1496 + appendProtocol(viewport.applet.getParameter("tree")));
1498 if (viewport.applet.getParameter("treeFile") != null)
1501 + appendProtocol(viewport.applet.getParameter("treeFile")));
1504 showURL(url.toString(), "FULL_APP");
1507 String removeWhiteSpace(String colour)
1509 StringBuffer sb = new StringBuffer();
1510 for (int i = 0; i < colour.length(); i++)
1512 if (Character.isWhitespace(colour.charAt(i)))
1518 sb.append(colour.charAt(i));
1522 return sb.toString();
1525 String appendProtocol(String url)
1530 url = URLEncoder.encode(url);
1533 * When we finally deprecate 1.1 compatibility, we can start to use
1534 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1535 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1536 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1537 * ex.printStackTrace(); }
1539 catch (java.net.MalformedURLException ex)
1541 url = viewport.applet.getCodeBase() + url;
1546 public void closeMenuItem_actionPerformed()
1548 PaintRefresher.RemoveComponent(alignPanel);
1549 if (alignPanel.seqPanel != null
1550 && alignPanel.seqPanel.seqCanvas != null)
1552 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1554 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1556 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1559 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1574 void updateEditMenuBar()
1577 if (viewport.getHistoryList().size() > 0)
1579 undoMenuItem.setEnabled(true);
1580 CommandI command = viewport.getHistoryList().peek();
1581 undoMenuItem.setLabel(MessageManager.formatMessage(
1582 "label.undo_command",
1583 new Object[] { command.getDescription() }));
1587 undoMenuItem.setEnabled(false);
1588 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1591 if (viewport.getRedoList().size() > 0)
1593 redoMenuItem.setEnabled(true);
1595 CommandI command = viewport.getRedoList().peek();
1596 redoMenuItem.setLabel(MessageManager.formatMessage(
1597 "label.redo_command",
1598 new Object[] { command.getDescription() }));
1602 redoMenuItem.setEnabled(false);
1603 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1611 public void addHistoryItem(CommandI command)
1613 if (command.getSize() > 0)
1615 viewport.addToHistoryList(command);
1616 viewport.clearRedoList();
1617 updateEditMenuBar();
1618 viewport.updateHiddenColumns();
1623 * TODO: JAL-1104 DOCUMENT ME!
1628 protected void undoMenuItem_actionPerformed()
1630 if (viewport.getHistoryList().isEmpty())
1635 CommandI command = viewport.getHistoryList().pop();
1636 viewport.addToRedoList(command);
1637 command.undoCommand(null);
1639 AlignmentViewport originalSource = getOriginatingSource(command);
1641 if (originalSource != viewport)
1644 .println("Warning: Viewport object mismatch whilst undoing");
1646 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1647 // viewport.getColumnSelection().getHiddenColumns()
1649 updateEditMenuBar();
1650 originalSource.firePropertyChange("alignment", null, originalSource
1651 .getAlignment().getSequences());
1655 * TODO: JAL-1104 DOCUMENT ME!
1660 protected void redoMenuItem_actionPerformed()
1662 if (viewport.getRedoList().isEmpty())
1667 CommandI command = viewport.getRedoList().pop();
1668 viewport.addToHistoryList(command);
1669 command.doCommand(null);
1671 AlignmentViewport originalSource = getOriginatingSource(command);
1673 if (originalSource != viewport)
1676 .println("Warning: Viewport object mismatch whilst re-doing");
1678 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1679 // viewport.getColumnSelection().getHiddenColumns()
1682 updateEditMenuBar();
1683 originalSource.firePropertyChange("alignment", null, originalSource
1684 .getAlignment().getSequences());
1687 AlignmentViewport getOriginatingSource(CommandI command)
1689 AlignmentViewport originalSource = null;
1690 // For sequence removal and addition, we need to fire
1691 // the property change event FROM the viewport where the
1692 // original alignment was altered
1693 AlignmentI al = null;
1694 if (command instanceof EditCommand)
1696 EditCommand editCommand = (EditCommand) command;
1697 al = editCommand.getAlignment();
1698 Vector comps = (Vector) PaintRefresher.components.get(viewport
1699 .getSequenceSetId());
1700 for (int i = 0; i < comps.size(); i++)
1702 if (comps.elementAt(i) instanceof AlignmentPanel)
1704 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1706 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1713 if (originalSource == null)
1715 // The original view is closed, we must validate
1716 // the current view against the closed view first
1719 PaintRefresher.validateSequences(al, viewport.getAlignment());
1722 originalSource = viewport;
1725 return originalSource;
1729 * Move the currently selected sequences up or down one position in the
1734 public void moveSelectedSequences(boolean up)
1736 SequenceGroup sg = viewport.getSelectionGroup();
1741 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1742 up ? null : viewport.getHiddenRepSequences(), up);
1743 alignPanel.paintAlignment(true);
1746 * Also move cDNA/protein complement sequences
1748 AlignViewportI complement = viewport.getCodingComplement();
1749 if (complement != null)
1751 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1752 viewport, complement);
1753 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1754 up ? null : complement.getHiddenRepSequences(), up);
1755 // TODO need to trigger a repaint of the complementary panel - how?
1756 // would prefer to handle in SplitFrame but it is not overriding key
1761 synchronized void slideSequences(boolean right, int size)
1763 List<SequenceI> sg = new Vector<SequenceI>();
1764 if (viewport.cursorMode)
1766 sg.add(viewport.getAlignment().getSequenceAt(
1767 alignPanel.seqPanel.seqCanvas.cursorY));
1769 else if (viewport.getSelectionGroup() != null
1770 && viewport.getSelectionGroup().getSize() != viewport
1771 .getAlignment().getHeight())
1773 sg = viewport.getSelectionGroup().getSequences(
1774 viewport.getHiddenRepSequences());
1782 Vector<SequenceI> invertGroup = new Vector();
1784 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1786 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1788 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1792 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1794 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1796 for (int i = 0; i < invertGroup.size(); i++)
1798 seqs2[i] = invertGroup.elementAt(i);
1801 SlideSequencesCommand ssc;
1804 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1805 size, viewport.getGapCharacter());
1809 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1810 size, viewport.getGapCharacter());
1813 int groupAdjustment = 0;
1814 if (ssc.getGapsInsertedBegin() && right)
1816 if (viewport.cursorMode)
1818 alignPanel.seqPanel.moveCursor(size, 0);
1822 groupAdjustment = size;
1825 else if (!ssc.getGapsInsertedBegin() && !right)
1827 if (viewport.cursorMode)
1829 alignPanel.seqPanel.moveCursor(-size, 0);
1833 groupAdjustment = -size;
1837 if (groupAdjustment != 0)
1839 viewport.getSelectionGroup().setStartRes(
1840 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1841 viewport.getSelectionGroup().setEndRes(
1842 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1845 boolean appendHistoryItem = false;
1846 Deque<CommandI> historyList = viewport.getHistoryList();
1847 if (historyList != null && historyList.size() > 0
1848 && historyList.peek() instanceof SlideSequencesCommand)
1850 appendHistoryItem = ssc
1851 .appendSlideCommand((SlideSequencesCommand) historyList
1855 if (!appendHistoryItem)
1857 addHistoryItem(ssc);
1863 static StringBuffer copiedSequences;
1865 static Vector copiedHiddenColumns;
1867 protected void copy_actionPerformed()
1869 if (viewport.getSelectionGroup() == null)
1874 SequenceGroup sg = viewport.getSelectionGroup();
1875 copiedSequences = new StringBuffer();
1876 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1877 for (int i = 0; i < sg.getSize(); i++)
1879 SequenceI seq = sg.getSequenceAt(i);
1880 int index = viewport.getAlignment().findIndex(seq);
