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 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1759 synchronized void slideSequences(boolean right, int size)
1761 List<SequenceI> sg = new Vector<SequenceI>();
1762 if (viewport.cursorMode)
1764 sg.add(viewport.getAlignment().getSequenceAt(
1765 alignPanel.seqPanel.seqCanvas.cursorY));
1767 else if (viewport.getSelectionGroup() != null
1768 && viewport.getSelectionGroup().getSize() != viewport
1769 .getAlignment().getHeight())
1771 sg = viewport.getSelectionGroup().getSequences(
1772 viewport.getHiddenRepSequences());
1780 Vector<SequenceI> invertGroup = new Vector();
1782 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1784 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1786 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1790 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1792 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1794 for (int i = 0; i < invertGroup.size(); i++)
1796 seqs2[i] = invertGroup.elementAt(i);
1799 SlideSequencesCommand ssc;
1802 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1803 size, viewport.getGapCharacter());
1807 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1808 size, viewport.getGapCharacter());
1811 int groupAdjustment = 0;
1812 if (ssc.getGapsInsertedBegin() && right)
1814 if (viewport.cursorMode)
1816 alignPanel.seqPanel.moveCursor(size, 0);
1820 groupAdjustment = size;
1823 else if (!ssc.getGapsInsertedBegin() && !right)
1825 if (viewport.cursorMode)
1827 alignPanel.seqPanel.moveCursor(-size, 0);
1831 groupAdjustment = -size;
1835 if (groupAdjustment != 0)
1837 viewport.getSelectionGroup().setStartRes(
1838 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1839 viewport.getSelectionGroup().setEndRes(
1840 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1843 boolean appendHistoryItem = false;
1844 Deque<CommandI> historyList = viewport.getHistoryList();
1845 if (historyList != null && historyList.size() > 0
1846 && historyList.peek() instanceof SlideSequencesCommand)
1848 appendHistoryItem = ssc
1849 .appendSlideCommand((SlideSequencesCommand) historyList
1853 if (!appendHistoryItem)
1855 addHistoryItem(ssc);
1861 static StringBuffer copiedSequences;
1863 static Vector copiedHiddenColumns;
1865 protected void copy_actionPerformed()
1867 if (viewport.getSelectionGroup() == null)
1872 SequenceGroup sg = viewport.getSelectionGroup();
1873 copiedSequences = new StringBuffer();
1874 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1875 for (int i = 0; i < sg.getSize(); i++)
1877 SequenceI seq = sg.getSequenceAt(i);
1878 int index = viewport.getAlignment().findIndex(seq);
1879 orderedSeqs.put(index, seq);
1882 int index = 0, startRes, endRes;
1885 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1887 copiedHiddenColumns = new Vector();
1888 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1889 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1891 copiedHiddenColumns.addElement(new int[] {
1892 region[0] - hiddenOffset, region[1] - hiddenOffset });
1897 copiedHiddenColumns = null;
1900 for (int i = 0; i < sg.getSize(); i++)
1902 SequenceI seq = null;
1906 if (orderedSeqs.containsKey(index))
1908 seq = orderedSeqs.get(index);
1919 // Returns residue following index if gap
1920 startRes = seq.findPosition(sg.getStartRes());
1923 // Need to find the residue preceeding index if gap
1926 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1928 ch = seq.getCharAt(j);
1929 if (!jalview.util.Comparison.isGap((ch)))
1937 endRes += seq.getStart() - 1;
1940 copiedSequences.append(seq.getName()
1946 + seq.getSequenceAsString(sg.getStartRes(),
1947 sg.getEndRes() + 1) + "\n");
1952 protected void pasteNew_actionPerformed()
1957 protected void pasteThis_actionPerformed()
1962 void paste(boolean newAlignment)
1967 if (copiedSequences == null)
1972 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1973 Vector seqs = new Vector();
1974 while (st.hasMoreElements())
1976 String name = st.nextToken();
1977 int start = Integer.parseInt(st.nextToken());
1978 int end = Integer.parseInt(st.nextToken());
1979 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1981 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1982 for (int i = 0; i < seqs.size(); i++)
1984 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1989 String newtitle = MessageManager
1990 .getString("label.copied_sequences");
1991 if (getTitle().startsWith(
1992 MessageManager.getString("label.copied_sequences")))
1994 newtitle = getTitle();
1998 newtitle = newtitle.concat(MessageManager.formatMessage(
1999 "label.from_msname", new String[] { getTitle() }));
2001 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2002 viewport.applet, newtitle, false);
2003 if (copiedHiddenColumns != null)
2005 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2007 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2008 af.viewport.hideColumns(region[0], region[1]);
2012 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2017 addSequences(newSeqs);
2020 } catch (Exception ex)
2022 } // could be anything being pasted in here
2026 void addSequences(SequenceI[] seqs)
2028 for (int i = 0; i < seqs.length; i++)
2030 viewport.getAlignment().addSequence(seqs[i]);
2034 addHistoryItem(new EditCommand(
2035 MessageManager.getString("label.add_sequences"), Action.PASTE,
2036 seqs, 0, viewport.getAlignment().getWidth(),
2037 viewport.getAlignment()));
2039 viewport.setEndSeq(viewport.getAlignment().getHeight());
2040 viewport.getAlignment().getWidth();
2041 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2046 protected void cut_actionPerformed()
2048 copy_actionPerformed();
2049 delete_actionPerformed();
2052 protected void delete_actionPerformed()
2055 SequenceGroup sg = viewport.getSelectionGroup();
2061 Vector seqs = new Vector();
2063 for (int i = 0; i < sg.getSize(); i++)
2065 seq = sg.getSequenceAt(i);
2066 seqs.addElement(seq);
2070 * If the cut affects all sequences, warn, remove highlighted columns
2072 if (sg.getSize() == viewport.getAlignment().getHeight())
2074 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2075 .getAlignment().getWidth()) ? true : false;
2076 if (isEntireAlignWidth)
2078 String title = MessageManager.getString("label.delete_all");
2079 Panel infoPanel = new Panel();
2080 infoPanel.setLayout(new FlowLayout());
2082 .add(new Label(MessageManager.getString("warn.delete_all")));
2084 final JVDialog dialog = new JVDialog(this, title, true, 400,
2086 dialog.setMainPanel(infoPanel);
2087 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2088 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2089 dialog.setVisible(true);
2096 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2097 sg.getEndRes() + 1);
2100 SequenceI[] cut = new SequenceI[seqs.size()];
2101 for (int i = 0; i < seqs.size(); i++)
2103 cut[i] = (SequenceI) seqs.elementAt(i);
2107 * //ADD HISTORY ITEM
2109 addHistoryItem(new EditCommand(
2110 MessageManager.getString("label.cut_sequences"), Action.CUT,
2111 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2112 viewport.getAlignment()));
2114 viewport.setSelectionGroup(null);
2115 viewport.getAlignment().deleteGroup(sg);
2117 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2120 if (viewport.getAlignment().getHeight() < 1)
2122 this.setVisible(false);
2124 viewport.sendSelection();
2128 * group consensus toggled
2131 protected void showGroupConsensus_actionPerformed()
2133 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2134 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2139 * group conservation toggled.
