2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.api.FeatureSettingsControllerI;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.OrderCommand;
37 import jalview.commands.RemoveGapColCommand;
38 import jalview.commands.RemoveGapsCommand;
39 import jalview.commands.SlideSequencesCommand;
40 import jalview.commands.TrimRegionCommand;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AnnotationFile;
51 import jalview.io.AppletFormatAdapter;
52 import jalview.io.DataSourceType;
53 import jalview.io.FeaturesFile;
54 import jalview.io.FileFormat;
55 import jalview.io.FileFormatI;
56 import jalview.io.FileFormats;
57 import jalview.io.TCoffeeScoreFile;
58 import jalview.schemes.Blosum62ColourScheme;
59 import jalview.schemes.BuriedColourScheme;
60 import jalview.schemes.ClustalxColourScheme;
61 import jalview.schemes.ColourSchemeI;
62 import jalview.schemes.HelixColourScheme;
63 import jalview.schemes.HydrophobicColourScheme;
64 import jalview.schemes.NucleotideColourScheme;
65 import jalview.schemes.PIDColourScheme;
66 import jalview.schemes.PurinePyrimidineColourScheme;
67 import jalview.schemes.RNAHelicesColourChooser;
68 import jalview.schemes.StrandColourScheme;
69 import jalview.schemes.TCoffeeColourScheme;
70 import jalview.schemes.TaylorColourScheme;
71 import jalview.schemes.TurnColourScheme;
72 import jalview.schemes.ZappoColourScheme;
73 import jalview.structure.StructureSelectionManager;
74 import jalview.structures.models.AAStructureBindingModel;
75 import jalview.util.MappingUtils;
76 import jalview.util.MessageManager;
77 import jalview.viewmodel.AlignmentViewport;
79 import java.awt.BorderLayout;
80 import java.awt.Canvas;
81 import java.awt.CheckboxMenuItem;
82 import java.awt.Color;
83 import java.awt.FlowLayout;
85 import java.awt.FontMetrics;
86 import java.awt.Frame;
87 import java.awt.Graphics;
88 import java.awt.Label;
90 import java.awt.MenuBar;
91 import java.awt.MenuItem;
92 import java.awt.Panel;
93 import java.awt.event.ActionEvent;
94 import java.awt.event.ActionListener;
95 import java.awt.event.FocusEvent;
96 import java.awt.event.FocusListener;
97 import java.awt.event.ItemEvent;
98 import java.awt.event.ItemListener;
99 import java.awt.event.KeyEvent;
100 import java.awt.event.KeyListener;
101 import java.awt.event.WindowAdapter;
102 import java.awt.event.WindowEvent;
103 import java.io.IOException;
105 import java.net.URLEncoder;
106 import java.util.Arrays;
107 import java.util.Deque;
108 import java.util.HashMap;
109 import java.util.List;
110 import java.util.Map;
111 import java.util.StringTokenizer;
112 import java.util.Vector;
114 import org.jmol.viewer.Viewer;
116 public class AlignFrame extends EmbmenuFrame implements ActionListener,
117 ItemListener, KeyListener, AlignViewControllerGuiI
119 public AlignViewControllerI avc;
121 public AlignmentPanel alignPanel;
123 public AlignViewport viewport;
125 // width and height may be overridden by applet parameters
126 int frameWidth = 700;
128 int frameHeight = 500;
130 String jalviewServletURL;
133 * Flag for showing autocalculated consensus above or below other consensus
136 private boolean showAutoCalculatedAbove;
138 private SequenceAnnotationOrder annotationSortOrder;
141 * Constructor that creates the frame and adds it to the display.
148 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
151 this(al, applet, title, embedded, true);
155 * Constructor that optionally allows the frame to be displayed or only
162 * @param addToDisplay
164 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
165 boolean embedded, boolean addToDisplay)
167 this(al, null, null, applet, title, embedded, addToDisplay);
170 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
171 ColumnSelection columnSelection, JalviewLite applet,
172 String title, boolean embedded)
174 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
177 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
178 ColumnSelection columnSelection, JalviewLite applet,
179 String title, boolean embedded, boolean addToDisplay)
183 jalviewServletURL = applet.getParameter("APPLICATION_URL");
189 } catch (Exception ex)
191 ex.printStackTrace();
193 // need to get window geometry before we calculate alignment layout
199 param = applet.getParameter("windowWidth");
202 int width = Integer.parseInt(param);
205 param = applet.getParameter("windowHeight");
208 int height = Integer.parseInt(param);
209 frameHeight = height;
211 } catch (Exception ex)
215 viewport = new AlignViewport(al, applet);
217 if (hiddenSeqs != null && hiddenSeqs.length > 0)
219 viewport.hideSequence(hiddenSeqs);
221 if (columnSelection != null)
223 viewport.setColumnSelection(columnSelection);
225 viewport.setScaleAboveWrapped(scaleAbove.getState());
227 alignPanel = new AlignmentPanel(this, viewport);
228 avc = new jalview.controller.AlignViewController(this, viewport,
230 viewport.updateConservation(alignPanel);
231 viewport.updateConsensus(alignPanel);
233 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
234 followMouseOverFlag.setState(viewport.isFollowHighlight());
235 showGroupConsensus.setState(viewport.isShowGroupConsensus());
236 showGroupConservation.setState(viewport.isShowGroupConservation());
237 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
238 showSequenceLogo.setState(viewport.isShowSequenceLogo());
239 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
240 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
241 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
242 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
243 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
244 showAlignmentAnnotations.setState(true);
245 showSequenceAnnotations.setState(false);
247 seqLimits.setState(viewport.getShowJVSuffix());
251 String param = applet.getParameter("sortBy");
254 if (param.equalsIgnoreCase("Id"))
256 sortIDMenuItem_actionPerformed();
258 else if (param.equalsIgnoreCase("Pairwise Identity"))
260 sortPairwiseMenuItem_actionPerformed();
262 else if (param.equalsIgnoreCase("Length"))
264 sortLengthMenuItem_actionPerformed();
268 param = applet.getParameter("wrap");
271 if (param.equalsIgnoreCase("true"))
273 wrapMenuItem.setState(true);
274 wrapMenuItem_actionPerformed();
277 param = applet.getParameter("centrecolumnlabels");
280 centreColumnLabelFlag.setState(true);
281 centreColumnLabelFlag_stateChanged();
285 if (viewport.getAlignment().isNucleotide())
287 viewport.updateStrucConsensus(alignPanel);
288 if (viewport.getAlignment().hasRNAStructure())
290 RNAHelixColour.setEnabled(true);
294 RNAHelixColour.setEnabled(false);
299 RNAHelixColour.setEnabled(false);
300 purinePyrimidineColour.setEnabled(false);
302 // Some JVMS send keyevents to Top frame or lowest panel,
303 // Havent worked out why yet. So add to both this frame and seqCanvas for