1881 orderedSeqs.put(index, seq);
1884 int index = 0, startRes, endRes;
1887 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1889 copiedHiddenColumns = new Vector();
1890 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1891 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1893 copiedHiddenColumns.addElement(new int[] {
1894 region[0] - hiddenOffset, region[1] - hiddenOffset });
1899 copiedHiddenColumns = null;
1902 for (int i = 0; i < sg.getSize(); i++)
1904 SequenceI seq = null;
1908 if (orderedSeqs.containsKey(index))
1910 seq = orderedSeqs.get(index);
1921 // Returns residue following index if gap
1922 startRes = seq.findPosition(sg.getStartRes());
1925 // Need to find the residue preceeding index if gap
1928 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1930 ch = seq.getCharAt(j);
1931 if (!jalview.util.Comparison.isGap((ch)))
1939 endRes += seq.getStart() - 1;
1942 copiedSequences.append(seq.getName()
1948 + seq.getSequenceAsString(sg.getStartRes(),
1949 sg.getEndRes() + 1) + "\n");
1954 protected void pasteNew_actionPerformed()
1959 protected void pasteThis_actionPerformed()
1964 void paste(boolean newAlignment)
1969 if (copiedSequences == null)
1974 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1975 Vector seqs = new Vector();
1976 while (st.hasMoreElements())
1978 String name = st.nextToken();
1979 int start = Integer.parseInt(st.nextToken());
1980 int end = Integer.parseInt(st.nextToken());
1981 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1983 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1984 for (int i = 0; i < seqs.size(); i++)
1986 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1991 String newtitle = MessageManager
1992 .getString("label.copied_sequences");
1993 if (getTitle().startsWith(
1994 MessageManager.getString("label.copied_sequences")))
1996 newtitle = getTitle();
2000 newtitle = newtitle.concat(MessageManager.formatMessage(
2001 "label.from_msname", new String[] { getTitle() }));
2003 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2004 viewport.applet, newtitle, false);
2005 if (copiedHiddenColumns != null)
2007 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2009 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2010 af.viewport.hideColumns(region[0], region[1]);
2014 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2019 addSequences(newSeqs);
2022 } catch (Exception ex)
2024 } // could be anything being pasted in here
2028 void addSequences(SequenceI[] seqs)
2030 for (int i = 0; i < seqs.length; i++)
2032 viewport.getAlignment().addSequence(seqs[i]);
2036 addHistoryItem(new EditCommand(
2037 MessageManager.getString("label.add_sequences"), Action.PASTE,
2038 seqs, 0, viewport.getAlignment().getWidth(),
2039 viewport.getAlignment()));
2041 viewport.setEndSeq(viewport.getAlignment().getHeight());
2042 viewport.getAlignment().getWidth();
2043 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2048 protected void cut_actionPerformed()
2050 copy_actionPerformed();
2051 delete_actionPerformed();
2054 protected void delete_actionPerformed()
2057 SequenceGroup sg = viewport.getSelectionGroup();
2063 Vector seqs = new Vector();
2065 for (int i = 0; i < sg.getSize(); i++)
2067 seq = sg.getSequenceAt(i);
2068 seqs.addElement(seq);
2072 * If the cut affects all sequences, warn, remove highlighted columns
2074 if (sg.getSize() == viewport.getAlignment().getHeight())
2076 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2077 .getAlignment().getWidth()) ? true : false;
2078 if (isEntireAlignWidth)
2080 String title = MessageManager.getString("label.delete_all");
2081 Panel infoPanel = new Panel();
2082 infoPanel.setLayout(new FlowLayout());
2084 .add(new Label(MessageManager.getString("warn.delete_all")));
2086 final JVDialog dialog = new JVDialog(this, title, true, 400,
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.size() > 0)
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",
2301 TrimRegionCommand.TRIM_LEFT, seqs, column,
2302 viewport.getAlignment(), viewport.getColumnSelection(),
2303 viewport.getSelectionGroup());
2304 viewport.setStartRes(0);
2308 trimRegion = new TrimRegionCommand("Remove Right",
2309 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2310 viewport.getAlignment(), viewport.getColumnSelection(),
2311 viewport.getSelectionGroup());
2314 statusBar.setText(MessageManager.formatMessage(
2315 "label.removed_columns",
2316 new String[] { Integer.valueOf(trimRegion.getSize())
2318 addHistoryItem(trimRegion);
2320 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2322 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2323 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2325 viewport.getAlignment().deleteGroup(sg);
2329 viewport.firePropertyChange("alignment", null, viewport
2330 .getAlignment().getSequences());
2334 public void removeGappedColumnMenuItem_actionPerformed()
2336 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2339 if (viewport.getSelectionGroup() != null)
2341 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2342 viewport.getHiddenRepSequences());
2343 start = viewport.getSelectionGroup().getStartRes();
2344 end = viewport.getSelectionGroup().getEndRes();
2348 seqs = viewport.getAlignment().getSequencesArray();
2351 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2352 "Remove Gapped Columns", seqs, start, end,
2353 viewport.getAlignment());
2355 addHistoryItem(removeGapCols);
2357 statusBar.setText(MessageManager.formatMessage(
2358 "label.removed_empty_columns",
2359 new String[] { Integer.valueOf(removeGapCols.getSize())
2362 // This is to maintain viewport position on first residue
2363 // of first sequence
2364 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2365 int startRes = seq.findPosition(viewport.startRes);
2366 // ShiftList shifts;
2367 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2368 // edit.alColumnChanges=shifts.getInverse();
2369 // if (viewport.hasHiddenColumns)
2370 // viewport.getColumnSelection().compensateForEdits(shifts);
2371 viewport.setStartRes(seq.findIndex(startRes) - 1);
2372 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2377 public void removeAllGapsMenuItem_actionPerformed()
2379 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2382 if (viewport.getSelectionGroup() != null)
2384 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385 viewport.getHiddenRepSequences());
2386 start = viewport.getSelectionGroup().getStartRes();
2387 end = viewport.getSelectionGroup().getEndRes();
2391 seqs = viewport.getAlignment().getSequencesArray();
2394 // This is to maintain viewport position on first residue
2395 // of first sequence
2396 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2397 int startRes = seq.findPosition(viewport.startRes);
2399 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2400 viewport.getAlignment()));
2402 viewport.setStartRes(seq.findIndex(startRes) - 1);
2404 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2409 public void findMenuItem_actionPerformed()
2411 new Finder(alignPanel);
2415 * create a new view derived from the current view
2418 * @return frame for the new view
2420 public AlignFrame newView(String viewtitle)
2423 if (viewport.hasHiddenRows())
2425 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2426 .getFullAlignment().getSequencesArray());
2430 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2433 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2435 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2437 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2439 newal.addAnnotation(viewport.getAlignment()
2440 .getAlignmentAnnotation()[i]);
2445 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2447 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2448 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2449 PaintRefresher.Register(newaf.alignPanel,
2450 newaf.alignPanel.av.getSequenceSetId());
2452 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2453 newaf.alignPanel.av.getSequenceSetId());