2141 protected void showGroupConservation_actionPerformed()
2143 viewport.setShowGroupConservation(showGroupConservation.getState());
2144 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2151 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2152 * .event.ActionEvent)
2154 protected void showConsensusHistogram_actionPerformed()
2156 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2157 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2164 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2165 * .event.ActionEvent)
2167 protected void showSequenceLogo_actionPerformed()
2169 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2170 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2173 protected void normSequenceLogo_actionPerformed()
2175 showSequenceLogo.setState(true);
2176 viewport.setShowSequenceLogo(true);
2177 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2178 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181 protected void applyAutoAnnotationSettings_actionPerformed()
2183 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2186 protected void makeGrpsFromSelection_actionPerformed()
2188 if (avc.makeGroupsFromSelection())
2190 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2191 alignPanel.updateAnnotation();
2192 alignPanel.paintAlignment(true);
2196 protected void createGroup_actionPerformed()
2201 protected void unGroup_actionPerformed()
2205 alignPanel.alignmentChanged();
2209 protected void deleteGroups_actionPerformed()
2211 if (avc.deleteGroups())
2213 alignPanel.alignmentChanged();
2217 public void selectAllSequenceMenuItem_actionPerformed()
2219 SequenceGroup sg = new SequenceGroup();
2220 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2222 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2224 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2225 viewport.setSelectionGroup(sg);
2226 alignPanel.paintAlignment(true);
2227 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2228 viewport.sendSelection();
2231 public void deselectAllSequenceMenuItem_actionPerformed()
2233 if (viewport.cursorMode)
2235 alignPanel.seqPanel.keyboardNo1 = null;
2236 alignPanel.seqPanel.keyboardNo2 = null;
2238 viewport.setSelectionGroup(null);
2239 viewport.getColumnSelection().clear();
2240 viewport.setSelectionGroup(null);
2241 alignPanel.idPanel.idCanvas.searchResults = null;
2242 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2243 alignPanel.paintAlignment(true);
2244 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2245 viewport.sendSelection();
2248 public void invertSequenceMenuItem_actionPerformed()
2250 SequenceGroup sg = viewport.getSelectionGroup();
2251 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2253 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2256 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257 viewport.sendSelection();
2260 public void invertColSel_actionPerformed()
2262 viewport.invertColumnSelection();
2263 alignPanel.paintAlignment(true);
2264 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2265 viewport.sendSelection();
2268 void trimAlignment(boolean trimLeft)
2270 ColumnSelection colSel = viewport.getColumnSelection();
2273 if (colSel.size() > 0)
2277 column = colSel.getMin();
2281 column = colSel.getMax();
2285 if (viewport.getSelectionGroup() != null)
2287 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2288 viewport.getHiddenRepSequences());
2292 seqs = viewport.getAlignment().getSequencesArray();
2295 TrimRegionCommand trimRegion;
2298 trimRegion = new TrimRegionCommand("Remove Left",
2299 TrimRegionCommand.TRIM_LEFT, seqs, column,
2300 viewport.getAlignment(), viewport.getColumnSelection(),
2301 viewport.getSelectionGroup());
2302 viewport.setStartRes(0);
2306 trimRegion = new TrimRegionCommand("Remove Right",
2307 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2308 viewport.getAlignment(), viewport.getColumnSelection(),
2309 viewport.getSelectionGroup());
2312 statusBar.setText(MessageManager.formatMessage(
2313 "label.removed_columns",
2314 new String[] { Integer.valueOf(trimRegion.getSize())
2316 addHistoryItem(trimRegion);
2318 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2320 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2321 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2323 viewport.getAlignment().deleteGroup(sg);
2327 viewport.firePropertyChange("alignment", null, viewport
2328 .getAlignment().getSequences());
2332 public void removeGappedColumnMenuItem_actionPerformed()
2334 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2337 if (viewport.getSelectionGroup() != null)
2339 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2340 viewport.getHiddenRepSequences());
2341 start = viewport.getSelectionGroup().getStartRes();
2342 end = viewport.getSelectionGroup().getEndRes();
2346 seqs = viewport.getAlignment().getSequencesArray();
2349 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2350 "Remove Gapped Columns", seqs, start, end,
2351 viewport.getAlignment());
2353 addHistoryItem(removeGapCols);
2355 statusBar.setText(MessageManager.formatMessage(
2356 "label.removed_empty_columns",
2357 new String[] { Integer.valueOf(removeGapCols.getSize())
2360 // This is to maintain viewport position on first residue
2361 // of first sequence
2362 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2363 int startRes = seq.findPosition(viewport.startRes);
2364 // ShiftList shifts;
2365 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2366 // edit.alColumnChanges=shifts.getInverse();
2367 // if (viewport.hasHiddenColumns)
2368 // viewport.getColumnSelection().compensateForEdits(shifts);
2369 viewport.setStartRes(seq.findIndex(startRes) - 1);
2370 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2375 public void removeAllGapsMenuItem_actionPerformed()
2377 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2380 if (viewport.getSelectionGroup() != null)
2382 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2383 viewport.getHiddenRepSequences());
2384 start = viewport.getSelectionGroup().getStartRes();
2385 end = viewport.getSelectionGroup().getEndRes();
2389 seqs = viewport.getAlignment().getSequencesArray();
2392 // This is to maintain viewport position on first residue
2393 // of first sequence
2394 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2395 int startRes = seq.findPosition(viewport.startRes);
2397 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2398 viewport.getAlignment()));
2400 viewport.setStartRes(seq.findIndex(startRes) - 1);
2402 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2407 public void findMenuItem_actionPerformed()
2409 new Finder(alignPanel);
2413 * create a new view derived from the current view
2416 * @return frame for the new view
2418 public AlignFrame newView(String viewtitle)
2421 if (viewport.hasHiddenRows())
2423 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2424 .getFullAlignment().getSequencesArray());
2428 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2431 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2433 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2435 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2437 newal.addAnnotation(viewport.getAlignment()
2438 .getAlignmentAnnotation()[i]);
2443 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2445 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2446 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2447 PaintRefresher.Register(newaf.alignPanel,
2448 newaf.alignPanel.av.getSequenceSetId());
2450 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2451 newaf.alignPanel.av.getSequenceSetId());
2452 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2453 newaf.alignPanel.av.getSequenceSetId());
2455 Vector comps = (Vector) PaintRefresher.components.get(viewport
2456 .getSequenceSetId());
2458 for (int i = 0; i < comps.size(); i++)
2460 if (comps.elementAt(i) instanceof AlignmentPanel)
2466 String title = new String(this.getTitle());
2467 if (viewtitle != null)
2469 title = viewtitle + " ( " + title + ")";
2473 if (title.indexOf("(View") > -1)
2475 title = title.substring(0, title.indexOf("(View"));
2477 title += "(View " + viewSize + ")";
2480 newaf.setTitle(title.toString());