305 this.addKeyListener(this);
306 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
307 alignPanel.idPanel.idCanvas.addKeyListener(this);
308 alignPanel.scalePanel.addKeyListener(this);
309 alignPanel.annotationPanel.addKeyListener(this);
310 alignPanel.annotationPanelHolder.addKeyListener(this);
311 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
312 alignPanel.alabels.addKeyListener(this);
314 setAnnotationsVisibility();
318 addToDisplay(embedded);
325 public void addToDisplay(boolean embedded)
327 createAlignFrameWindow(embedded);
329 alignPanel.adjustAnnotationHeight();
330 alignPanel.paintAlignment(true);
333 public AlignViewport getAlignViewport()
338 public SeqCanvas getSeqcanvas()
340 return alignPanel.seqPanel.seqCanvas;
344 * Load a features file onto the alignment
347 * file URL, content, or other resolvable path
349 * is protocol for accessing data referred to by file
352 public boolean parseFeaturesFile(String file, DataSourceType type)
354 return parseFeaturesFile(file, type, true);
358 * Load a features file onto the alignment
361 * file URL, content, or other resolvable path
363 * is protocol for accessing data referred to by file
364 * @param autoenabledisplay
365 * when true, display features flag will be automatically enabled if
366 * features are loaded
367 * @return true if data parsed as a features file
369 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
370 boolean autoenabledisplay)
372 boolean featuresFile = false;
375 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
376 .getFeatureRenderer().getFeatureColours();
377 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
378 "relaxedidmatch", false);
379 featuresFile = new FeaturesFile(file, sourceType).parse(
380 viewport.getAlignment(), colours, true, relaxedIdMatching);
381 } catch (Exception ex)
383 ex.printStackTrace();
388 if (autoenabledisplay)
390 viewport.setShowSequenceFeatures(true);
391 sequenceFeatures.setState(true);
393 if (alignPanel.seqPanel.seqCanvas.fr != null)
395 // update the min/max ranges where necessary
396 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
398 if (viewport.featureSettings != null)
400 viewport.featureSettings.refreshTable();
402 alignPanel.paintAlignment(true);
403 statusBar.setText(MessageManager
404 .getString("label.successfully_added_features_alignment"));
410 public void keyPressed(KeyEvent evt)
412 if (viewport.cursorMode
413 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
414 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
415 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
416 && Character.isDigit(evt.getKeyChar()))
418 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
421 switch (evt.getKeyCode())
423 case 27: // escape key
424 deselectAllSequenceMenuItem_actionPerformed();
426 alignPanel.alabels.cancelDrag();
429 if (evt.isControlDown() || evt.isMetaDown())
431 cut_actionPerformed();
435 if (viewport.cursorMode && !evt.isControlDown())
437 alignPanel.seqPanel.setCursorColumn();
439 if (evt.isControlDown() || evt.isMetaDown())
441 copy_actionPerformed();
445 if (evt.isControlDown())
447 paste(evt.isShiftDown());
451 if (evt.isControlDown() || evt.isMetaDown())
453 selectAllSequenceMenuItem_actionPerformed();
456 case KeyEvent.VK_DOWN:
457 if (viewport.cursorMode)
459 alignPanel.seqPanel.moveCursor(0, 1);
463 moveSelectedSequences(false);
468 if (viewport.cursorMode)
470 alignPanel.seqPanel.moveCursor(0, -1);
474 moveSelectedSequences(true);
478 case KeyEvent.VK_LEFT:
479 if (evt.isAltDown() || !viewport.cursorMode)
481 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
485 alignPanel.seqPanel.moveCursor(-1, 0);
489 case KeyEvent.VK_RIGHT:
490 if (evt.isAltDown() || !viewport.cursorMode)
492 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
496 alignPanel.seqPanel.moveCursor(1, 0);
500 case KeyEvent.VK_SPACE:
501 if (viewport.cursorMode)
503 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
504 || evt.isShiftDown() || evt.isAltDown());
508 case KeyEvent.VK_DELETE:
509 case KeyEvent.VK_BACK_SPACE:
510 if (viewport.cursorMode)
512 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
513 || evt.isShiftDown() || evt.isAltDown());
517 cut_actionPerformed();
518 alignPanel.seqPanel.seqCanvas.repaint();
523 if (viewport.cursorMode)
525 alignPanel.seqPanel.setCursorRow();
529 if (viewport.cursorMode)
531 alignPanel.seqPanel.setCursorPosition();
535 case KeyEvent.VK_ENTER:
536 case KeyEvent.VK_COMMA:
537 if (viewport.cursorMode)
539 alignPanel.seqPanel.setCursorRowAndColumn();
544 if (viewport.cursorMode)
546 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
550 if (viewport.cursorMode)
552 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
557 viewport.cursorMode = !viewport.cursorMode;
558 statusBar.setText(MessageManager.formatMessage(
559 "label.keyboard_editing_mode",
560 new String[] { (viewport.cursorMode ? "on" : "off") }));
561 if (viewport.cursorMode)
563 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
564 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
569 if (evt.isControlDown())
571 findMenuItem_actionPerformed();
577 boolean toggleSeqs = !evt.isControlDown();
578 boolean toggleCols = !evt.isShiftDown();
579 toggleHiddenRegions(toggleSeqs, toggleCols);
583 case KeyEvent.VK_PAGE_UP:
584 if (viewport.getWrapAlignment())
586 alignPanel.scrollUp(true);
590 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
591 - viewport.endSeq + viewport.startSeq);
595 case KeyEvent.VK_PAGE_DOWN:
596 if (viewport.getWrapAlignment())
598 alignPanel.scrollUp(false);
602 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
603 + viewport.endSeq - viewport.startSeq);
608 if (evt.isControlDown())
610 undoMenuItem_actionPerformed();
615 if (evt.isControlDown())
617 redoMenuItem_actionPerformed();
622 if (evt.isControlDown())
629 if (evt.isControlDown())
631 trimAlignment(false);
636 if (evt.isControlDown())
638 if (evt.isShiftDown())
640 this.removeAllGapsMenuItem_actionPerformed();
644 removeGappedColumnMenuItem_actionPerformed();
649 if (evt.isControlDown())
653 invertColSel_actionPerformed();
657 invertSequenceMenuItem_actionPerformed();
663 if (evt.isControlDown())
665 if (evt.isShiftDown())
667 this.unGroup_actionPerformed();
671 this.createGroup_actionPerformed();
677 if (evt.isControlDown())
679 this.deleteGroups_actionPerformed();
684 if (evt.isControlDown())
691 alignPanel.paintAlignment(true);
695 * called by key handler and the hide all/show all menu items
700 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
702 boolean hide = false;
703 SequenceGroup sg = viewport.getSelectionGroup();
704 if (!toggleSeqs && !toggleCols)
706 // Hide everything by the current selection - this is a hack - we do the
707 // invert and then hide
708 // first check that there will be visible columns after the invert.