2454 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2455 newaf.alignPanel.av.getSequenceSetId());
2457 Vector comps = (Vector) PaintRefresher.components.get(viewport
2458 .getSequenceSetId());
2460 for (int i = 0; i < comps.size(); i++)
2462 if (comps.elementAt(i) instanceof AlignmentPanel)
2468 String title = new String(this.getTitle());
2469 if (viewtitle != null)
2471 title = viewtitle + " ( " + title + ")";
2475 if (title.indexOf("(View") > -1)
2477 title = title.substring(0, title.indexOf("(View"));
2479 title += "(View " + viewSize + ")";
2482 newaf.setTitle(title.toString());
2484 newaf.viewport.setHistoryList(viewport.getHistoryList());
2485 newaf.viewport.setRedoList(viewport.getRedoList());
2491 * @return list of feature groups on the view
2493 public String[] getFeatureGroups()
2495 FeatureRenderer fr = null;
2496 if (alignPanel != null
2497 && (fr = alignPanel.getFeatureRenderer()) != null)
2499 List<String> gps = fr.getFeatureGroups();
2500 String[] _gps = gps.toArray(new String[gps.size()]);
2507 * get sequence feature groups that are hidden or shown
2513 public String[] getFeatureGroupsOfState(boolean visible)
2515 FeatureRenderer fr = null;
2516 if (alignPanel != null
2517 && (fr = alignPanel.getFeatureRenderer()) != null)
2519 List<String> gps = fr.getGroups(visible);
2520 String[] _gps = gps.toArray(new String[gps.size()]);
2527 * Change the display state for the given feature groups
2530 * list of group strings
2532 * visible or invisible
2534 public void setFeatureGroupState(String[] groups, boolean state)
2536 FeatureRenderer fr = null;
2537 this.sequenceFeatures.setState(true);
2538 viewport.setShowSequenceFeatures(true);
2539 if (alignPanel != null
2540 && (fr = alignPanel.getFeatureRenderer()) != null)
2543 fr.setGroupVisibility(Arrays.asList(groups), state);
2544 alignPanel.seqPanel.seqCanvas.repaint();
2545 if (alignPanel.overviewPanel != null)
2547 alignPanel.overviewPanel.updateOverviewImage();
2552 public void seqLimits_itemStateChanged()
2554 viewport.setShowJVSuffix(seqLimits.getState());
2555 alignPanel.fontChanged();
2556 alignPanel.paintAlignment(true);
2559 protected void colourTextMenuItem_actionPerformed()
2561 viewport.setColourText(colourTextMenuItem.getState());
2562 alignPanel.paintAlignment(true);
2565 protected void displayNonconservedMenuItem_actionPerformed()
2567 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2568 alignPanel.paintAlignment(true);
2571 protected void wrapMenuItem_actionPerformed()
2573 viewport.setWrapAlignment(wrapMenuItem.getState());
2574 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2575 scaleAbove.setEnabled(wrapMenuItem.getState());
2576 scaleLeft.setEnabled(wrapMenuItem.getState());
2577 scaleRight.setEnabled(wrapMenuItem.getState());
2578 alignPanel.paintAlignment(true);
2581 public void overviewMenuItem_actionPerformed()
2583 if (alignPanel.overviewPanel != null)
2588 Frame frame = new Frame();
2589 OverviewPanel overview = new OverviewPanel(alignPanel);
2590 frame.add(overview);
2591 // +50 must allow for applet frame window
2592 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2593 "label.overview_params", new String[] { this.getTitle() }),
2594 overview.getPreferredSize().width,
2595 overview.getPreferredSize().height + 50);
2598 final AlignmentPanel ap = alignPanel;
2599 frame.addWindowListener(new WindowAdapter()
2602 public void windowClosing(WindowEvent e)
2606 ap.setOverviewPanel(null);
2611 alignPanel.setOverviewPanel(overview);
2615 public void changeColour(ColourSchemeI cs)
2620 if (viewport.getAbovePIDThreshold())
2622 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2626 if (viewport.getConservationSelected())
2628 cs.setConservationApplied(true);
2629 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2634 cs.setConservationApplied(false);
2637 viewport.setGlobalColourScheme(cs);
2639 alignPanel.paintAlignment(true);
2642 protected void modifyPID_actionPerformed()
2644 if (viewport.getAbovePIDThreshold()
2645 && viewport.getGlobalColourScheme() != null)
2647 SliderPanel.setPIDSliderSource(alignPanel,
2648 viewport.getGlobalColourScheme(), "Background");
2649 SliderPanel.showPIDSlider();
2653 protected void modifyConservation_actionPerformed()
2655 if (viewport.getConservationSelected()
2656 && viewport.getGlobalColourScheme() != null)
2658 SliderPanel.setConservationSlider(alignPanel,
2659 viewport.getGlobalColourScheme(), "Background");
2660 SliderPanel.showConservationSlider();
2664 protected void conservationMenuItem_actionPerformed()
2666 viewport.setConservationSelected(conservationMenuItem.getState());
2668 viewport.setAbovePIDThreshold(false);
2669 abovePIDThreshold.setState(false);
2671 changeColour(viewport.getGlobalColourScheme());
2673 modifyConservation_actionPerformed();
2676 public void abovePIDThreshold_actionPerformed()
2678 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2680 conservationMenuItem.setState(false);
2681 viewport.setConservationSelected(false);
2683 changeColour(viewport.getGlobalColourScheme());
2685 modifyPID_actionPerformed();
2688 public void sortPairwiseMenuItem_actionPerformed()
2690 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2691 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2692 .getAlignment().getSequenceAt(0), null);
2694 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2695 viewport.getAlignment()));
2696 alignPanel.paintAlignment(true);
2699 public void sortIDMenuItem_actionPerformed()
2701 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2702 AlignmentSorter.sortByID(viewport.getAlignment());
2703 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2704 viewport.getAlignment()));
2705 alignPanel.paintAlignment(true);
2708 public void sortLengthMenuItem_actionPerformed()
2710 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2711 AlignmentSorter.sortByLength(viewport.getAlignment());
2712 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2713 viewport.getAlignment()));
2714 alignPanel.paintAlignment(true);
2717 public void sortGroupMenuItem_actionPerformed()
2719 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2720 AlignmentSorter.sortByGroup(viewport.getAlignment());
2721 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2722 viewport.getAlignment()));
2723 alignPanel.paintAlignment(true);
2727 public void removeRedundancyMenuItem_actionPerformed()
2729 new RedundancyPanel(alignPanel);
2732 public void pairwiseAlignmentMenuItem_actionPerformed()
2734 if (viewport.getSelectionGroup() != null
2735 && viewport.getSelectionGroup().getSize() > 1)
2737 Frame frame = new Frame();
2738 frame.add(new PairwiseAlignPanel(alignPanel));
2739 jalview.bin.JalviewLite.addFrame(frame,
2740 MessageManager.getString("action.pairwise_alignment"), 600,
2745 public void PCAMenuItem_actionPerformed()
2747 // are the sequences aligned?
2748 if (!viewport.getAlignment().isAligned(false))
2751 int Width = viewport.getAlignment().getWidth();
2753 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2755 current = viewport.getAlignment().getSequenceAt(i);
2757 if (current.getLength() < Width)
2759 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2762 alignPanel.paintAlignment(true);
2765 if ((viewport.getSelectionGroup() != null
2766 && viewport.getSelectionGroup().getSize() < 4 && viewport
2767 .getSelectionGroup().getSize() > 0)
2768 || viewport.getAlignment().getHeight() < 4)
2775 new PCAPanel(viewport);
2776 } catch (java.lang.OutOfMemoryError ex)
2782 public void averageDistanceTreeMenuItem_actionPerformed()
2784 NewTreePanel("AV", "PID", "Average distance tree using PID");
2787 public void neighbourTreeMenuItem_actionPerformed()
2789 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2792 protected void njTreeBlosumMenuItem_actionPerformed()
2794 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2797 protected void avTreeBlosumMenuItem_actionPerformed()
2799 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2802 void NewTreePanel(String type, String pwType, String title)
2804 // are the sequences aligned?