2482 newaf.viewport.setHistoryList(viewport.getHistoryList());
2483 newaf.viewport.setRedoList(viewport.getRedoList());
2489 * @return list of feature groups on the view
2491 public String[] getFeatureGroups()
2493 FeatureRenderer fr = null;
2494 if (alignPanel != null
2495 && (fr = alignPanel.getFeatureRenderer()) != null)
2497 List<String> gps = fr.getFeatureGroups();
2498 String[] _gps = gps.toArray(new String[gps.size()]);
2505 * get sequence feature groups that are hidden or shown
2511 public String[] getFeatureGroupsOfState(boolean visible)
2513 FeatureRenderer fr = null;
2514 if (alignPanel != null
2515 && (fr = alignPanel.getFeatureRenderer()) != null)
2517 List<String> gps = fr.getGroups(visible);
2518 String[] _gps = gps.toArray(new String[gps.size()]);
2525 * Change the display state for the given feature groups
2528 * list of group strings
2530 * visible or invisible
2532 public void setFeatureGroupState(String[] groups, boolean state)
2534 FeatureRenderer fr = null;
2535 this.sequenceFeatures.setState(true);
2536 viewport.setShowSequenceFeatures(true);
2537 if (alignPanel != null
2538 && (fr = alignPanel.getFeatureRenderer()) != null)
2541 fr.setGroupVisibility(Arrays.asList(groups), state);
2542 alignPanel.seqPanel.seqCanvas.repaint();
2543 if (alignPanel.overviewPanel != null)
2545 alignPanel.overviewPanel.updateOverviewImage();
2550 public void seqLimits_itemStateChanged()
2552 viewport.setShowJVSuffix(seqLimits.getState());
2553 alignPanel.fontChanged();
2554 alignPanel.paintAlignment(true);
2557 protected void colourTextMenuItem_actionPerformed()
2559 viewport.setColourText(colourTextMenuItem.getState());
2560 alignPanel.paintAlignment(true);
2563 protected void displayNonconservedMenuItem_actionPerformed()
2565 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2566 alignPanel.paintAlignment(true);
2569 protected void wrapMenuItem_actionPerformed()
2571 viewport.setWrapAlignment(wrapMenuItem.getState());
2572 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2573 scaleAbove.setEnabled(wrapMenuItem.getState());
2574 scaleLeft.setEnabled(wrapMenuItem.getState());
2575 scaleRight.setEnabled(wrapMenuItem.getState());
2576 alignPanel.paintAlignment(true);
2579 public void overviewMenuItem_actionPerformed()
2581 if (alignPanel.overviewPanel != null)
2586 Frame frame = new Frame();
2587 OverviewPanel overview = new OverviewPanel(alignPanel);
2588 frame.add(overview);
2589 // +50 must allow for applet frame window
2590 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2591 "label.overview_params", new String[] { this.getTitle() }),
2592 overview.getPreferredSize().width,
2593 overview.getPreferredSize().height + 50);
2596 final AlignmentPanel ap = alignPanel;
2597 frame.addWindowListener(new WindowAdapter()
2600 public void windowClosing(WindowEvent e)
2604 ap.setOverviewPanel(null);
2609 alignPanel.setOverviewPanel(overview);
2613 public void changeColour(ColourSchemeI cs)
2618 if (viewport.getAbovePIDThreshold())
2620 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2624 if (viewport.getConservationSelected())
2626 cs.setConservationApplied(true);
2627 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2632 cs.setConservationApplied(false);
2635 viewport.setGlobalColourScheme(cs);
2637 alignPanel.paintAlignment(true);
2640 protected void modifyPID_actionPerformed()
2642 if (viewport.getAbovePIDThreshold()
2643 && viewport.getGlobalColourScheme() != null)
2645 SliderPanel.setPIDSliderSource(alignPanel,
2646 viewport.getGlobalColourScheme(), "Background");
2647 SliderPanel.showPIDSlider();
2651 protected void modifyConservation_actionPerformed()
2653 if (viewport.getConservationSelected()
2654 && viewport.getGlobalColourScheme() != null)
2656 SliderPanel.setConservationSlider(alignPanel,
2657 viewport.getGlobalColourScheme(), "Background");
2658 SliderPanel.showConservationSlider();
2662 protected void conservationMenuItem_actionPerformed()
2664 viewport.setConservationSelected(conservationMenuItem.getState());
2666 viewport.setAbovePIDThreshold(false);
2667 abovePIDThreshold.setState(false);
2669 changeColour(viewport.getGlobalColourScheme());
2671 modifyConservation_actionPerformed();
2674 public void abovePIDThreshold_actionPerformed()
2676 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2678 conservationMenuItem.setState(false);
2679 viewport.setConservationSelected(false);
2681 changeColour(viewport.getGlobalColourScheme());
2683 modifyPID_actionPerformed();
2686 public void sortPairwiseMenuItem_actionPerformed()
2688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2689 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2690 .getAlignment().getSequenceAt(0), null);
2692 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2693 viewport.getAlignment()));
2694 alignPanel.paintAlignment(true);
2697 public void sortIDMenuItem_actionPerformed()
2699 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2700 AlignmentSorter.sortByID(viewport.getAlignment());
2701 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2702 viewport.getAlignment()));
2703 alignPanel.paintAlignment(true);
2706 public void sortLengthMenuItem_actionPerformed()
2708 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2709 AlignmentSorter.sortByLength(viewport.getAlignment());
2710 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2711 viewport.getAlignment()));
2712 alignPanel.paintAlignment(true);
2715 public void sortGroupMenuItem_actionPerformed()
2717 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2718 AlignmentSorter.sortByGroup(viewport.getAlignment());
2719 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2720 viewport.getAlignment()));
2721 alignPanel.paintAlignment(true);
2725 public void removeRedundancyMenuItem_actionPerformed()
2727 new RedundancyPanel(alignPanel);
2730 public void pairwiseAlignmentMenuItem_actionPerformed()
2732 if (viewport.getSelectionGroup() != null
2733 && viewport.getSelectionGroup().getSize() > 1)
2735 Frame frame = new Frame();
2736 frame.add(new PairwiseAlignPanel(alignPanel));
2737 jalview.bin.JalviewLite.addFrame(frame,
2738 MessageManager.getString("action.pairwise_alignment"), 600,
2743 public void PCAMenuItem_actionPerformed()
2745 // are the sequences aligned?
2746 if (!viewport.getAlignment().isAligned(false))
2749 int Width = viewport.getAlignment().getWidth();
2751 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2753 current = viewport.getAlignment().getSequenceAt(i);
2755 if (current.getLength() < Width)
2757 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2760 alignPanel.paintAlignment(true);
2763 if ((viewport.getSelectionGroup() != null
2764 && viewport.getSelectionGroup().getSize() < 4 && viewport
2765 .getSelectionGroup().getSize() > 0)
2766 || viewport.getAlignment().getHeight() < 4)
2773 new PCAPanel(viewport);
2774 } catch (java.lang.OutOfMemoryError ex)
2780 public void averageDistanceTreeMenuItem_actionPerformed()
2782 NewTreePanel("AV", "PID", "Average distance tree using PID");
2785 public void neighbourTreeMenuItem_actionPerformed()
2787 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2790 protected void njTreeBlosumMenuItem_actionPerformed()
2792 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2795 protected void avTreeBlosumMenuItem_actionPerformed()
2797 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2800 void NewTreePanel(String type, String pwType, String title)
2802 // are the sequences aligned?
2803 if (!viewport.getAlignment().isAligned(false))
2806 int Width = viewport.getAlignment().getWidth();
2808 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2810 current = viewport.getAlignment().getSequenceAt(i);
2812 if (current.getLength() < Width)
2814 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2817 alignPanel.paintAlignment(true);
2821 if ((viewport.getSelectionGroup() != null && viewport
2822 .getSelectionGroup().getSize() > 1)
2823 || (viewport.getAlignment().getHeight() > 1))
2825 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2827 addTreeMenuItem(tp, title);
2829 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2833 void loadTree_actionPerformed()
2835 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2836 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2837 cap.setTreeImport();