709 if (viewport.hasSelectedColumns()
710 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
713 // now invert the sequence set, if required - empty selection implies
714 // that no hiding is required.
717 invertSequenceMenuItem_actionPerformed();
718 sg = viewport.getSelectionGroup();
722 viewport.expandColSelection(sg, true);
723 // finally invert the column selection and get the new sequence
724 // selection and indicate it should be hidden.
725 invertColSel_actionPerformed();
732 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
735 viewport.hideAllSelectedSeqs();
737 else if (!(toggleCols && viewport.hasSelectedColumns()))
739 viewport.showAllHiddenSeqs();
745 if (viewport.hasSelectedColumns())
747 viewport.hideSelectedColumns();
750 viewport.setSelectionGroup(sg);
755 viewport.showAllHiddenColumns();
757 viewport.sendSelection();
762 public void keyReleased(KeyEvent evt)
767 public void keyTyped(KeyEvent evt)
772 public void itemStateChanged(ItemEvent evt)
774 final Object source = evt.getSource();
775 if (source == displayNonconservedMenuItem)
777 displayNonconservedMenuItem_actionPerformed();
779 else if (source == colourTextMenuItem)
781 colourTextMenuItem_actionPerformed();
783 else if (source == wrapMenuItem)
785 wrapMenuItem_actionPerformed();
787 else if (source == scaleAbove)
789 viewport.setScaleAboveWrapped(scaleAbove.getState());
791 else if (source == scaleLeft)
793 viewport.setScaleLeftWrapped(scaleLeft.getState());
795 else if (source == scaleRight)
797 viewport.setScaleRightWrapped(scaleRight.getState());
799 else if (source == seqLimits)
801 seqLimits_itemStateChanged();
803 else if (source == viewBoxesMenuItem)
805 viewport.setShowBoxes(viewBoxesMenuItem.getState());
807 else if (source == viewTextMenuItem)
809 viewport.setShowText(viewTextMenuItem.getState());
811 else if (source == renderGapsMenuItem)
813 viewport.setRenderGaps(renderGapsMenuItem.getState());
815 else if (source == annotationPanelMenuItem)
817 boolean showAnnotations = annotationPanelMenuItem.getState();
818 showAlignmentAnnotations.setEnabled(showAnnotations);
819 showSequenceAnnotations.setEnabled(showAnnotations);
820 viewport.setShowAnnotation(showAnnotations);
821 alignPanel.setAnnotationVisible(showAnnotations);
823 else if (source == sequenceFeatures)
825 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
826 alignPanel.seqPanel.seqCanvas.repaint();
828 else if (source == showAlignmentAnnotations)
830 setAnnotationsVisibility();
832 else if (source == showSequenceAnnotations)
834 setAnnotationsVisibility();
836 else if (source == sortAnnBySequence)
838 boolean newState = sortAnnBySequence.getState();
839 sortAnnByLabel.setState(false);
840 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
841 : SequenceAnnotationOrder.NONE);
842 setViewportAnnotationOrder();
844 else if (source == sortAnnByLabel)
846 boolean newState = sortAnnByLabel.getState();
847 sortAnnBySequence.setState(false);
848 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
849 : SequenceAnnotationOrder.NONE);
850 setViewportAnnotationOrder();
852 else if (source == showAutoFirst)
854 showAutoLast.setState(!showAutoFirst.getState());
855 setShowAutoCalculatedAbove(showAutoFirst.getState());
856 setViewportAnnotationOrder();
858 else if (source == showAutoLast)
860 showAutoFirst.setState(!showAutoLast.getState());
861 setShowAutoCalculatedAbove(showAutoFirst.getState());
862 setViewportAnnotationOrder();
864 else if (source == conservationMenuItem)
866 conservationMenuItem_actionPerformed();
868 else if (source == abovePIDThreshold)
870 abovePIDThreshold_actionPerformed();
872 else if (source == applyToAllGroups)
874 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
876 else if (source == autoCalculate)
878 viewport.autoCalculateConsensus = autoCalculate.getState();
880 else if (source == sortByTree)
882 viewport.sortByTree = sortByTree.getState();
884 else if (source == this.centreColumnLabelFlag)
886 centreColumnLabelFlag_stateChanged();
888 else if (source == this.followMouseOverFlag)
890 mouseOverFlag_stateChanged();
892 else if (source == showGroupConsensus)
894 showGroupConsensus_actionPerformed();
896 else if (source == showGroupConservation)
898 showGroupConservation_actionPerformed();
900 else if (source == showSequenceLogo)
902 showSequenceLogo_actionPerformed();
904 else if (source == normSequenceLogo)
906 normSequenceLogo_actionPerformed();
908 else if (source == showConsensusHistogram)
910 showConsensusHistogram_actionPerformed();
912 else if (source == applyAutoAnnotationSettings)
914 applyAutoAnnotationSettings_actionPerformed();
916 alignPanel.paintAlignment(true);
920 * Set the visibility state of sequence-related and/or alignment-related
921 * annotations depending on checkbox selections, and repaint.