2805 if (!viewport.getAlignment().isAligned(false))
2808 int Width = viewport.getAlignment().getWidth();
2810 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2812 current = viewport.getAlignment().getSequenceAt(i);
2814 if (current.getLength() < Width)
2816 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2819 alignPanel.paintAlignment(true);
2823 if ((viewport.getSelectionGroup() != null && viewport
2824 .getSelectionGroup().getSize() > 1)
2825 || (viewport.getAlignment().getHeight() > 1))
2827 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2829 addTreeMenuItem(tp, title);
2831 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2835 void loadTree_actionPerformed()
2837 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2838 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2839 cap.setTreeImport();
2840 Frame frame = new Frame();
2842 jalview.bin.JalviewLite.addFrame(frame,
2843 MessageManager.getString("label.paste_newick_file"), 400, 300);
2846 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2848 TreePanel tp = new TreePanel(alignPanel, treeFile,
2849 MessageManager.getString("label.load_tree_from_file"), tree);
2850 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2851 addTreeMenuItem(tp, treeFile);
2855 * sort the alignment using the given treePanel
2858 * tree used to sort view
2860 * string used for undo event name
2862 public void sortByTree(TreePanel treePanel, String title)
2864 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2866 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2867 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2868 // HistoryItem.SORT));
2869 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2870 "label.order_by_params", new String[] { title }), oldOrder,
2871 viewport.getAlignment()));
2872 alignPanel.paintAlignment(true);
2876 * Do any automatic reordering of the alignment and add the necessary bits to
2877 * the menu structure for the new tree
2882 protected void addTreeMenuItem(final TreePanel treePanel,
2885 final MenuItem item = new MenuItem(title);
2886 sortByTreeMenu.add(item);
2887 item.addActionListener(new java.awt.event.ActionListener()
2890 public void actionPerformed(ActionEvent evt)
2892 sortByTree(treePanel, title); // treePanel.getTitle());
2896 treePanel.addWindowListener(new WindowAdapter()
2899 public void windowOpened(WindowEvent e)
2901 if (viewport.sortByTree)
2903 sortByTree(treePanel, title);
2905 super.windowOpened(e);
2909 public void windowClosing(WindowEvent e)
2911 sortByTreeMenu.remove(item);
2916 public boolean sortBy(AlignmentOrder alorder, String undoname)
2918 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2919 if (viewport.applet.debug)
2921 System.err.println("Sorting " + alorder.getOrder().size()
2922 + " in alignment '" + getTitle() + "'");
2924 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2925 if (undoname != null)
2927 addHistoryItem(new OrderCommand(undoname, oldOrder,
2928 viewport.getAlignment()));
2930 alignPanel.paintAlignment(true);
2934 protected void documentation_actionPerformed()
2936 alignPanel.av.applet.openJalviewHelpUrl();
2939 protected void about_actionPerformed()
2942 class AboutPanel extends Canvas
2948 public AboutPanel(String version, String builddate)
2950 this.version = version;
2951 this.builddate = builddate;
2955 public void paint(Graphics g)
2957 g.setColor(Color.white);
2958 g.fillRect(0, 0, getSize().width, getSize().height);
2959 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2960 FontMetrics fm = g.getFontMetrics();
2961 int fh = fm.getHeight();
2963 g.setColor(Color.black);
2964 // TODO: update this text for each release or centrally store it for
2965 // lite and application
2966 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2967 g.drawString(MessageManager.formatMessage(
2968 "label.jalviewLite_release", new String[] { version }), x,
2970 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2971 g.drawString(MessageManager.formatMessage(
2972 "label.jaview_build_date", new String[] { builddate }), x,
2974 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2975 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2977 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2978 x + 50, y += fh + 8);
2980 MessageManager.getString("label.jalview_dev_managers"), x,
2982 g.drawString(MessageManager
2983 .getString("label.jalview_distribution_lists"), x, y += fh);
2984 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2987 MessageManager.getString("label.jalview_cite_1_authors"),
2990 MessageManager.getString("label.jalview_cite_1_title"), x,
2992 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2997 Frame frame = new Frame();
2998 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3000 jalview.bin.JalviewLite.addFrame(frame,
3001 MessageManager.getString("label.jalview"), 580, 220);
3005 public void showURL(String url, String target)
3007 if (viewport.applet == null)
3009 System.out.println("Not running as applet - no browser available.");
3013 viewport.applet.showURL(url, target);
3017 // ////////////////////////////////////////////////////////////////////////////////
3018 // JBuilder Graphics here
3020 MenuBar alignFrameMenuBar = new MenuBar();
3022 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3024 MenuItem loadApplication = new MenuItem(
3025 MessageManager.getString("label.view_full_application"));
3027 MenuItem loadTree = new MenuItem(
3028 MessageManager.getString("label.load_associated_tree"));
3030 MenuItem loadAnnotations = new MenuItem(
3031 MessageManager.getString("label.load_features_annotations"));
3033 MenuItem outputFeatures = new MenuItem(
3034 MessageManager.getString("label.export_features"));
3036 MenuItem outputAnnotations = new MenuItem(
3037 MessageManager.getString("label.export_annotations"));
3039 MenuItem closeMenuItem = new MenuItem(
3040 MessageManager.getString("action.close"));
3042 MenuItem selectAllSequenceMenuItem = new MenuItem(
3043 MessageManager.getString("action.select_all"));
3045 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3046 MessageManager.getString("action.deselect_all"));
3048 MenuItem invertSequenceMenuItem = new MenuItem(
3049 MessageManager.getString("action.invert_selection"));
3051 MenuItem remove2LeftMenuItem = new MenuItem();
3053 MenuItem remove2RightMenuItem = new MenuItem();
3055 MenuItem removeGappedColumnMenuItem = new MenuItem();
3057 MenuItem removeAllGapsMenuItem = new MenuItem();
3059 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3061 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3063 MenuItem sortPairwiseMenuItem = new MenuItem();
3065 MenuItem sortIDMenuItem = new MenuItem();
3067 MenuItem sortLengthMenuItem = new MenuItem();
3069 MenuItem sortGroupMenuItem = new MenuItem();
3071 MenuItem removeRedundancyMenuItem = new MenuItem();
3073 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3075 MenuItem PCAMenuItem = new MenuItem();
3077 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3079 MenuItem neighbourTreeMenuItem = new MenuItem();
3081 BorderLayout borderLayout1 = new BorderLayout();
3083 public Label statusBar = new Label();
3085 MenuItem clustalColour = new MenuItem();
3087 MenuItem zappoColour = new MenuItem();
3089 MenuItem taylorColour = new MenuItem();
3091 MenuItem hydrophobicityColour = new MenuItem();
3093 MenuItem helixColour = new MenuItem();
3095 MenuItem strandColour = new MenuItem();
3097 MenuItem turnColour = new MenuItem();
3099 MenuItem buriedColour = new MenuItem();
3101 MenuItem purinePyrimidineColour = new MenuItem();
3103 // MenuItem RNAInteractionColour = new MenuItem();
3105 MenuItem RNAHelixColour = new MenuItem();
3107 MenuItem userDefinedColour = new MenuItem();
3109 MenuItem PIDColour = new MenuItem();
3111 MenuItem BLOSUM62Colour = new MenuItem();
3113 MenuItem tcoffeeColour = new MenuItem();
3115 MenuItem njTreeBlosumMenuItem = new MenuItem();
3117 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3119 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3121 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3123 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3125 MenuItem alProperties = new MenuItem(
3126 MessageManager.getString("label.alignment_props"));
3128 MenuItem overviewMenuItem = new MenuItem();
3130 MenuItem undoMenuItem = new MenuItem();
3132 MenuItem redoMenuItem = new MenuItem();
3134 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3136 MenuItem noColourmenuItem = new MenuItem();