2838 Frame frame = new Frame();
2840 jalview.bin.JalviewLite.addFrame(frame,
2841 MessageManager.getString("label.paste_newick_file"), 400, 300);
2844 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2846 TreePanel tp = new TreePanel(alignPanel, treeFile,
2847 MessageManager.getString("label.load_tree_from_file"), tree);
2848 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2849 addTreeMenuItem(tp, treeFile);
2853 * sort the alignment using the given treePanel
2856 * tree used to sort view
2858 * string used for undo event name
2860 public void sortByTree(TreePanel treePanel, String title)
2862 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2864 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2865 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2866 // HistoryItem.SORT));
2867 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2868 "label.order_by_params", new String[] { title }), oldOrder,
2869 viewport.getAlignment()));
2870 alignPanel.paintAlignment(true);
2874 * Do any automatic reordering of the alignment and add the necessary bits to
2875 * the menu structure for the new tree
2880 protected void addTreeMenuItem(final TreePanel treePanel,
2883 final MenuItem item = new MenuItem(title);
2884 sortByTreeMenu.add(item);
2885 item.addActionListener(new java.awt.event.ActionListener()
2888 public void actionPerformed(ActionEvent evt)
2890 sortByTree(treePanel, title); // treePanel.getTitle());
2894 treePanel.addWindowListener(new WindowAdapter()
2897 public void windowOpened(WindowEvent e)
2899 if (viewport.sortByTree)
2901 sortByTree(treePanel, title);
2903 super.windowOpened(e);
2907 public void windowClosing(WindowEvent e)
2909 sortByTreeMenu.remove(item);
2914 public boolean sortBy(AlignmentOrder alorder, String undoname)
2916 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2917 if (viewport.applet.debug)
2919 System.err.println("Sorting " + alorder.getOrder().size()
2920 + " in alignment '" + getTitle() + "'");
2922 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2923 if (undoname != null)
2925 addHistoryItem(new OrderCommand(undoname, oldOrder,
2926 viewport.getAlignment()));
2928 alignPanel.paintAlignment(true);
2932 protected void documentation_actionPerformed()
2934 alignPanel.av.applet.openJalviewHelpUrl();
2937 protected void about_actionPerformed()
2940 class AboutPanel extends Canvas
2946 public AboutPanel(String version, String builddate)
2948 this.version = version;
2949 this.builddate = builddate;
2953 public void paint(Graphics g)
2955 g.setColor(Color.white);
2956 g.fillRect(0, 0, getSize().width, getSize().height);
2957 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2958 FontMetrics fm = g.getFontMetrics();
2959 int fh = fm.getHeight();
2961 g.setColor(Color.black);
2962 // TODO: update this text for each release or centrally store it for
2963 // lite and application
2964 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2965 g.drawString(MessageManager.formatMessage(
2966 "label.jalviewLite_release", new String[] { version }), x,
2968 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2969 g.drawString(MessageManager.formatMessage(
2970 "label.jaview_build_date", new String[] { builddate }), x,
2972 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2973 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2975 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2976 x + 50, y += fh + 8);
2978 MessageManager.getString("label.jalview_dev_managers"), x,
2980 g.drawString(MessageManager
2981 .getString("label.jalview_distribution_lists"), x, y += fh);
2982 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2985 MessageManager.getString("label.jalview_cite_1_authors"),
2988 MessageManager.getString("label.jalview_cite_1_title"), x,
2990 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2995 Frame frame = new Frame();
2996 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2998 jalview.bin.JalviewLite.addFrame(frame,
2999 MessageManager.getString("label.jalview"), 580, 220);
3003 public void showURL(String url, String target)
3005 if (viewport.applet == null)
3007 System.out.println("Not running as applet - no browser available.");
3011 viewport.applet.showURL(url, target);
3015 // ////////////////////////////////////////////////////////////////////////////////
3016 // JBuilder Graphics here
3018 MenuBar alignFrameMenuBar = new MenuBar();
3020 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3022 MenuItem loadApplication = new MenuItem(
3023 MessageManager.getString("label.view_full_application"));
3025 MenuItem loadTree = new MenuItem(
3026 MessageManager.getString("label.load_associated_tree"));
3028 MenuItem loadAnnotations = new MenuItem(
3029 MessageManager.getString("label.load_features_annotations"));
3031 MenuItem outputFeatures = new MenuItem(
3032 MessageManager.getString("label.export_features"));
3034 MenuItem outputAnnotations = new MenuItem(
3035 MessageManager.getString("label.export_annotations"));
3037 MenuItem closeMenuItem = new MenuItem(
3038 MessageManager.getString("action.close"));
3040 MenuItem selectAllSequenceMenuItem = new MenuItem(
3041 MessageManager.getString("action.select_all"));
3043 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3044 MessageManager.getString("action.deselect_all"));
3046 MenuItem invertSequenceMenuItem = new MenuItem(
3047 MessageManager.getString("action.invert_selection"));
3049 MenuItem remove2LeftMenuItem = new MenuItem();
3051 MenuItem remove2RightMenuItem = new MenuItem();
3053 MenuItem removeGappedColumnMenuItem = new MenuItem();
3055 MenuItem removeAllGapsMenuItem = new MenuItem();
3057 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3059 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3061 MenuItem sortPairwiseMenuItem = new MenuItem();
3063 MenuItem sortIDMenuItem = new MenuItem();
3065 MenuItem sortLengthMenuItem = new MenuItem();
3067 MenuItem sortGroupMenuItem = new MenuItem();
3069 MenuItem removeRedundancyMenuItem = new MenuItem();
3071 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3073 MenuItem PCAMenuItem = new MenuItem();
3075 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3077 MenuItem neighbourTreeMenuItem = new MenuItem();
3079 BorderLayout borderLayout1 = new BorderLayout();
3081 public Label statusBar = new Label();
3083 MenuItem clustalColour = new MenuItem();
3085 MenuItem zappoColour = new MenuItem();
3087 MenuItem taylorColour = new MenuItem();
3089 MenuItem hydrophobicityColour = new MenuItem();
3091 MenuItem helixColour = new MenuItem();
3093 MenuItem strandColour = new MenuItem();
3095 MenuItem turnColour = new MenuItem();
3097 MenuItem buriedColour = new MenuItem();
3099 MenuItem purinePyrimidineColour = new MenuItem();
3101 // MenuItem RNAInteractionColour = new MenuItem();
3103 MenuItem RNAHelixColour = new MenuItem();
3105 MenuItem userDefinedColour = new MenuItem();
3107 MenuItem PIDColour = new MenuItem();
3109 MenuItem BLOSUM62Colour = new MenuItem();
3111 MenuItem tcoffeeColour = new MenuItem();
3113 MenuItem njTreeBlosumMenuItem = new MenuItem();
3115 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3117 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3119 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3121 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3123 MenuItem alProperties = new MenuItem(
3124 MessageManager.getString("label.alignment_props"));
3126 MenuItem overviewMenuItem = new MenuItem();
3128 MenuItem undoMenuItem = new MenuItem();
3130 MenuItem redoMenuItem = new MenuItem();
3132 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3134 MenuItem noColourmenuItem = new MenuItem();
3136 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3138 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3140 MenuItem findMenuItem = new MenuItem();
3142 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3144 MenuItem nucleotideColour = new MenuItem();
3146 MenuItem deleteGroups = new MenuItem();
3148 MenuItem grpsFromSelection = new MenuItem();
3150 MenuItem createGroup = new MenuItem();
3152 MenuItem unGroup = new MenuItem();
3154 MenuItem delete = new MenuItem();
3156 MenuItem copy = new MenuItem();
3158 MenuItem cut = new MenuItem();