925 private void setAnnotationsVisibility()
927 boolean showForAlignment = showAlignmentAnnotations.getState();
928 boolean showForSequences = showSequenceAnnotations.getState();
929 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
931 for (AlignmentAnnotation aa : alignPanel.getAlignment()
932 .getAlignmentAnnotation())
934 boolean visible = (aa.sequenceRef == null ? showForAlignment
936 aa.visible = visible;
939 alignPanel.validateAnnotationDimensions(true);
944 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
946 this.annotationSortOrder = order;
950 * Set flags on the viewport that control annotation ordering
952 private void setViewportAnnotationOrder()
954 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
956 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
959 private void setShowAutoCalculatedAbove(boolean showAbove)
961 this.showAutoCalculatedAbove = showAbove;
964 private void mouseOverFlag_stateChanged()
966 viewport.setFollowHighlight(followMouseOverFlag.getState());
967 // TODO: could kick the scrollTo mechanism to reset view for current
971 private void centreColumnLabelFlag_stateChanged()
973 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
974 this.alignPanel.annotationPanel.repaint();
978 public void actionPerformed(ActionEvent evt)
980 viewport.applet.currentAlignFrame = this;
982 Object source = evt.getSource();
984 if (source == inputText)
986 inputText_actionPerformed();
988 else if (source == loadTree)
990 loadTree_actionPerformed();
992 else if (source == loadApplication)
994 launchFullApplication();
996 else if (source == loadAnnotations)
1000 else if (source == outputAnnotations)
1002 outputAnnotations(true);
1004 else if (source == outputFeatures)
1006 outputFeatures(true, "Jalview");
1008 else if (source == closeMenuItem)
1010 closeMenuItem_actionPerformed();
1012 else if (source == copy)
1014 copy_actionPerformed();
1016 else if (source == undoMenuItem)
1018 undoMenuItem_actionPerformed();
1020 else if (source == redoMenuItem)
1022 redoMenuItem_actionPerformed();
1024 else if (source == inputText)
1026 inputText_actionPerformed();
1028 else if (source == closeMenuItem)
1030 closeMenuItem_actionPerformed();
1032 else if (source == undoMenuItem)
1034 undoMenuItem_actionPerformed();
1036 else if (source == redoMenuItem)
1038 redoMenuItem_actionPerformed();
1040 else if (source == copy)
1042 copy_actionPerformed();
1044 else if (source == pasteNew)
1046 pasteNew_actionPerformed();
1048 else if (source == pasteThis)
1050 pasteThis_actionPerformed();
1052 else if (source == cut)
1054 cut_actionPerformed();
1056 else if (source == delete)
1058 delete_actionPerformed();
1060 else if (source == grpsFromSelection)
1062 makeGrpsFromSelection_actionPerformed();
1064 else if (source == deleteGroups)
1066 deleteGroups_actionPerformed();
1068 else if (source == selectAllSequenceMenuItem)
1070 selectAllSequenceMenuItem_actionPerformed();
1072 else if (source == deselectAllSequenceMenuItem)
1074 deselectAllSequenceMenuItem_actionPerformed();
1076 else if (source == invertSequenceMenuItem)
1078 invertSequenceMenuItem_actionPerformed();
1079 // uncomment to slave sequence selections in split frame
1080 // viewport.sendSelection();
1082 else if (source == invertColSel)
1084 viewport.invertColumnSelection();
1085 alignPanel.paintAlignment(true);
1086 viewport.sendSelection();
1088 else if (source == remove2LeftMenuItem)
1090 trimAlignment(true);
1092 else if (source == remove2RightMenuItem)
1094 trimAlignment(false);
1096 else if (source == removeGappedColumnMenuItem)
1098 removeGappedColumnMenuItem_actionPerformed();
1100 else if (source == removeAllGapsMenuItem)
1102 removeAllGapsMenuItem_actionPerformed();
1104 else if (source == findMenuItem)
1106 findMenuItem_actionPerformed();
1108 else if (source == font)
1110 new FontChooser(alignPanel);
1112 else if (source == newView)
1116 else if (source == showColumns)
1118 viewport.showAllHiddenColumns();
1119 alignPanel.paintAlignment(true);
1120 viewport.sendSelection();
1122 else if (source == showSeqs)
1124 viewport.showAllHiddenSeqs();
1125 alignPanel.paintAlignment(true);
1126 // uncomment if we want to slave sequence selections in split frame
1127 // viewport.sendSelection();
1129 else if (source == hideColumns)
1131 viewport.hideSelectedColumns();
1132 alignPanel.paintAlignment(true);
1133 viewport.sendSelection();
1135 else if (source == hideSequences
1136 && viewport.getSelectionGroup() != null)
1138 viewport.hideAllSelectedSeqs();
1139 alignPanel.paintAlignment(true);
1140 // uncomment if we want to slave sequence selections in split frame
1141 // viewport.sendSelection();
1143 else if (source == hideAllButSelection)
1145 toggleHiddenRegions(false, false);
1146 alignPanel.paintAlignment(true);
1147 viewport.sendSelection();
1149 else if (source == hideAllSelection)
1151 SequenceGroup sg = viewport.getSelectionGroup();
1152 viewport.expandColSelection(sg, false);
1153 viewport.hideAllSelectedSeqs();
1154 viewport.hideSelectedColumns();
1155 alignPanel.paintAlignment(true);
1156 viewport.sendSelection();
1158 else if (source == showAllHidden)
1160 viewport.showAllHiddenColumns();
1161 viewport.showAllHiddenSeqs();
1162 alignPanel.paintAlignment(true);
1163 viewport.sendSelection();
1165 else if (source == showGroupConsensus)
1167 showGroupConsensus_actionPerformed();
1169 else if (source == showGroupConservation)
1171 showGroupConservation_actionPerformed();
1173 else if (source == showSequenceLogo)
1175 showSequenceLogo_actionPerformed();
1177 else if (source == normSequenceLogo)
1179 normSequenceLogo_actionPerformed();
1181 else if (source == showConsensusHistogram)
1183 showConsensusHistogram_actionPerformed();
1185 else if (source == applyAutoAnnotationSettings)
1187 applyAutoAnnotationSettings_actionPerformed();
1189 else if (source == featureSettings)
1191 new FeatureSettings(alignPanel);
1193 else if (source == alProperties)
1195 StringBuffer contents = new jalview.io.AlignmentProperties(
1196 viewport.getAlignment()).formatAsString();
1197 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1198 cap.setText(contents.toString());
1199 Frame frame = new Frame();
1201 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1202 "label.alignment_properties", new String[] { getTitle() }),
1205 else if (source == overviewMenuItem)
1207 overviewMenuItem_actionPerformed();
1209 else if (source == noColourmenuItem)
1213 else if (source == clustalColour)
1215 abovePIDThreshold.setState(false);
1216 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1218 else if (source == zappoColour)
1220 changeColour(new ZappoColourScheme());
1222 else if (source == taylorColour)
1224 changeColour(new TaylorColourScheme());
1226 else if (source == hydrophobicityColour)
1228 changeColour(new HydrophobicColourScheme());
1230 else if (source == helixColour)
1232 changeColour(new HelixColourScheme());
1234 else if (source == strandColour)
1236 changeColour(new StrandColourScheme());
1238 else if (source == turnColour)
1240 changeColour(new TurnColourScheme());
1242 else if (source == buriedColour)
1244 changeColour(new BuriedColourScheme());
1246 else if (source == nucleotideColour)
1248 changeColour(new NucleotideColourScheme());
1250 else if (source == purinePyrimidineColour)
1252 changeColour(new PurinePyrimidineColourScheme());
1254 // else if (source == RNAInteractionColour)
1256 // changeColour(new RNAInteractionColourScheme());
1258 else if (source == RNAHelixColour)
1260 new RNAHelicesColourChooser(viewport, alignPanel);
1262 else if (source == modifyPID)
1264 modifyPID_actionPerformed();
1266 else if (source == modifyConservation)
1268 modifyConservation_actionPerformed();
1270 else if (source == userDefinedColour)
1272 new UserDefinedColours(alignPanel, null);
1274 else if (source == PIDColour)