3138 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3140 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3142 MenuItem findMenuItem = new MenuItem();
3144 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3146 MenuItem nucleotideColour = new MenuItem();
3148 MenuItem deleteGroups = new MenuItem();
3150 MenuItem grpsFromSelection = new MenuItem();
3152 MenuItem createGroup = new MenuItem();
3154 MenuItem unGroup = new MenuItem();
3156 MenuItem delete = new MenuItem();
3158 MenuItem copy = new MenuItem();
3160 MenuItem cut = new MenuItem();
3162 Menu pasteMenu = new Menu();
3164 MenuItem pasteNew = new MenuItem();
3166 MenuItem pasteThis = new MenuItem();
3168 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3170 MenuItem font = new MenuItem();
3172 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3174 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3176 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3178 MenuItem modifyPID = new MenuItem();
3180 MenuItem modifyConservation = new MenuItem();
3182 CheckboxMenuItem autoCalculate = null;
3184 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3185 "Sort Alignment With New Tree", true);
3187 Menu sortByTreeMenu = new Menu();
3189 MenuItem inputText = new MenuItem();
3191 MenuItem documentation = new MenuItem();
3193 MenuItem about = new MenuItem();
3195 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3197 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3199 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3201 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3203 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3205 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3207 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3209 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3211 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3214 * Initialise menus and other items
3218 private void jbInit() throws Exception
3220 setMenuBar(alignFrameMenuBar);
3223 * Configure File menu items and actions
3226 .setLabel(MessageManager.getString("label.input_from_textbox"));
3227 inputText.addActionListener(this);
3228 Menu outputTextboxMenu = new Menu(
3229 MessageManager.getString("label.out_to_textbox"));
3230 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3233 MenuItem item = new MenuItem(
3234 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3236 item.addActionListener(new java.awt.event.ActionListener()
3239 public void actionPerformed(ActionEvent e)
3241 outputText_actionPerformed(e);
3245 outputTextboxMenu.add(item);
3247 closeMenuItem.addActionListener(this);
3248 loadApplication.addActionListener(this);
3249 loadTree.addActionListener(this);
3250 loadAnnotations.addActionListener(this);
3251 outputFeatures.addActionListener(this);
3252 outputAnnotations.addActionListener(this);
3255 * Configure Edit menu items and actions
3257 undoMenuItem.setEnabled(false);
3258 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3259 undoMenuItem.addActionListener(this);
3260 redoMenuItem.setEnabled(false);
3261 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3262 redoMenuItem.addActionListener(this);
3263 copy.setLabel(MessageManager.getString("action.copy"));
3264 copy.addActionListener(this);
3265 cut.setLabel(MessageManager.getString("action.cut"));
3266 cut.addActionListener(this);
3267 delete.setLabel(MessageManager.getString("action.delete"));
3268 delete.addActionListener(this);
3269 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3270 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3271 pasteNew.addActionListener(this);
3272 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3273 pasteThis.addActionListener(this);
3274 remove2LeftMenuItem.setLabel(MessageManager
3275 .getString("action.remove_left"));
3276 remove2LeftMenuItem.addActionListener(this);
3277 remove2RightMenuItem.setLabel(MessageManager
3278 .getString("action.remove_right"));
3279 remove2RightMenuItem.addActionListener(this);
3280 removeGappedColumnMenuItem.setLabel(MessageManager
3281 .getString("action.remove_empty_columns"));
3282 removeGappedColumnMenuItem.addActionListener(this);
3283 removeAllGapsMenuItem.setLabel(MessageManager
3284 .getString("action.remove_all_gaps"));
3285 removeAllGapsMenuItem.addActionListener(this);
3286 removeRedundancyMenuItem.setLabel(MessageManager
3287 .getString("action.remove_redundancy"));
3288 removeRedundancyMenuItem.addActionListener(this);
3291 * Configure Select menu items and actions
3293 findMenuItem.setLabel(MessageManager.getString("action.find"));
3294 findMenuItem.addActionListener(this);
3295 selectAllSequenceMenuItem.addActionListener(this);
3296 deselectAllSequenceMenuItem.addActionListener(this);
3297 invertSequenceMenuItem.setLabel(MessageManager
3298 .getString("action.invert_sequence_selection"));
3299 invertSequenceMenuItem.addActionListener(this);
3300 invertColSel.setLabel(MessageManager
3301 .getString("action.invert_column_selection"));
3302 invertColSel.addActionListener(this);
3303 deleteGroups.setLabel(MessageManager
3304 .getString("action.undefine_groups"));
3305 deleteGroups.addActionListener(this);
3306 grpsFromSelection.setLabel(MessageManager
3307 .getString("action.make_groups_selection"));
3308 grpsFromSelection.addActionListener(this);
3309 createGroup.setLabel(MessageManager.getString("action.create_group"));
3310 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3311 annotationColumnSelection.setLabel(MessageManager
3312 .getString("action.select_by_annotation"));
3313 annotationColumnSelection.addActionListener(this);
3316 * Configure View menu items and actions
3318 newView.setLabel(MessageManager.getString("action.new_view"));
3319 newView.addActionListener(this);
3320 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3321 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3322 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3323 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3325 .setLabel(MessageManager.getString("label.selected_columns"));
3326 hideSequences.setLabel(MessageManager
3327 .getString("label.selected_sequences"));
3328 hideAllButSelection.setLabel(MessageManager
3329 .getString("label.all_but_selected_region"));
3330 hideAllSelection.setLabel(MessageManager
3331 .getString("label.selected_region"));
3332 showAllHidden.setLabel(MessageManager
3333 .getString("label.all_sequences_columns"));
3334 showColumns.addActionListener(this);
3335 showSeqs.addActionListener(this);
3336 hideColumns.addActionListener(this);
3337 hideSequences.addActionListener(this);
3338 hideAllButSelection.addActionListener(this);
3339 hideAllSelection.addActionListener(this);
3340 showAllHidden.addActionListener(this);
3341 featureSettings.setLabel(MessageManager
3342 .getString("action.feature_settings"));
3343 featureSettings.addActionListener(this);
3344 sequenceFeatures.setLabel(MessageManager
3345 .getString("label.show_sequence_features"));
3346 sequenceFeatures.addItemListener(this);
3347 sequenceFeatures.setState(false);
3348 followMouseOverFlag.setLabel(MessageManager
3349 .getString("label.automatic_scrolling"));
3350 followMouseOverFlag.addItemListener(this);
3351 alProperties.addActionListener(this);
3352 overviewMenuItem.setLabel(MessageManager
3353 .getString("label.overview_window"));
3354 overviewMenuItem.addActionListener(this);
3357 * Configure Annotations menu items and actions
3359 annotationPanelMenuItem.setLabel(MessageManager
3360 .getString("label.show_annotations"));
3361 annotationPanelMenuItem.addItemListener(this);
3362 showGroupConsensus.setLabel(MessageManager
3363 .getString("label.group_consensus"));
3364 showGroupConservation.setLabel(MessageManager
3365 .getString("label.group_conservation"));
3366 showConsensusHistogram.setLabel(MessageManager
3367 .getString("label.show_consensus_histogram"));
3368 showSequenceLogo.setLabel(MessageManager
3369 .getString("label.show_consensus_logo"));
3370 normSequenceLogo.setLabel(MessageManager
3371 .getString("label.norm_consensus_logo"));
3372 applyAutoAnnotationSettings.setLabel(MessageManager
3373 .getString("label.apply_all_groups"));
3374 applyAutoAnnotationSettings.setState(true);
3375 Menu autoAnnMenu = new Menu(
3376 MessageManager.getString("label.autocalculated_annotation"));
3377 showGroupConsensus.addItemListener(this);
3378 showGroupConservation.addItemListener(this);