3160 Menu pasteMenu = new Menu();
3162 MenuItem pasteNew = new MenuItem();
3164 MenuItem pasteThis = new MenuItem();
3166 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3168 MenuItem font = new MenuItem();
3170 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3172 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3174 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3176 MenuItem modifyPID = new MenuItem();
3178 MenuItem modifyConservation = new MenuItem();
3180 CheckboxMenuItem autoCalculate = null;
3182 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3183 "Sort Alignment With New Tree", true);
3185 Menu sortByTreeMenu = new Menu();
3187 MenuItem inputText = new MenuItem();
3189 MenuItem documentation = new MenuItem();
3191 MenuItem about = new MenuItem();
3193 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3195 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3197 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3199 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3201 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3203 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3205 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3207 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3209 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3212 * Initialise menus and other items
3216 private void jbInit() throws Exception
3218 setMenuBar(alignFrameMenuBar);
3221 * Configure File menu items and actions
3224 .setLabel(MessageManager.getString("label.input_from_textbox"));
3225 inputText.addActionListener(this);
3226 Menu outputTextboxMenu = new Menu(
3227 MessageManager.getString("label.out_to_textbox"));
3228 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3231 MenuItem item = new MenuItem(
3232 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3234 item.addActionListener(new java.awt.event.ActionListener()
3237 public void actionPerformed(ActionEvent e)
3239 outputText_actionPerformed(e);
3243 outputTextboxMenu.add(item);
3245 closeMenuItem.addActionListener(this);
3246 loadApplication.addActionListener(this);
3247 loadTree.addActionListener(this);
3248 loadAnnotations.addActionListener(this);
3249 outputFeatures.addActionListener(this);
3250 outputAnnotations.addActionListener(this);
3253 * Configure Edit menu items and actions
3255 undoMenuItem.setEnabled(false);
3256 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3257 undoMenuItem.addActionListener(this);
3258 redoMenuItem.setEnabled(false);
3259 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3260 redoMenuItem.addActionListener(this);
3261 copy.setLabel(MessageManager.getString("action.copy"));
3262 copy.addActionListener(this);
3263 cut.setLabel(MessageManager.getString("action.cut"));
3264 cut.addActionListener(this);
3265 delete.setLabel(MessageManager.getString("action.delete"));
3266 delete.addActionListener(this);
3267 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3268 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3269 pasteNew.addActionListener(this);
3270 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3271 pasteThis.addActionListener(this);
3272 remove2LeftMenuItem.setLabel(MessageManager
3273 .getString("action.remove_left"));
3274 remove2LeftMenuItem.addActionListener(this);
3275 remove2RightMenuItem.setLabel(MessageManager
3276 .getString("action.remove_right"));
3277 remove2RightMenuItem.addActionListener(this);
3278 removeGappedColumnMenuItem.setLabel(MessageManager
3279 .getString("action.remove_empty_columns"));
3280 removeGappedColumnMenuItem.addActionListener(this);
3281 removeAllGapsMenuItem.setLabel(MessageManager
3282 .getString("action.remove_all_gaps"));
3283 removeAllGapsMenuItem.addActionListener(this);
3284 removeRedundancyMenuItem.setLabel(MessageManager
3285 .getString("action.remove_redundancy"));
3286 removeRedundancyMenuItem.addActionListener(this);
3289 * Configure Select menu items and actions
3291 findMenuItem.setLabel(MessageManager.getString("action.find"));
3292 findMenuItem.addActionListener(this);
3293 selectAllSequenceMenuItem.addActionListener(this);
3294 deselectAllSequenceMenuItem.addActionListener(this);
3295 invertSequenceMenuItem.setLabel(MessageManager
3296 .getString("action.invert_sequence_selection"));
3297 invertSequenceMenuItem.addActionListener(this);
3298 invertColSel.setLabel(MessageManager
3299 .getString("action.invert_column_selection"));
3300 invertColSel.addActionListener(this);
3301 deleteGroups.setLabel(MessageManager
3302 .getString("action.undefine_groups"));
3303 deleteGroups.addActionListener(this);
3304 grpsFromSelection.setLabel(MessageManager
3305 .getString("action.make_groups_selection"));
3306 grpsFromSelection.addActionListener(this);
3307 createGroup.setLabel(MessageManager.getString("action.create_group"));
3308 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3309 annotationColumnSelection.setLabel(MessageManager
3310 .getString("action.select_by_annotation"));
3311 annotationColumnSelection.addActionListener(this);
3314 * Configure View menu items and actions
3316 newView.setLabel(MessageManager.getString("action.new_view"));
3317 newView.addActionListener(this);
3318 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3319 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3320 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3321 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3323 .setLabel(MessageManager.getString("label.selected_columns"));
3324 hideSequences.setLabel(MessageManager
3325 .getString("label.selected_sequences"));
3326 hideAllButSelection.setLabel(MessageManager
3327 .getString("label.all_but_selected_region"));
3328 hideAllSelection.setLabel(MessageManager
3329 .getString("label.selected_region"));
3330 showAllHidden.setLabel(MessageManager
3331 .getString("label.all_sequences_columns"));
3332 showColumns.addActionListener(this);
3333 showSeqs.addActionListener(this);
3334 hideColumns.addActionListener(this);
3335 hideSequences.addActionListener(this);
3336 hideAllButSelection.addActionListener(this);
3337 hideAllSelection.addActionListener(this);
3338 showAllHidden.addActionListener(this);
3339 featureSettings.setLabel(MessageManager
3340 .getString("action.feature_settings"));
3341 featureSettings.addActionListener(this);
3342 sequenceFeatures.setLabel(MessageManager
3343 .getString("label.show_sequence_features"));
3344 sequenceFeatures.addItemListener(this);
3345 sequenceFeatures.setState(false);
3346 followMouseOverFlag.setLabel(MessageManager
3347 .getString("label.automatic_scrolling"));
3348 followMouseOverFlag.addItemListener(this);
3349 alProperties.addActionListener(this);
3350 overviewMenuItem.setLabel(MessageManager
3351 .getString("label.overview_window"));
3352 overviewMenuItem.addActionListener(this);
3355 * Configure Annotations menu items and actions
3357 annotationPanelMenuItem.setLabel(MessageManager
3358 .getString("label.show_annotations"));
3359 annotationPanelMenuItem.addItemListener(this);
3360 showGroupConsensus.setLabel(MessageManager
3361 .getString("label.group_consensus"));
3362 showGroupConservation.setLabel(MessageManager
3363 .getString("label.group_conservation"));
3364 showConsensusHistogram.setLabel(MessageManager
3365 .getString("label.show_consensus_histogram"));
3366 showSequenceLogo.setLabel(MessageManager
3367 .getString("label.show_consensus_logo"));
3368 normSequenceLogo.setLabel(MessageManager
3369 .getString("label.norm_consensus_logo"));
3370 applyAutoAnnotationSettings.setLabel(MessageManager
3371 .getString("label.apply_all_groups"));
3372 applyAutoAnnotationSettings.setState(true);
3373 Menu autoAnnMenu = new Menu(
3374 MessageManager.getString("label.autocalculated_annotation"));
3375 showGroupConsensus.addItemListener(this);
3376 showGroupConservation.addItemListener(this);
3377 showConsensusHistogram.addItemListener(this);
3378 showSequenceLogo.addItemListener(this);
3379 normSequenceLogo.addItemListener(this);
3380 applyAutoAnnotationSettings.addItemListener(this);
3381 showAlignmentAnnotations = new CheckboxMenuItem(
3382 MessageManager.getString("label.show_all_al_annotations"));
3383 showSequenceAnnotations = new CheckboxMenuItem(
3384 MessageManager.getString("label.show_all_seq_annotations"));