1276 changeColour(new PIDColourScheme());
1278 else if (source == BLOSUM62Colour)
1280 changeColour(new Blosum62ColourScheme());
1282 else if (source == tcoffeeColour)
1284 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1286 else if (source == annotationColour)
1288 new AnnotationColourChooser(viewport, alignPanel);
1290 else if (source == annotationColumnSelection)
1292 new AnnotationColumnChooser(viewport, alignPanel);
1294 else if (source == sortPairwiseMenuItem)
1296 sortPairwiseMenuItem_actionPerformed();
1298 else if (source == sortIDMenuItem)
1300 sortIDMenuItem_actionPerformed();
1302 else if (source == sortLengthMenuItem)
1304 sortLengthMenuItem_actionPerformed();
1306 else if (source == sortGroupMenuItem)
1308 sortGroupMenuItem_actionPerformed();
1310 else if (source == removeRedundancyMenuItem)
1312 removeRedundancyMenuItem_actionPerformed();
1314 else if (source == pairwiseAlignmentMenuItem)
1316 pairwiseAlignmentMenuItem_actionPerformed();
1318 else if (source == PCAMenuItem)
1320 PCAMenuItem_actionPerformed();
1322 else if (source == averageDistanceTreeMenuItem)
1324 averageDistanceTreeMenuItem_actionPerformed();
1326 else if (source == neighbourTreeMenuItem)
1328 neighbourTreeMenuItem_actionPerformed();
1330 else if (source == njTreeBlosumMenuItem)
1332 njTreeBlosumMenuItem_actionPerformed();
1334 else if (source == avDistanceTreeBlosumMenuItem)
1336 avTreeBlosumMenuItem_actionPerformed();
1338 else if (source == documentation)
1340 documentation_actionPerformed();
1342 else if (source == about)
1344 about_actionPerformed();
1349 public void inputText_actionPerformed()
1351 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352 Frame frame = new Frame();
1354 jalview.bin.JalviewLite.addFrame(frame,
1355 MessageManager.getString("label.input_cut_paste"), 500, 500);
1358 protected void outputText_actionPerformed(ActionEvent e)
1360 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361 Frame frame = new Frame();
1363 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364 "label.alignment_output_command",
1365 new Object[] { e.getActionCommand() }), 600, 500);
1367 FileFormatI fileFormat = FileFormats.getInstance().forName(
1368 e.getActionCommand());
1369 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1370 fileFormat, viewport.getAlignment(),
1371 viewport.getShowJVSuffix()));
1374 public void loadAnnotations()
1376 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377 cap.setText(MessageManager
1378 .getString("label.paste_features_annotations_Tcoffee_here"));
1379 cap.setAnnotationImport();
1380 Frame frame = new Frame();
1382 jalview.bin.JalviewLite.addFrame(frame,
1383 MessageManager.getString("action.paste_annotations"), 400, 300);
1387 public String outputAnnotations(boolean displayTextbox)
1389 String annotation = new AnnotationFile()
1390 .printAnnotationsForView(viewport);
1394 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1395 Frame frame = new Frame();
1397 jalview.bin.JalviewLite.addFrame(frame,
1398 MessageManager.getString("label.annotations"), 600, 500);
1399 cap.setText(annotation);
1405 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1407 if (alignPanel.getFeatureRenderer() != null
1408 && viewport.getFeaturesDisplayed() != null)
1410 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1416 public String outputFeatures(boolean displayTextbox, String format)
1419 FeaturesFile formatter = new FeaturesFile();
1420 if (format.equalsIgnoreCase("Jalview"))
1422 features = formatter.printJalviewFormat(viewport.getAlignment()
1423 .getSequencesArray(), getDisplayedFeatureCols());
1427 features = formatter.printGffFormat(viewport.getAlignment()
1428 .getSequencesArray(), getDisplayedFeatureCols());
1433 boolean frimport = false;
1434 if (features == null || features.equals("No Features Visible"))
1436 features = "# No features visible - paste some and import them here.";
1440 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1443 cap.setAnnotationImport();
1445 Frame frame = new Frame();
1447 jalview.bin.JalviewLite.addFrame(frame,
1448 MessageManager.getString("label.features"), 600, 500);
1449 cap.setText(features);
1453 if (features == null)
1462 void launchFullApplication()
1464 StringBuffer url = new StringBuffer(jalviewServletURL);
1466 // allow servlet parameters to be passed in applet parameter
1467 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1469 url.append(firstSep);
1472 + appendProtocol(viewport.applet.getParameter("file")));
1474 if (viewport.applet.getParameter("features") != null)
1476 url.append("&features=");
1477 url.append(appendProtocol(viewport.applet.getParameter("features")));
1480 if (viewport.applet.getParameter("annotations") != null)
1482 url.append("&annotations=");
1483 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1486 if (viewport.applet.getParameter("jnetfile") != null
1487 || viewport.applet.getParameter("jpredfile") != null)
1489 url.append("&annotations=");
1490 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1491 .getParameter("jnetfile") : viewport.applet
1492 .getParameter("jpredfile")));
1495 if (viewport.applet.getParameter("defaultColour") != null)
1497 url.append("&colour="
1498 + removeWhiteSpace(viewport.applet
1499 .getParameter("defaultColour")));
1502 if (viewport.applet.getParameter("userDefinedColour") != null)
1504 url.append("&colour="
1505 + removeWhiteSpace(viewport.applet
1506 .getParameter("userDefinedColour")));
1508 if (viewport.applet.getParameter("tree") != null)
1511 + appendProtocol(viewport.applet.getParameter("tree")));
1513 if (viewport.applet.getParameter("treeFile") != null)
1516 + appendProtocol(viewport.applet.getParameter("treeFile")));
1519 showURL(url.toString(), "FULL_APP");
1522 String removeWhiteSpace(String colour)
1524 StringBuffer sb = new StringBuffer();
1525 for (int i = 0; i < colour.length(); i++)
1527 if (Character.isWhitespace(colour.charAt(i)))
1533 sb.append(colour.charAt(i));
1537 return sb.toString();
1540 String appendProtocol(String url)
1545 url = URLEncoder.encode(url);
1548 * When we finally deprecate 1.1 compatibility, we can start to use
1549 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1550 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1551 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1552 * ex.printStackTrace(); }
1554 catch (java.net.MalformedURLException ex)
1556 url = viewport.applet.getCodeBase() + url;
1561 public void closeMenuItem_actionPerformed()
1563 PaintRefresher.RemoveComponent(alignPanel);
1564 if (alignPanel.seqPanel != null
1565 && alignPanel.seqPanel.seqCanvas != null)
1567 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1569 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1571 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1574 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1589 void updateEditMenuBar()
1592 if (viewport.getHistoryList().size() > 0)
1594 undoMenuItem.setEnabled(true);
1595 CommandI command = viewport.getHistoryList().peek();
1596 undoMenuItem.setLabel(MessageManager.formatMessage(
1597 "label.undo_command",
1598 new Object[] { command.getDescription() }));
1602 undoMenuItem.setEnabled(false);
1603 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1606 if (viewport.getRedoList().size() > 0)
1608 redoMenuItem.setEnabled(true);
1610 CommandI command = viewport.getRedoList().peek();
1611 redoMenuItem.setLabel(MessageManager.formatMessage(
1612 "label.redo_command",
1613 new Object[] { command.getDescription() }));
1617 redoMenuItem.setEnabled(false);
1618 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1626 public void addHistoryItem(CommandI command)
1628 if (command.getSize() > 0)
1630 viewport.addToHistoryList(command);
1631 viewport.clearRedoList();
1632 updateEditMenuBar();
1633 viewport.updateHiddenColumns();
1638 * TODO: JAL-1104 DOCUMENT ME!