3379 showConsensusHistogram.addItemListener(this);
3380 showSequenceLogo.addItemListener(this);
3381 normSequenceLogo.addItemListener(this);
3382 applyAutoAnnotationSettings.addItemListener(this);
3383 showAlignmentAnnotations = new CheckboxMenuItem(
3384 MessageManager.getString("label.show_all_al_annotations"));
3385 showSequenceAnnotations = new CheckboxMenuItem(
3386 MessageManager.getString("label.show_all_seq_annotations"));
3387 sortAnnBySequence = new CheckboxMenuItem(
3388 MessageManager.getString("label.sort_annotations_by_sequence"));
3389 sortAnnByLabel = new CheckboxMenuItem(
3390 MessageManager.getString("label.sort_annotations_by_label"));
3391 showAutoFirst = new CheckboxMenuItem(
3392 MessageManager.getString("label.show_first"));
3393 showAutoFirst.setState(false); // pending applet parameter
3394 setShowAutoCalculatedAbove(showAutoFirst.getState());
3395 showAutoLast = new CheckboxMenuItem(
3396 MessageManager.getString("label.show_last"));
3397 showAutoLast.setState(!showAutoFirst.getState());
3398 showAlignmentAnnotations.addItemListener(this);
3399 showSequenceAnnotations.addItemListener(this);
3400 sortAnnBySequence.addItemListener(this);
3401 sortAnnByLabel.addItemListener(this);
3402 showAutoFirst.addItemListener(this);
3403 showAutoLast.addItemListener(this);
3406 * Configure Format menu items and actions
3408 font.setLabel(MessageManager.getString("action.font"));
3409 font.addActionListener(this);
3410 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3411 scaleAbove.setState(true);
3412 scaleAbove.setEnabled(false);
3413 scaleAbove.addItemListener(this);
3414 scaleLeft.setEnabled(false);
3415 scaleLeft.setState(true);
3416 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3417 scaleLeft.addItemListener(this);
3418 scaleRight.setEnabled(false);
3419 scaleRight.setState(true);
3420 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3421 scaleRight.addItemListener(this);
3422 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3423 viewBoxesMenuItem.setState(true);
3424 viewBoxesMenuItem.addItemListener(this);
3425 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3426 viewTextMenuItem.setState(true);
3427 viewTextMenuItem.addItemListener(this);
3428 colourTextMenuItem.setLabel(MessageManager
3429 .getString("label.colour_text"));
3430 colourTextMenuItem.addItemListener(this);
3431 displayNonconservedMenuItem.setLabel(MessageManager
3432 .getString("label.show_non_conversed"));
3433 displayNonconservedMenuItem.addItemListener(this);
3434 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3435 wrapMenuItem.addItemListener(this);
3436 renderGapsMenuItem.setLabel(MessageManager
3437 .getString("action.show_gaps"));
3438 renderGapsMenuItem.setState(true);
3439 renderGapsMenuItem.addItemListener(this);
3440 centreColumnLabelFlag.setLabel(MessageManager
3441 .getString("label.centre_column_labels"));
3442 centreColumnLabelFlag.addItemListener(this);
3443 seqLimits.setState(true);
3444 seqLimits.setLabel(MessageManager
3445 .getString("label.show_sequence_limits"));
3446 seqLimits.addItemListener(this);
3449 * Configure Colour menu items and actions
3451 applyToAllGroups.setLabel(MessageManager
3452 .getString("label.apply_colour_to_all_groups"));
3453 applyToAllGroups.setState(true);
3454 applyToAllGroups.addItemListener(this);
3455 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3456 clustalColour.addActionListener(this);
3457 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3458 zappoColour.addActionListener(this);
3459 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3460 taylorColour.addActionListener(this);
3461 hydrophobicityColour.setLabel(MessageManager
3462 .getString("label.hydrophobicity"));
3463 hydrophobicityColour.addActionListener(this);
3465 .setLabel(MessageManager.getString("label.helix_propensity"));
3466 helixColour.addActionListener(this);
3467 strandColour.setLabel(MessageManager
3468 .getString("label.strand_propensity"));
3469 strandColour.addActionListener(this);
3470 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3471 turnColour.addActionListener(this);
3472 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3473 buriedColour.addActionListener(this);
3474 purinePyrimidineColour.setLabel(MessageManager
3475 .getString("label.purine_pyrimidine"));
3476 purinePyrimidineColour.addActionListener(this);
3477 // RNAInteractionColour.setLabel(MessageManager
3478 // .getString("label.rna_interaction"));
3479 // RNAInteractionColour.addActionListener(this);
3480 RNAHelixColour.setLabel(MessageManager
3481 .getString("action.by_rna_helixes"));
3482 RNAHelixColour.addActionListener(this);
3483 userDefinedColour.setLabel(MessageManager
3484 .getString("action.user_defined"));
3485 userDefinedColour.addActionListener(this);
3486 PIDColour.setLabel(MessageManager
3487 .getString("label.percentage_identity"));
3488 PIDColour.addActionListener(this);
3489 BLOSUM62Colour.setLabel(MessageManager
3490 .getString("label.blosum62_score"));
3491 BLOSUM62Colour.addActionListener(this);
3493 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3494 // it will be enabled only if a score file is provided
3495 tcoffeeColour.setEnabled(false);
3496 tcoffeeColour.addActionListener(this);
3497 conservationMenuItem.setLabel(MessageManager
3498 .getString("action.by_conservation"));
3499 conservationMenuItem.addItemListener(this);
3500 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3501 noColourmenuItem.addActionListener(this);
3502 abovePIDThreshold.setLabel(MessageManager
3503 .getString("label.above_identity_threshold"));
3504 abovePIDThreshold.addItemListener(this);
3505 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3506 nucleotideColour.addActionListener(this);
3507 modifyPID.setLabel(MessageManager
3508 .getString("label.modify_identity_thereshold"));
3509 modifyPID.addActionListener(this);
3510 modifyConservation.setLabel(MessageManager
3511 .getString("label.modify_conservation_thereshold"));
3512 modifyConservation.addActionListener(this);
3513 annotationColour.setLabel(MessageManager
3514 .getString("action.by_annotation"));
3515 annotationColour.addActionListener(this);
3518 * Configure Calculate menu items and actions
3520 sortPairwiseMenuItem.setLabel(MessageManager
3521 .getString("action.by_pairwise_id"));
3522 sortPairwiseMenuItem.addActionListener(this);
3523 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3524 sortIDMenuItem.addActionListener(this);
3525 sortLengthMenuItem.setLabel(MessageManager
3526 .getString("action.by_length"));
3527 sortLengthMenuItem.addActionListener(this);
3528 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3529 sortGroupMenuItem.addActionListener(this);
3530 pairwiseAlignmentMenuItem.setLabel(MessageManager
3531 .getString("action.pairwise_alignment"));
3532 pairwiseAlignmentMenuItem.addActionListener(this);
3533 PCAMenuItem.setLabel(MessageManager
3534 .getString("label.principal_component_analysis"));
3535 PCAMenuItem.addActionListener(this);
3536 autoCalculate = new CheckboxMenuItem(
3537 MessageManager.getString("label.autocalculate_consensus"), true);
3538 averageDistanceTreeMenuItem.setLabel(MessageManager
3539 .getString("label.average_distance_identity"));
3540 averageDistanceTreeMenuItem.addActionListener(this);
3541 neighbourTreeMenuItem.setLabel(MessageManager
3542 .getString("label.neighbour_joining_identity"));
3543 neighbourTreeMenuItem.addActionListener(this);
3544 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3545 .getString("label.average_distance_bloslum62"));
3546 avDistanceTreeBlosumMenuItem.addActionListener(this);
3547 njTreeBlosumMenuItem.setLabel(MessageManager
3548 .getString("label.neighbour_blosum62"));
3549 njTreeBlosumMenuItem.addActionListener(this);
3550 sortByTreeMenu.setLabel(MessageManager
3551 .getString("action.by_tree_order"));
3552 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3553 Menu calculateTreeMenu = new Menu(
3554 MessageManager.getString("action.calculate_tree"));
3555 autoCalculate.addItemListener(this);
3556 sortByTree.addItemListener(this);
3559 * Configure Help menu items and actions
3561 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3562 documentation.setLabel(MessageManager.getString("label.documentation"));
3563 documentation.addActionListener(this);
3564 about.setLabel(MessageManager.getString("label.about"));
3565 about.addActionListener(this);
3568 * Add top level menus to frame
3570 alignFrameMenuBar.add(fileMenu);