3385 sortAnnBySequence = new CheckboxMenuItem(
3386 MessageManager.getString("label.sort_annotations_by_sequence"));
3387 sortAnnByLabel = new CheckboxMenuItem(
3388 MessageManager.getString("label.sort_annotations_by_label"));
3389 showAutoFirst = new CheckboxMenuItem(
3390 MessageManager.getString("label.show_first"));
3391 showAutoFirst.setState(false); // pending applet parameter
3392 setShowAutoCalculatedAbove(showAutoFirst.getState());
3393 showAutoLast = new CheckboxMenuItem(
3394 MessageManager.getString("label.show_last"));
3395 showAutoLast.setState(!showAutoFirst.getState());
3396 showAlignmentAnnotations.addItemListener(this);
3397 showSequenceAnnotations.addItemListener(this);
3398 sortAnnBySequence.addItemListener(this);
3399 sortAnnByLabel.addItemListener(this);
3400 showAutoFirst.addItemListener(this);
3401 showAutoLast.addItemListener(this);
3404 * Configure Format menu items and actions
3406 font.setLabel(MessageManager.getString("action.font"));
3407 font.addActionListener(this);
3408 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3409 scaleAbove.setState(true);
3410 scaleAbove.setEnabled(false);
3411 scaleAbove.addItemListener(this);
3412 scaleLeft.setEnabled(false);
3413 scaleLeft.setState(true);
3414 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3415 scaleLeft.addItemListener(this);
3416 scaleRight.setEnabled(false);
3417 scaleRight.setState(true);
3418 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3419 scaleRight.addItemListener(this);
3420 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3421 viewBoxesMenuItem.setState(true);
3422 viewBoxesMenuItem.addItemListener(this);
3423 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3424 viewTextMenuItem.setState(true);
3425 viewTextMenuItem.addItemListener(this);
3426 colourTextMenuItem.setLabel(MessageManager
3427 .getString("label.colour_text"));
3428 colourTextMenuItem.addItemListener(this);
3429 displayNonconservedMenuItem.setLabel(MessageManager
3430 .getString("label.show_non_conversed"));
3431 displayNonconservedMenuItem.addItemListener(this);
3432 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3433 wrapMenuItem.addItemListener(this);
3434 renderGapsMenuItem.setLabel(MessageManager
3435 .getString("action.show_gaps"));
3436 renderGapsMenuItem.setState(true);
3437 renderGapsMenuItem.addItemListener(this);
3438 centreColumnLabelFlag.setLabel(MessageManager
3439 .getString("label.centre_column_labels"));
3440 centreColumnLabelFlag.addItemListener(this);
3441 seqLimits.setState(true);
3442 seqLimits.setLabel(MessageManager
3443 .getString("label.show_sequence_limits"));
3444 seqLimits.addItemListener(this);
3447 * Configure Colour menu items and actions
3449 applyToAllGroups.setLabel(MessageManager
3450 .getString("label.apply_colour_to_all_groups"));
3451 applyToAllGroups.setState(true);
3452 applyToAllGroups.addItemListener(this);
3453 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3454 clustalColour.addActionListener(this);
3455 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3456 zappoColour.addActionListener(this);
3457 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3458 taylorColour.addActionListener(this);
3459 hydrophobicityColour.setLabel(MessageManager
3460 .getString("label.hydrophobicity"));
3461 hydrophobicityColour.addActionListener(this);
3463 .setLabel(MessageManager.getString("label.helix_propensity"));
3464 helixColour.addActionListener(this);
3465 strandColour.setLabel(MessageManager
3466 .getString("label.strand_propensity"));
3467 strandColour.addActionListener(this);
3468 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3469 turnColour.addActionListener(this);
3470 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3471 buriedColour.addActionListener(this);
3472 purinePyrimidineColour.setLabel(MessageManager
3473 .getString("label.purine_pyrimidine"));
3474 purinePyrimidineColour.addActionListener(this);
3475 // RNAInteractionColour.setLabel(MessageManager
3476 // .getString("label.rna_interaction"));
3477 // RNAInteractionColour.addActionListener(this);
3478 RNAHelixColour.setLabel(MessageManager
3479 .getString("action.by_rna_helixes"));
3480 RNAHelixColour.addActionListener(this);
3481 userDefinedColour.setLabel(MessageManager
3482 .getString("action.user_defined"));
3483 userDefinedColour.addActionListener(this);
3484 PIDColour.setLabel(MessageManager
3485 .getString("label.percentage_identity"));
3486 PIDColour.addActionListener(this);
3487 BLOSUM62Colour.setLabel(MessageManager
3488 .getString("label.blosum62_score"));
3489 BLOSUM62Colour.addActionListener(this);
3491 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3492 // it will be enabled only if a score file is provided
3493 tcoffeeColour.setEnabled(false);
3494 tcoffeeColour.addActionListener(this);
3495 conservationMenuItem.setLabel(MessageManager
3496 .getString("action.by_conservation"));
3497 conservationMenuItem.addItemListener(this);
3498 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3499 noColourmenuItem.addActionListener(this);
3500 abovePIDThreshold.setLabel(MessageManager
3501 .getString("label.above_identity_threshold"));
3502 abovePIDThreshold.addItemListener(this);
3503 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3504 nucleotideColour.addActionListener(this);
3505 modifyPID.setLabel(MessageManager
3506 .getString("label.modify_identity_thereshold"));
3507 modifyPID.addActionListener(this);
3508 modifyConservation.setLabel(MessageManager
3509 .getString("label.modify_conservation_thereshold"));
3510 modifyConservation.addActionListener(this);
3511 annotationColour.setLabel(MessageManager
3512 .getString("action.by_annotation"));
3513 annotationColour.addActionListener(this);
3516 * Configure Calculate menu items and actions
3518 sortPairwiseMenuItem.setLabel(MessageManager
3519 .getString("action.by_pairwise_id"));
3520 sortPairwiseMenuItem.addActionListener(this);
3521 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3522 sortIDMenuItem.addActionListener(this);
3523 sortLengthMenuItem.setLabel(MessageManager
3524 .getString("action.by_length"));
3525 sortLengthMenuItem.addActionListener(this);
3526 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3527 sortGroupMenuItem.addActionListener(this);
3528 pairwiseAlignmentMenuItem.setLabel(MessageManager
3529 .getString("action.pairwise_alignment"));
3530 pairwiseAlignmentMenuItem.addActionListener(this);
3531 PCAMenuItem.setLabel(MessageManager
3532 .getString("label.principal_component_analysis"));
3533 PCAMenuItem.addActionListener(this);
3534 autoCalculate = new CheckboxMenuItem(
3535 MessageManager.getString("label.autocalculate_consensus"), true);
3536 averageDistanceTreeMenuItem.setLabel(MessageManager
3537 .getString("label.average_distance_identity"));
3538 averageDistanceTreeMenuItem.addActionListener(this);
3539 neighbourTreeMenuItem.setLabel(MessageManager
3540 .getString("label.neighbour_joining_identity"));
3541 neighbourTreeMenuItem.addActionListener(this);
3542 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3543 .getString("label.average_distance_bloslum62"));
3544 avDistanceTreeBlosumMenuItem.addActionListener(this);
3545 njTreeBlosumMenuItem.setLabel(MessageManager
3546 .getString("label.neighbour_blosum62"));
3547 njTreeBlosumMenuItem.addActionListener(this);
3548 sortByTreeMenu.setLabel(MessageManager
3549 .getString("action.by_tree_order"));
3550 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3551 Menu calculateTreeMenu = new Menu(
3552 MessageManager.getString("action.calculate_tree"));
3553 autoCalculate.addItemListener(this);
3554 sortByTree.addItemListener(this);
3557 * Configure Help menu items and actions
3559 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3560 documentation.setLabel(MessageManager.getString("label.documentation"));
3561 documentation.addActionListener(this);
3562 about.setLabel(MessageManager.getString("label.about"));
3563 about.addActionListener(this);
3566 * Add top level menus to frame
3568 alignFrameMenuBar.add(fileMenu);
3569 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3570 alignFrameMenuBar.add(editMenu);
3571 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3572 alignFrameMenuBar.add(selectMenu);