1643 protected void undoMenuItem_actionPerformed()
1645 if (viewport.getHistoryList().isEmpty())
1650 CommandI command = viewport.getHistoryList().pop();
1651 viewport.addToRedoList(command);
1652 command.undoCommand(null);
1654 AlignmentViewport originalSource = getOriginatingSource(command);
1656 if (originalSource != viewport)
1659 .println("Warning: Viewport object mismatch whilst undoing");
1661 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1662 // viewport.getColumnSelection().getHiddenColumns()
1664 updateEditMenuBar();
1665 originalSource.firePropertyChange("alignment", null, originalSource
1666 .getAlignment().getSequences());
1670 * TODO: JAL-1104 DOCUMENT ME!
1675 protected void redoMenuItem_actionPerformed()
1677 if (viewport.getRedoList().isEmpty())
1682 CommandI command = viewport.getRedoList().pop();
1683 viewport.addToHistoryList(command);
1684 command.doCommand(null);
1686 AlignmentViewport originalSource = getOriginatingSource(command);
1688 if (originalSource != viewport)
1691 .println("Warning: Viewport object mismatch whilst re-doing");
1693 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1694 // viewport.getColumnSelection().getHiddenColumns()
1697 updateEditMenuBar();
1698 originalSource.firePropertyChange("alignment", null, originalSource
1699 .getAlignment().getSequences());
1702 AlignmentViewport getOriginatingSource(CommandI command)
1704 AlignmentViewport originalSource = null;
1705 // For sequence removal and addition, we need to fire
1706 // the property change event FROM the viewport where the
1707 // original alignment was altered
1708 AlignmentI al = null;
1709 if (command instanceof EditCommand)
1711 EditCommand editCommand = (EditCommand) command;
1712 al = editCommand.getAlignment();
1713 Vector comps = (Vector) PaintRefresher.components.get(viewport
1714 .getSequenceSetId());
1715 for (int i = 0; i < comps.size(); i++)
1717 if (comps.elementAt(i) instanceof AlignmentPanel)
1719 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1721 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1728 if (originalSource == null)
1730 // The original view is closed, we must validate
1731 // the current view against the closed view first
1734 PaintRefresher.validateSequences(al, viewport.getAlignment());
1737 originalSource = viewport;
1740 return originalSource;
1744 * Move the currently selected sequences up or down one position in the
1749 public void moveSelectedSequences(boolean up)
1751 SequenceGroup sg = viewport.getSelectionGroup();
1756 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1757 up ? null : viewport.getHiddenRepSequences(), up);
1758 alignPanel.paintAlignment(true);
1761 * Also move cDNA/protein complement sequences
1763 AlignViewportI complement = viewport.getCodingComplement();
1764 if (complement != null)
1766 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1767 viewport, complement);
1768 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1769 up ? null : complement.getHiddenRepSequences(), up);
1770 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1774 synchronized void slideSequences(boolean right, int size)
1776 List<SequenceI> sg = new Vector<SequenceI>();
1777 if (viewport.cursorMode)
1779 sg.add(viewport.getAlignment().getSequenceAt(
1780 alignPanel.seqPanel.seqCanvas.cursorY));
1782 else if (viewport.getSelectionGroup() != null
1783 && viewport.getSelectionGroup().getSize() != viewport
1784 .getAlignment().getHeight())
1786 sg = viewport.getSelectionGroup().getSequences(
1787 viewport.getHiddenRepSequences());
1795 Vector<SequenceI> invertGroup = new Vector();
1797 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1799 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1801 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1805 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1807 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1809 for (int i = 0; i < invertGroup.size(); i++)
1811 seqs2[i] = invertGroup.elementAt(i);
1814 SlideSequencesCommand ssc;
1817 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1818 size, viewport.getGapCharacter());
1822 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1823 size, viewport.getGapCharacter());
1826 int groupAdjustment = 0;
1827 if (ssc.getGapsInsertedBegin() && right)
1829 if (viewport.cursorMode)
1831 alignPanel.seqPanel.moveCursor(size, 0);
1835 groupAdjustment = size;
1838 else if (!ssc.getGapsInsertedBegin() && !right)
1840 if (viewport.cursorMode)
1842 alignPanel.seqPanel.moveCursor(-size, 0);
1846 groupAdjustment = -size;
1850 if (groupAdjustment != 0)
1852 viewport.getSelectionGroup().setStartRes(
1853 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1854 viewport.getSelectionGroup().setEndRes(
1855 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1858 boolean appendHistoryItem = false;
1859 Deque<CommandI> historyList = viewport.getHistoryList();
1860 if (historyList != null && historyList.size() > 0
1861 && historyList.peek() instanceof SlideSequencesCommand)
1863 appendHistoryItem = ssc
1864 .appendSlideCommand((SlideSequencesCommand) historyList
1868 if (!appendHistoryItem)
1870 addHistoryItem(ssc);
1876 static StringBuffer copiedSequences;
1878 static Vector copiedHiddenColumns;
1880 protected void copy_actionPerformed()