3571 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3572 alignFrameMenuBar.add(editMenu);
3573 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3574 alignFrameMenuBar.add(selectMenu);
3575 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3576 alignFrameMenuBar.add(viewMenu);
3577 Menu annotationsMenu = new Menu(
3578 MessageManager.getString("action.annotations"));
3579 alignFrameMenuBar.add(annotationsMenu);
3580 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3581 alignFrameMenuBar.add(formatMenu);
3582 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3583 alignFrameMenuBar.add(colourMenu);
3584 Menu calculateMenu = new Menu(
3585 MessageManager.getString("action.calculate"));
3586 alignFrameMenuBar.add(calculateMenu);
3587 alignFrameMenuBar.add(helpMenu);
3592 fileMenu.add(inputText);
3593 fileMenu.add(loadTree);
3594 fileMenu.add(loadAnnotations);
3595 fileMenu.addSeparator();
3596 fileMenu.add(outputTextboxMenu);
3597 fileMenu.add(outputFeatures);
3598 fileMenu.add(outputAnnotations);
3599 if (jalviewServletURL != null)
3601 fileMenu.add(loadApplication);
3603 fileMenu.addSeparator();
3604 fileMenu.add(closeMenuItem);
3609 editMenu.add(undoMenuItem);
3610 editMenu.add(redoMenuItem);
3613 pasteMenu.add(pasteNew);
3614 pasteMenu.add(pasteThis);
3615 editMenu.add(pasteMenu);
3616 editMenu.add(delete);
3617 editMenu.addSeparator();
3618 editMenu.add(remove2LeftMenuItem);
3619 editMenu.add(remove2RightMenuItem);
3620 editMenu.add(removeGappedColumnMenuItem);
3621 editMenu.add(removeAllGapsMenuItem);
3622 editMenu.add(removeRedundancyMenuItem);
3627 selectMenu.add(findMenuItem);
3628 selectMenu.addSeparator();
3629 selectMenu.add(selectAllSequenceMenuItem);
3630 selectMenu.add(deselectAllSequenceMenuItem);
3631 selectMenu.add(invertSequenceMenuItem);
3632 selectMenu.add(invertColSel);
3633 selectMenu.add(createGroup);
3634 selectMenu.add(unGroup);
3635 selectMenu.add(grpsFromSelection);
3636 selectMenu.add(deleteGroups);
3637 selectMenu.add(annotationColumnSelection);
3642 viewMenu.add(newView);
3643 viewMenu.addSeparator();
3644 showMenu.add(showColumns);
3645 showMenu.add(showSeqs);
3646 showMenu.add(showAllHidden);
3647 viewMenu.add(showMenu);
3648 hideMenu.add(hideColumns);
3649 hideMenu.add(hideSequences);
3650 hideMenu.add(hideAllSelection);
3651 hideMenu.add(hideAllButSelection);
3652 viewMenu.add(hideMenu);
3653 viewMenu.addSeparator();
3654 viewMenu.add(followMouseOverFlag);
3655 viewMenu.addSeparator();
3656 viewMenu.add(sequenceFeatures);
3657 viewMenu.add(featureSettings);
3658 viewMenu.addSeparator();
3659 viewMenu.add(alProperties);
3660 viewMenu.addSeparator();
3661 viewMenu.add(overviewMenuItem);
3666 annotationsMenu.add(annotationPanelMenuItem);
3667 annotationsMenu.addSeparator();
3668 annotationsMenu.add(showAlignmentAnnotations);
3669 annotationsMenu.add(showSequenceAnnotations);
3670 annotationsMenu.add(sortAnnBySequence);
3671 annotationsMenu.add(sortAnnByLabel);
3672 annotationsMenu.addSeparator();
3673 autoAnnMenu.add(showAutoFirst);
3674 autoAnnMenu.add(showAutoLast);
3675 autoAnnMenu.addSeparator();
3676 autoAnnMenu.add(applyAutoAnnotationSettings);
3677 autoAnnMenu.add(showConsensusHistogram);
3678 autoAnnMenu.add(showSequenceLogo);
3679 autoAnnMenu.add(normSequenceLogo);
3680 autoAnnMenu.addSeparator();
3681 autoAnnMenu.add(showGroupConservation);
3682 autoAnnMenu.add(showGroupConsensus);
3683 annotationsMenu.add(autoAnnMenu);
3688 formatMenu.add(font);
3689 formatMenu.add(seqLimits);
3690 formatMenu.add(wrapMenuItem);
3691 formatMenu.add(scaleAbove);
3692 formatMenu.add(scaleLeft);
3693 formatMenu.add(scaleRight);
3694 formatMenu.add(viewBoxesMenuItem);
3695 formatMenu.add(viewTextMenuItem);
3696 formatMenu.add(colourTextMenuItem);
3697 formatMenu.add(displayNonconservedMenuItem);
3698 formatMenu.add(renderGapsMenuItem);
3699 formatMenu.add(centreColumnLabelFlag);
3704 colourMenu.add(applyToAllGroups);
3705 colourMenu.addSeparator();
3706 colourMenu.add(noColourmenuItem);
3707 colourMenu.add(clustalColour);
3708 colourMenu.add(BLOSUM62Colour);
3709 colourMenu.add(PIDColour);
3710 colourMenu.add(zappoColour);
3711 colourMenu.add(taylorColour);
3712 colourMenu.add(hydrophobicityColour);
3713 colourMenu.add(helixColour);
3714 colourMenu.add(strandColour);
3715 colourMenu.add(turnColour);
3716 colourMenu.add(buriedColour);
3717 colourMenu.add(nucleotideColour);
3718 colourMenu.add(purinePyrimidineColour);
3719 // colourMenu.add(RNAInteractionColour);
3720 colourMenu.add(tcoffeeColour);
3721 colourMenu.add(userDefinedColour);
3722 colourMenu.addSeparator();
3723 colourMenu.add(conservationMenuItem);
3724 colourMenu.add(modifyConservation);
3725 colourMenu.add(abovePIDThreshold);
3726 colourMenu.add(modifyPID);
3727 colourMenu.add(annotationColour);
3728 colourMenu.add(RNAHelixColour);
3733 sortMenu.add(sortIDMenuItem);
3734 sortMenu.add(sortLengthMenuItem);
3735 sortMenu.add(sortByTreeMenu);
3736 sortMenu.add(sortGroupMenuItem);
3737 sortMenu.add(sortPairwiseMenuItem);
3738 calculateMenu.add(sortMenu);
3739 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3740 calculateTreeMenu.add(neighbourTreeMenuItem);
3741 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3742 calculateTreeMenu.add(njTreeBlosumMenuItem);
3743 calculateMenu.add(calculateTreeMenu);
3744 calculateMenu.addSeparator();
3745 calculateMenu.add(pairwiseAlignmentMenuItem);
3746 calculateMenu.add(PCAMenuItem);
3747 calculateMenu.add(autoCalculate);
3748 calculateMenu.add(sortByTree);
3753 helpMenu.add(documentation);
3754 helpMenu.add(about);
3759 statusBar.setBackground(Color.white);
3760 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3761 statusBar.setText(MessageManager.getString("label.status_bar"));
3762 this.add(statusBar, BorderLayout.SOUTH);
3765 public void setStatus(String string)
3767 statusBar.setText(string);
3770 MenuItem featureSettings = new MenuItem();
3772 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3774 MenuItem annotationColour = new MenuItem();
3776 MenuItem annotationColumnSelection = new MenuItem();
3778 MenuItem invertColSel = new MenuItem();
3780 MenuItem showColumns = new MenuItem();
3782 MenuItem showSeqs = new MenuItem();
3784 MenuItem hideColumns = new MenuItem();
3786 MenuItem hideSequences = new MenuItem();
3788 MenuItem hideAllButSelection = new MenuItem();
3790 MenuItem hideAllSelection = new MenuItem();
3792 MenuItem showAllHidden = new MenuItem();
3794 MenuItem newView = new MenuItem();
3796 private CheckboxMenuItem showAlignmentAnnotations;
3798 private CheckboxMenuItem showSequenceAnnotations;
3800 private CheckboxMenuItem sortAnnBySequence;
3802 private CheckboxMenuItem sortAnnByLabel;
3804 private CheckboxMenuItem showAutoFirst;
3806 private CheckboxMenuItem showAutoLast;
3808 private SplitFrame splitFrame;
3811 * Attach the alignFrame panels after embedding menus, if necessary. This used
3812 * to be called setEmbedded, but is now creates the dropdown menus in a
3813 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3815 * @param reallyEmbedded
3816 * true to attach the view to the applet area on the page rather than
3819 public void createAlignFrameWindow(boolean reallyEmbedded)
3823 embedAlignFrameInApplet(viewport.applet);
3828 // test and embed menu bar if necessary.
3830 if (embedMenuIfNeeded(alignPanel))
3833 * adjust for status bar height too. ? pointless as overridden by layout
3836 alignPanel.setSize(getSize().width,
3837 getSize().height - statusBar.getHeight());
3839 add(statusBar, BorderLayout.SOUTH);
3840 add(alignPanel, BorderLayout.CENTER);
3841 // and register with the applet so it can pass external API calls to us
3842 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3848 * Add the components of this AlignFrame to the applet container.
3852 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3855 // Explicitly build the embedded menu panel for the on-page applet
3857 // view cannot be closed if its actually on the page
3858 fileMenu.remove(closeMenuItem);
3859 fileMenu.remove(3); // Remove Separator
3860 // construct embedded menu, using default font
3861 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3862 // and actually add the components to the applet area
3863 theApplet.setLayout(new BorderLayout());
3864 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3865 theApplet.add(statusBar, BorderLayout.SOUTH);
3866 // TODO should size be left to the layout manager?