3573 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3574 alignFrameMenuBar.add(viewMenu);
3575 Menu annotationsMenu = new Menu(
3576 MessageManager.getString("action.annotations"));
3577 alignFrameMenuBar.add(annotationsMenu);
3578 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3579 alignFrameMenuBar.add(formatMenu);
3580 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3581 alignFrameMenuBar.add(colourMenu);
3582 Menu calculateMenu = new Menu(
3583 MessageManager.getString("action.calculate"));
3584 alignFrameMenuBar.add(calculateMenu);
3585 alignFrameMenuBar.add(helpMenu);
3590 fileMenu.add(inputText);
3591 fileMenu.add(loadTree);
3592 fileMenu.add(loadAnnotations);
3593 fileMenu.addSeparator();
3594 fileMenu.add(outputTextboxMenu);
3595 fileMenu.add(outputFeatures);
3596 fileMenu.add(outputAnnotations);
3597 if (jalviewServletURL != null)
3599 fileMenu.add(loadApplication);
3601 fileMenu.addSeparator();
3602 fileMenu.add(closeMenuItem);
3607 editMenu.add(undoMenuItem);
3608 editMenu.add(redoMenuItem);
3611 pasteMenu.add(pasteNew);
3612 pasteMenu.add(pasteThis);
3613 editMenu.add(pasteMenu);
3614 editMenu.add(delete);
3615 editMenu.addSeparator();
3616 editMenu.add(remove2LeftMenuItem);
3617 editMenu.add(remove2RightMenuItem);
3618 editMenu.add(removeGappedColumnMenuItem);
3619 editMenu.add(removeAllGapsMenuItem);
3620 editMenu.add(removeRedundancyMenuItem);
3625 selectMenu.add(findMenuItem);
3626 selectMenu.addSeparator();
3627 selectMenu.add(selectAllSequenceMenuItem);
3628 selectMenu.add(deselectAllSequenceMenuItem);
3629 selectMenu.add(invertSequenceMenuItem);
3630 selectMenu.add(invertColSel);
3631 selectMenu.add(createGroup);
3632 selectMenu.add(unGroup);
3633 selectMenu.add(grpsFromSelection);
3634 selectMenu.add(deleteGroups);
3635 selectMenu.add(annotationColumnSelection);
3640 viewMenu.add(newView);
3641 viewMenu.addSeparator();
3642 showMenu.add(showColumns);
3643 showMenu.add(showSeqs);
3644 showMenu.add(showAllHidden);
3645 viewMenu.add(showMenu);
3646 hideMenu.add(hideColumns);
3647 hideMenu.add(hideSequences);
3648 hideMenu.add(hideAllSelection);
3649 hideMenu.add(hideAllButSelection);
3650 viewMenu.add(hideMenu);
3651 viewMenu.addSeparator();
3652 viewMenu.add(followMouseOverFlag);
3653 viewMenu.addSeparator();
3654 viewMenu.add(sequenceFeatures);
3655 viewMenu.add(featureSettings);
3656 viewMenu.addSeparator();
3657 viewMenu.add(alProperties);
3658 viewMenu.addSeparator();
3659 viewMenu.add(overviewMenuItem);
3664 annotationsMenu.add(annotationPanelMenuItem);
3665 annotationsMenu.addSeparator();
3666 annotationsMenu.add(showAlignmentAnnotations);
3667 annotationsMenu.add(showSequenceAnnotations);
3668 annotationsMenu.add(sortAnnBySequence);
3669 annotationsMenu.add(sortAnnByLabel);
3670 annotationsMenu.addSeparator();
3671 autoAnnMenu.add(showAutoFirst);
3672 autoAnnMenu.add(showAutoLast);
3673 autoAnnMenu.addSeparator();
3674 autoAnnMenu.add(applyAutoAnnotationSettings);
3675 autoAnnMenu.add(showConsensusHistogram);
3676 autoAnnMenu.add(showSequenceLogo);
3677 autoAnnMenu.add(normSequenceLogo);
3678 autoAnnMenu.addSeparator();
3679 autoAnnMenu.add(showGroupConservation);
3680 autoAnnMenu.add(showGroupConsensus);
3681 annotationsMenu.add(autoAnnMenu);
3686 formatMenu.add(font);
3687 formatMenu.add(seqLimits);
3688 formatMenu.add(wrapMenuItem);
3689 formatMenu.add(scaleAbove);
3690 formatMenu.add(scaleLeft);
3691 formatMenu.add(scaleRight);
3692 formatMenu.add(viewBoxesMenuItem);
3693 formatMenu.add(viewTextMenuItem);
3694 formatMenu.add(colourTextMenuItem);
3695 formatMenu.add(displayNonconservedMenuItem);
3696 formatMenu.add(renderGapsMenuItem);
3697 formatMenu.add(centreColumnLabelFlag);
3702 colourMenu.add(applyToAllGroups);
3703 colourMenu.addSeparator();
3704 colourMenu.add(noColourmenuItem);
3705 colourMenu.add(clustalColour);
3706 colourMenu.add(BLOSUM62Colour);
3707 colourMenu.add(PIDColour);
3708 colourMenu.add(zappoColour);
3709 colourMenu.add(taylorColour);
3710 colourMenu.add(hydrophobicityColour);
3711 colourMenu.add(helixColour);
3712 colourMenu.add(strandColour);
3713 colourMenu.add(turnColour);
3714 colourMenu.add(buriedColour);
3715 colourMenu.add(nucleotideColour);
3716 colourMenu.add(purinePyrimidineColour);
3717 // colourMenu.add(RNAInteractionColour);
3718 colourMenu.add(tcoffeeColour);
3719 colourMenu.add(userDefinedColour);
3720 colourMenu.addSeparator();
3721 colourMenu.add(conservationMenuItem);
3722 colourMenu.add(modifyConservation);
3723 colourMenu.add(abovePIDThreshold);
3724 colourMenu.add(modifyPID);
3725 colourMenu.add(annotationColour);
3726 colourMenu.add(RNAHelixColour);
3731 sortMenu.add(sortIDMenuItem);
3732 sortMenu.add(sortLengthMenuItem);
3733 sortMenu.add(sortByTreeMenu);
3734 sortMenu.add(sortGroupMenuItem);
3735 sortMenu.add(sortPairwiseMenuItem);
3736 calculateMenu.add(sortMenu);
3737 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3738 calculateTreeMenu.add(neighbourTreeMenuItem);
3739 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3740 calculateTreeMenu.add(njTreeBlosumMenuItem);
3741 calculateMenu.add(calculateTreeMenu);
3742 calculateMenu.addSeparator();
3743 calculateMenu.add(pairwiseAlignmentMenuItem);
3744 calculateMenu.add(PCAMenuItem);
3745 calculateMenu.add(autoCalculate);
3746 calculateMenu.add(sortByTree);
3751 helpMenu.add(documentation);
3752 helpMenu.add(about);
3757 statusBar.setBackground(Color.white);
3758 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3759 statusBar.setText(MessageManager.getString("label.status_bar"));
3760 this.add(statusBar, BorderLayout.SOUTH);
3763 public void setStatus(String string)
3765 statusBar.setText(string);
3768 MenuItem featureSettings = new MenuItem();
3770 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3772 MenuItem annotationColour = new MenuItem();
3774 MenuItem annotationColumnSelection = new MenuItem();
3776 MenuItem invertColSel = new MenuItem();
3778 MenuItem showColumns = new MenuItem();
3780 MenuItem showSeqs = new MenuItem();
3782 MenuItem hideColumns = new MenuItem();
3784 MenuItem hideSequences = new MenuItem();
3786 MenuItem hideAllButSelection = new MenuItem();
3788 MenuItem hideAllSelection = new MenuItem();
3790 MenuItem showAllHidden = new MenuItem();
3792 MenuItem newView = new MenuItem();
3794 private CheckboxMenuItem showAlignmentAnnotations;
3796 private CheckboxMenuItem showSequenceAnnotations;
3798 private CheckboxMenuItem sortAnnBySequence;
3800 private CheckboxMenuItem sortAnnByLabel;
3802 private CheckboxMenuItem showAutoFirst;
3804 private CheckboxMenuItem showAutoLast;
3806 private SplitFrame splitFrame;
3809 * Attach the alignFrame panels after embedding menus, if necessary. This used
3810 * to be called setEmbedded, but is now creates the dropdown menus in a
3811 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3813 * @param reallyEmbedded
3814 * true to attach the view to the applet area on the page rather than
3817 public void createAlignFrameWindow(boolean reallyEmbedded)
3821 embedAlignFrameInApplet(viewport.applet);
3826 // test and embed menu bar if necessary.
3828 if (embedMenuIfNeeded(alignPanel))
3831 * adjust for status bar height too. ? pointless as overridden by layout
3834 alignPanel.setSize(getSize().width,
3835 getSize().height - statusBar.getHeight());
3837 add(statusBar, BorderLayout.SOUTH);
3838 add(alignPanel, BorderLayout.CENTER);
3839 // and register with the applet so it can pass external API calls to us
3840 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3846 * Add the components of this AlignFrame to the applet container.
3850 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3853 // Explicitly build the embedded menu panel for the on-page applet
3855 // view cannot be closed if its actually on the page
3856 fileMenu.remove(closeMenuItem);
3857 fileMenu.remove(3); // Remove Separator
3858 // construct embedded menu, using default font
3859 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3860 // and actually add the components to the applet area
3861 theApplet.setLayout(new BorderLayout());
3862 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3863 theApplet.add(statusBar, BorderLayout.SOUTH);
3864 // TODO should size be left to the layout manager?