1882 if (viewport.getSelectionGroup() == null)
1887 SequenceGroup sg = viewport.getSelectionGroup();
1888 copiedSequences = new StringBuffer();
1889 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1890 for (int i = 0; i < sg.getSize(); i++)
1892 SequenceI seq = sg.getSequenceAt(i);
1893 int index = viewport.getAlignment().findIndex(seq);
1894 orderedSeqs.put(index, seq);
1897 int index = 0, startRes, endRes;
1900 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1902 copiedHiddenColumns = new Vector();
1903 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1904 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1906 copiedHiddenColumns.addElement(new int[] {
1907 region[0] - hiddenOffset, region[1] - hiddenOffset });
1912 copiedHiddenColumns = null;
1915 for (int i = 0; i < sg.getSize(); i++)
1917 SequenceI seq = null;
1921 if (orderedSeqs.containsKey(index))
1923 seq = orderedSeqs.get(index);
1934 // Returns residue following index if gap
1935 startRes = seq.findPosition(sg.getStartRes());
1938 // Need to find the residue preceeding index if gap
1941 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1943 ch = seq.getCharAt(j);
1944 if (!jalview.util.Comparison.isGap((ch)))
1952 endRes += seq.getStart() - 1;
1955 copiedSequences.append(seq.getName()
1961 + seq.getSequenceAsString(sg.getStartRes(),
1962 sg.getEndRes() + 1) + "\n");
1967 protected void pasteNew_actionPerformed()
1972 protected void pasteThis_actionPerformed()
1977 void paste(boolean newAlignment)
1982 if (copiedSequences == null)
1987 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1988 Vector seqs = new Vector();
1989 while (st.hasMoreElements())
1991 String name = st.nextToken();
1992 int start = Integer.parseInt(st.nextToken());
1993 int end = Integer.parseInt(st.nextToken());
1994 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1996 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1997 for (int i = 0; i < seqs.size(); i++)
1999 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2004 String newtitle = MessageManager
2005 .getString("label.copied_sequences");
2006 if (getTitle().startsWith(
2007 MessageManager.getString("label.copied_sequences")))
2009 newtitle = getTitle();
2013 newtitle = newtitle.concat(MessageManager.formatMessage(
2014 "label.from_msname", new String[] { getTitle() }));
2016 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2017 viewport.applet, newtitle, false);
2018 if (copiedHiddenColumns != null)
2020 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2022 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2023 af.viewport.hideColumns(region[0], region[1]);
2027 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2032 addSequences(newSeqs);
2035 } catch (Exception ex)
2037 } // could be anything being pasted in here
2041 void addSequences(SequenceI[] seqs)
2043 for (int i = 0; i < seqs.length; i++)
2045 viewport.getAlignment().addSequence(seqs[i]);
2049 addHistoryItem(new EditCommand(
2050 MessageManager.getString("label.add_sequences"), Action.PASTE,
2051 seqs, 0, viewport.getAlignment().getWidth(),
2052 viewport.getAlignment()));
2054 viewport.setEndSeq(viewport.getAlignment().getHeight());
2055 viewport.getAlignment().getWidth();
2056 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2061 protected void cut_actionPerformed()
2063 copy_actionPerformed();
2064 delete_actionPerformed();
2067 protected void delete_actionPerformed()
2070 SequenceGroup sg = viewport.getSelectionGroup();
2076 Vector seqs = new Vector();
2078 for (int i = 0; i < sg.getSize(); i++)
2080 seq = sg.getSequenceAt(i);
2081 seqs.addElement(seq);
2085 * If the cut affects all sequences, warn, remove highlighted columns
2087 if (sg.getSize() == viewport.getAlignment().getHeight())
2089 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2090 .getAlignment().getWidth()) ? true : false;
2091 if (isEntireAlignWidth)
2093 String title = MessageManager.getString("label.delete_all");
2094 Panel infoPanel = new Panel();
2095 infoPanel.setLayout(new FlowLayout());
2097 .add(new Label(MessageManager.getString("warn.delete_all")));
2099 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2100 dialog.setMainPanel(infoPanel);
2101 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2102 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2103 dialog.setVisible(true);
2110 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2111 sg.getEndRes() + 1);
2114 SequenceI[] cut = new SequenceI[seqs.size()];
2115 for (int i = 0; i < seqs.size(); i++)
2117 cut[i] = (SequenceI) seqs.elementAt(i);
2121 * //ADD HISTORY ITEM
2123 addHistoryItem(new EditCommand(
2124 MessageManager.getString("label.cut_sequences"), Action.CUT,
2125 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2126 viewport.getAlignment()));
2128 viewport.setSelectionGroup(null);
2129 viewport.getAlignment().deleteGroup(sg);
2131 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2134 if (viewport.getAlignment().getHeight() < 1)
2136 this.setVisible(false);
2138 viewport.sendSelection();
2142 * group consensus toggled
2145 protected void showGroupConsensus_actionPerformed()
2147 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2148 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2153 * group conservation toggled.