3867 alignPanel.setSize(theApplet.getSize().width,
3868 theApplet.getSize().height - embeddedMenu.getHeight()
3869 - statusBar.getHeight());
3870 theApplet.add(alignPanel, BorderLayout.CENTER);
3871 final AlignFrame me = this;
3872 theApplet.addFocusListener(new FocusListener()
3876 public void focusLost(FocusEvent e)
3878 if (theApplet.currentAlignFrame == me)
3880 theApplet.currentAlignFrame = null;
3885 public void focusGained(FocusEvent e)
3887 theApplet.currentAlignFrame = me;
3890 theApplet.validate();
3894 * create a new binding between structures in an existing jmol viewer instance
3895 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3896 * this does not open a new Jmol window, or modify the display of the
3897 * structures in the original jmol window. Note This method doesn't work
3898 * without an additional javascript library to exchange messages between the
3899 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3902 * JmolViewer instance
3903 * @param sequenceIds
3904 * - sequence Ids to search for associations
3906 public SequenceStructureBinding addStructureViewInstance(
3907 Object jmolviewer, String[] sequenceIds)
3909 Viewer viewer = null;
3912 viewer = (Viewer) jmolviewer;
3913 } catch (ClassCastException ex)
3915 System.err.println("Unsupported viewer object :"
3916 + jmolviewer.getClass());
3920 System.err.println("Can't use this object as a structure viewer:"
3921 + jmolviewer.getClass());
3924 SequenceI[] seqs = null;
3925 if (sequenceIds == null || sequenceIds.length == 0)
3927 seqs = viewport.getAlignment().getSequencesArray();
3931 Vector sqi = new Vector();
3932 AlignmentI al = viewport.getAlignment();
3933 for (int sid = 0; sid < sequenceIds.length; sid++)
3935 SequenceI sq = al.findName(sequenceIds[sid]);
3943 seqs = new SequenceI[sqi.size()];
3944 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3946 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3954 AAStructureBindingModel jmv = null;
3955 // TODO: search for a jmv that involves viewer
3957 { // create a new viewer/jalview binding.
3958 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3965 * bind a pdb file to a sequence in the current view
3968 * - sequenceId within the dataset.
3969 * @param pdbEntryString
3970 * - the short name for the PDB file
3972 * - pdb file - either a URL or a valid PDB file.
3973 * @return true if binding was as success TODO: consider making an exception
3974 * structure for indicating when PDB parsing or sequenceId location
3977 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3980 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3981 boolean needtoadd = false;
3982 if (toaddpdb != null)
3984 Vector pdbe = toaddpdb.getAllPDBEntries();
3985 PDBEntry pdbentry = null;
3986 if (pdbe != null && pdbe.size() > 0)
3988 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3990 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3991 if (!pdbentry.getId().equals(pdbEntryString)
3992 && !pdbentry.getFile().equals(pdbFile))
4002 if (pdbentry == null)
4004 pdbentry = new PDBEntry();
4005 pdbentry.setId(pdbEntryString);
4006 pdbentry.setFile(pdbFile);
4007 needtoadd = true; // add this new entry to sequence.
4009 // resolve data source
4010 // TODO: this code should be a refactored to an io package
4011 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4012 if (protocol == null)
4018 // make a note of the access mode and add
4019 if (pdbentry.getProperty() == null)
4021 pdbentry.setProperty(new Hashtable());
4023 pdbentry.getProperty().put("protocol", protocol);
4024 toaddpdb.addPDBId(pdbentry);
4025 alignPanel.getStructureSelectionManager()
4026 .registerPDBEntry(pdbentry);
4032 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4036 Vector sequences = new Vector();
4037 for (int i = 0; i < seqs.length; i++)
4039 if (seqs[i] != null)
4041 sequences.addElement(new Object[] { seqs[i],
4042 (chains != null) ? chains[i] : null });
4045 seqs = new SequenceI[sequences.size()];
4046 chains = new String[sequences.size()];
4047 for (int i = 0, isize = sequences.size(); i < isize; i++)
4049 Object[] oj = (Object[]) sequences.elementAt(i);
4051 seqs[i] = (SequenceI) oj[0];
4052 chains[i] = (String) oj[1];
4055 return new Object[] { seqs, chains };
4059 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4060 SequenceI[] seqs, String[] chains, String protocol)
4062 // Scrub any null sequences from the array
4063 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4064 seqs = (SequenceI[]) sqch[0];
4065 chains = (String[]) sqch[1];
4066 if (seqs == null || seqs.length == 0)
4069 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4071 if (protocol == null || protocol.trim().length() == 0
4072 || protocol.equals("null"))
4074 protocol = (String) pdb.getProperty().get("protocol");
4075 if (protocol == null)
4077 System.err.println("Couldn't work out protocol to open structure: "
4082 if (applet.useXtrnalSviewer)
4084 // register the association(s) and quit, don't create any windows.
4085 if (StructureSelectionManager.getStructureSelectionManager(applet)
4086 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4088 System.err.println("Failed to map " + pdb.getFile() + " ("
4089 + protocol + ") to any sequences");
4093 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4095 // can only do alignments with Jmol
4096 // find the last jmol window assigned to this alignment
4097 jalview.appletgui.AppletJmol ajm = null, tajm;
4098 Vector jmols = applet
4099 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4100 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4102 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4103 if (tajm.ap.alignFrame == this)
4112 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4113 // try and add the pdb structure
4118 // otherwise, create a new window
4119 if (applet.jmolAvailable)
4121 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4123 applet.lastFrameX += 40;
4124 applet.lastFrameY += 40;
4128 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4133 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4134 SequenceI[][] seqs, String[][] chains, String[] protocols)
4136 // TODO Auto-generated method stub
4137 System.err.println("Aligned Structure View: Not yet implemented.");
4141 * modify the current selection, providing the user has not made a selection
4145 * - sequences from this alignment
4147 * - columns to be selected on the alignment
4149 public void select(SequenceGroup sel, ColumnSelection csel)
4151 alignPanel.seqPanel.selection(sel, csel, null);
4154 public void scrollTo(int row, int column)
4156 alignPanel.seqPanel.scrollTo(row, column);
4159 public void scrollToRow(int row)
4161 alignPanel.seqPanel.scrollToRow(row);
4164 public void scrollToColumn(int column)
4166 alignPanel.seqPanel.scrollToColumn(column);
4170 * @return the alignments unique ID.
4172 public String getSequenceSetId()
4174 return viewport.getSequenceSetId();
4178 * Load the (T-Coffee) score file from the specified url
4181 * File/URL/T-COFFEE score file contents
4182 * @throws IOException
4183 * @return true if alignment was annotated with data from source
4185 public boolean loadScoreFile(String source) throws IOException
4188 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4189 AppletFormatAdapter.checkProtocol(source));
4190 if (!file.isValid())
4192 // TODO: raise dialog for gui
4193 System.err.println("Problems parsing T-Coffee scores: "
4194 + file.getWarningMessage());
4195 System.err.println("Origin was:\n" + source);
4200 * check that the score matrix matches the alignment dimensions
4203 if ((aln = viewport.getAlignment()) != null
4204 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4207 // TODO: raise a dialog box here rather than bomb out.
4209 .println("The scores matrix does not match the alignment dimensions");
4213 // TODO add parameter to indicate if matching should be done
4214 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4216 alignPanel.fontChanged();
4217 tcoffeeColour.setEnabled(true);
4218 // switch to this color
4219 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4224 System.err.println("Problems resolving T-Coffee scores:");
4225 if (file.getWarningMessage() != null)
4227 System.err.println(file.getWarningMessage());
4233 public SplitFrame getSplitFrame()
4235 return this.splitFrame;
4238 public void setSplitFrame(SplitFrame sf)
4240 this.splitFrame = sf;
4243 // may not need this
4245 public void setShowSeqFeatures(boolean b)
4247 // showSeqFeatures.setSelected(b);
4248 viewport.setShowSequenceFeatures(b);
4253 public void setMenusForViewport()
4255 // setMenusFromViewport(viewport);
4260 public void refreshFeatureUI(boolean enableIfNecessary)
4262 if (enableIfNecessary)
4264 sequenceFeatures.setState(true);
4265 alignPanel.av.setShowSequenceFeatures(true);
4270 public FeatureSettingsControllerI getFeatureSettingsUI()
4272 return alignPanel.av.featureSettings;