3865 alignPanel.setSize(theApplet.getSize().width,
3866 theApplet.getSize().height - embeddedMenu.getHeight()
3867 - statusBar.getHeight());
3868 theApplet.add(alignPanel, BorderLayout.CENTER);
3869 final AlignFrame me = this;
3870 theApplet.addFocusListener(new FocusListener()
3874 public void focusLost(FocusEvent e)
3876 if (theApplet.currentAlignFrame == me)
3878 theApplet.currentAlignFrame = null;
3883 public void focusGained(FocusEvent e)
3885 theApplet.currentAlignFrame = me;
3888 theApplet.validate();
3892 * create a new binding between structures in an existing jmol viewer instance
3893 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3894 * this does not open a new Jmol window, or modify the display of the
3895 * structures in the original jmol window. Note This method doesn't work
3896 * without an additional javascript library to exchange messages between the
3897 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3900 * JmolViewer instance
3901 * @param sequenceIds
3902 * - sequence Ids to search for associations
3904 public SequenceStructureBinding addStructureViewInstance(
3905 Object jmolviewer, String[] sequenceIds)
3907 Viewer viewer = null;
3910 viewer = (Viewer) jmolviewer;
3911 } catch (ClassCastException ex)
3913 System.err.println("Unsupported viewer object :"
3914 + jmolviewer.getClass());
3918 System.err.println("Can't use this object as a structure viewer:"
3919 + jmolviewer.getClass());
3922 SequenceI[] seqs = null;
3923 if (sequenceIds == null || sequenceIds.length == 0)
3925 seqs = viewport.getAlignment().getSequencesArray();
3929 Vector sqi = new Vector();
3930 AlignmentI al = viewport.getAlignment();
3931 for (int sid = 0; sid < sequenceIds.length; sid++)
3933 SequenceI sq = al.findName(sequenceIds[sid]);
3941 seqs = new SequenceI[sqi.size()];
3942 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3944 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3952 AAStructureBindingModel jmv = null;
3953 // TODO: search for a jmv that involves viewer
3955 { // create a new viewer/jalview binding.
3956 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3963 * bind a pdb file to a sequence in the current view
3966 * - sequenceId within the dataset.
3967 * @param pdbEntryString
3968 * - the short name for the PDB file
3970 * - pdb file - either a URL or a valid PDB file.
3971 * @return true if binding was as success TODO: consider making an exception
3972 * structure for indicating when PDB parsing or sequenceId location
3975 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3978 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3979 boolean needtoadd = false;
3980 if (toaddpdb != null)
3982 Vector pdbe = toaddpdb.getAllPDBEntries();
3983 PDBEntry pdbentry = null;
3984 if (pdbe != null && pdbe.size() > 0)
3986 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3988 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3989 if (!pdbentry.getId().equals(pdbEntryString)
3990 && !pdbentry.getFile().equals(pdbFile))
4000 if (pdbentry == null)
4002 pdbentry = new PDBEntry();
4003 pdbentry.setId(pdbEntryString);
4004 pdbentry.setFile(pdbFile);
4005 needtoadd = true; // add this new entry to sequence.
4007 // resolve data source
4008 // TODO: this code should be a refactored to an io package
4009 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4010 if (protocol == null)
4016 // make a note of the access mode and add
4017 if (pdbentry.getProperty() == null)
4019 pdbentry.setProperty(new Hashtable());
4021 pdbentry.getProperty().put("protocol", protocol);
4022 toaddpdb.addPDBId(pdbentry);
4023 alignPanel.getStructureSelectionManager()
4024 .registerPDBEntry(pdbentry);
4030 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4034 Vector sequences = new Vector();
4035 for (int i = 0; i < seqs.length; i++)
4037 if (seqs[i] != null)
4039 sequences.addElement(new Object[] { seqs[i],
4040 (chains != null) ? chains[i] : null });
4043 seqs = new SequenceI[sequences.size()];
4044 chains = new String[sequences.size()];
4045 for (int i = 0, isize = sequences.size(); i < isize; i++)
4047 Object[] oj = (Object[]) sequences.elementAt(i);
4049 seqs[i] = (SequenceI) oj[0];
4050 chains[i] = (String) oj[1];
4053 return new Object[] { seqs, chains };
4057 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4058 SequenceI[] seqs, String[] chains, String protocol)
4060 // Scrub any null sequences from the array
4061 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4062 seqs = (SequenceI[]) sqch[0];
4063 chains = (String[]) sqch[1];
4064 if (seqs == null || seqs.length == 0)
4067 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4069 if (protocol == null || protocol.trim().length() == 0
4070 || protocol.equals("null"))
4072 protocol = (String) pdb.getProperty().get("protocol");
4073 if (protocol == null)
4075 System.err.println("Couldn't work out protocol to open structure: "
4080 if (applet.useXtrnalSviewer)
4082 // register the association(s) and quit, don't create any windows.
4083 if (StructureSelectionManager.getStructureSelectionManager(applet)
4084 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4086 System.err.println("Failed to map " + pdb.getFile() + " ("
4087 + protocol + ") to any sequences");
4091 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4093 // can only do alignments with Jmol
4094 // find the last jmol window assigned to this alignment
4095 jalview.appletgui.AppletJmol ajm = null, tajm;
4096 Vector jmols = applet
4097 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4098 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4100 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4101 if (tajm.ap.alignFrame == this)
4110 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4111 // try and add the pdb structure
4116 // otherwise, create a new window
4117 if (applet.jmolAvailable)
4119 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4121 applet.lastFrameX += 40;
4122 applet.lastFrameY += 40;
4126 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4131 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4132 SequenceI[][] seqs, String[][] chains, String[] protocols)
4134 // TODO Auto-generated method stub
4135 System.err.println("Aligned Structure View: Not yet implemented.");
4139 * modify the current selection, providing the user has not made a selection
4143 * - sequences from this alignment
4145 * - columns to be selected on the alignment
4147 public void select(SequenceGroup sel, ColumnSelection csel)
4149 alignPanel.seqPanel.selection(sel, csel, null);
4152 public void scrollTo(int row, int column)
4154 alignPanel.seqPanel.scrollTo(row, column);
4157 public void scrollToRow(int row)
4159 alignPanel.seqPanel.scrollToRow(row);
4162 public void scrollToColumn(int column)
4164 alignPanel.seqPanel.scrollToColumn(column);
4168 * @return the alignments unique ID.
4170 public String getSequenceSetId()
4172 return viewport.getSequenceSetId();
4176 * Load the (T-Coffee) score file from the specified url
4179 * File/URL/T-COFFEE score file contents
4180 * @throws IOException
4181 * @return true if alignment was annotated with data from source
4183 public boolean loadScoreFile(String source) throws IOException
4186 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4187 AppletFormatAdapter.checkProtocol(source));
4188 if (!file.isValid())
4190 // TODO: raise dialog for gui
4191 System.err.println("Problems parsing T-Coffee scores: "
4192 + file.getWarningMessage());
4193 System.err.println("Origin was:\n" + source);
4198 * check that the score matrix matches the alignment dimensions
4201 if ((aln = viewport.getAlignment()) != null
4202 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4205 // TODO: raise a dialog box here rather than bomb out.
4207 .println("The scores matrix does not match the alignment dimensions");
4211 // TODO add parameter to indicate if matching should be done
4212 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4214 alignPanel.fontChanged();
4215 tcoffeeColour.setEnabled(true);
4216 // switch to this color
4217 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4222 System.err.println("Problems resolving T-Coffee scores:");
4223 if (file.getWarningMessage() != null)
4225 System.err.println(file.getWarningMessage());
4231 public SplitFrame getSplitFrame()
4233 return this.splitFrame;
4236 public void setSplitFrame(SplitFrame sf)
4238 this.splitFrame = sf;
4241 // may not need this
4243 public void setShowSeqFeatures(boolean b)
4245 // showSeqFeatures.setSelected(b);
4246 viewport.setShowSequenceFeatures(b);
4251 public void setMenusForViewport()
4253 // setMenusFromViewport(viewport);
4258 public void refreshFeatureUI(boolean enableIfNecessary)
4260 if (enableIfNecessary)
4262 sequenceFeatures.setState(true);
4263 alignPanel.av.setShowSequenceFeatures(true);
4268 public FeatureSettingsControllerI getFeatureSettingsUI()
4270 return alignPanel.av.featureSettings;