2155 protected void showGroupConservation_actionPerformed()
2157 viewport.setShowGroupConservation(showGroupConservation.getState());
2158 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2165 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2166 * .event.ActionEvent)
2168 protected void showConsensusHistogram_actionPerformed()
2170 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2171 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2178 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2179 * .event.ActionEvent)
2181 protected void showSequenceLogo_actionPerformed()
2183 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2184 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187 protected void normSequenceLogo_actionPerformed()
2189 showSequenceLogo.setState(true);
2190 viewport.setShowSequenceLogo(true);
2191 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2192 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195 protected void applyAutoAnnotationSettings_actionPerformed()
2197 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200 protected void makeGrpsFromSelection_actionPerformed()
2202 if (avc.makeGroupsFromSelection())
2204 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2205 alignPanel.updateAnnotation();
2206 alignPanel.paintAlignment(true);
2210 protected void createGroup_actionPerformed()
2215 protected void unGroup_actionPerformed()
2219 alignPanel.alignmentChanged();
2223 protected void deleteGroups_actionPerformed()
2225 if (avc.deleteGroups())
2227 alignPanel.alignmentChanged();
2231 public void selectAllSequenceMenuItem_actionPerformed()
2233 SequenceGroup sg = new SequenceGroup();
2234 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2236 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2238 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2239 viewport.setSelectionGroup(sg);
2240 // JAL-2034 - should delegate to
2241 // alignPanel to decide if overview needs
2243 alignPanel.paintAlignment(false);
2244 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2245 viewport.sendSelection();
2248 public void deselectAllSequenceMenuItem_actionPerformed()
2250 if (viewport.cursorMode)
2252 alignPanel.seqPanel.keyboardNo1 = null;
2253 alignPanel.seqPanel.keyboardNo2 = null;
2255 viewport.setSelectionGroup(null);
2256 viewport.getColumnSelection().clear();
2257 viewport.setSelectionGroup(null);
2258 alignPanel.idPanel.idCanvas.searchResults = null;
2259 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2260 // JAL-2034 - should delegate to
2261 // alignPanel to decide if overview needs
2263 alignPanel.paintAlignment(false);
2264 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2265 viewport.sendSelection();
2268 public void invertSequenceMenuItem_actionPerformed()
2270 SequenceGroup sg = viewport.getSelectionGroup();
2271 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2273 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2276 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277 viewport.sendSelection();
2280 public void invertColSel_actionPerformed()
2282 viewport.invertColumnSelection();
2283 alignPanel.paintAlignment(true);
2284 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2285 viewport.sendSelection();
2288 void trimAlignment(boolean trimLeft)
2290 ColumnSelection colSel = viewport.getColumnSelection();
2293 if (!colSel.isEmpty())
2297 column = colSel.getMin();
2301 column = colSel.getMax();
2305 if (viewport.getSelectionGroup() != null)
2307 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2308 viewport.getHiddenRepSequences());
2312 seqs = viewport.getAlignment().getSequencesArray();
2315 TrimRegionCommand trimRegion;
2318 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2319 column, viewport.getAlignment());
2320 viewport.setStartRes(0);
2324 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2325 column, viewport.getAlignment());
2328 statusBar.setText(MessageManager.formatMessage(
2329 "label.removed_columns",
2330 new String[] { Integer.valueOf(trimRegion.getSize())
2332 addHistoryItem(trimRegion);
2334 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2336 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2337 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2339 viewport.getAlignment().deleteGroup(sg);
2343 viewport.firePropertyChange("alignment", null, viewport
2344 .getAlignment().getSequences());
2348 public void removeGappedColumnMenuItem_actionPerformed()
2350 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2353 if (viewport.getSelectionGroup() != null)
2355 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2356 viewport.getHiddenRepSequences());
2357 start = viewport.getSelectionGroup().getStartRes();
2358 end = viewport.getSelectionGroup().getEndRes();
2362 seqs = viewport.getAlignment().getSequencesArray();
2365 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2366 "Remove Gapped Columns", seqs, start, end,
2367 viewport.getAlignment());
2369 addHistoryItem(removeGapCols);
2371 statusBar.setText(MessageManager.formatMessage(
2372 "label.removed_empty_columns",
2373 new String[] { Integer.valueOf(removeGapCols.getSize())
2376 // This is to maintain viewport position on first residue
2377 // of first sequence
2378 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2379 int startRes = seq.findPosition(viewport.startRes);
2380 // ShiftList shifts;
2381 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2382 // edit.alColumnChanges=shifts.getInverse();
2383 // if (viewport.hasHiddenColumns)
2384 // viewport.getColumnSelection().compensateForEdits(shifts);
2385 viewport.setStartRes(seq.findIndex(startRes) - 1);
2386 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2391 public void removeAllGapsMenuItem_actionPerformed()
2393 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2396 if (viewport.getSelectionGroup() != null)
2398 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2399 viewport.getHiddenRepSequences());
2400 start = viewport.getSelectionGroup().getStartRes();
2401 end = viewport.getSelectionGroup().getEndRes();
2405 seqs = viewport.getAlignment().getSequencesArray();
2408 // This is to maintain viewport position on first residue
2409 // of first sequence
2410 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2411 int startRes = seq.findPosition(viewport.startRes);
2413 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2414 viewport.getAlignment()));
2416 viewport.setStartRes(seq.findIndex(startRes) - 1);
2418 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2423 public void findMenuItem_actionPerformed()
2425 new Finder(alignPanel);
2429 * create a new view derived from the current view
2432 * @return frame for the new view
2434 public AlignFrame newView(String viewtitle)
2437 if (viewport.hasHiddenRows())
2439 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2440 .getFullAlignment().getSequencesArray());
2444 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2447 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2449 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2451 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2453 newal.addAnnotation(viewport.getAlignment()
2454 .getAlignmentAnnotation()[i]);
2459 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2461 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2462 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2463 PaintRefresher.Register(newaf.alignPanel,
2464 newaf.alignPanel.av.getSequenceSetId());
2466 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2467 newaf.alignPanel.av.getSequenceSetId());
2468 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2469 newaf.alignPanel.av.getSequenceSetId());
2471 Vector comps = (Vector) PaintRefresher.components.get(viewport
2472 .getSequenceSetId());
2474 for (int i = 0; i < comps.size(); i++)
2476 if (comps.elementAt(i) instanceof AlignmentPanel)
2482 String title = new String(this.getTitle());
2483 if (viewtitle != null)
2485 title = viewtitle + " ( " + title + ")";
2489 if (title.indexOf("(View") > -1)
2491 title = title.substring(0, title.indexOf("(View"));
2493 title += "(View " + viewSize + ")";
2496 newaf.setTitle(title.toString());
2498 newaf.viewport.setHistoryList(viewport.getHistoryList());
2499 newaf.viewport.setRedoList(viewport.getRedoList());
2505 * @return list of feature groups on the view
2507 public String[] getFeatureGroups()
2509 FeatureRenderer fr = null;
2510 if (alignPanel != null
2511 && (fr = alignPanel.getFeatureRenderer()) != null)
2513 List<String> gps = fr.getFeatureGroups();
2514 String[] _gps = gps.toArray(new String[gps.size()]);
2521 * get sequence feature groups that are hidden or shown
2527 public String[] getFeatureGroupsOfState(boolean visible)
2529 FeatureRenderer fr = null;
2530 if (alignPanel != null
2531 && (fr = alignPanel.getFeatureRenderer()) != null)
2533 List<String> gps = fr.getGroups(visible);
2534 String[] _gps = gps.toArray(new String[gps.size()]);
2541 * Change the display state for the given feature groups
2544 * list of group strings
2546 * visible or invisible
2548 public void setFeatureGroupState(String[] groups, boolean state)
2550 FeatureRenderer fr = null;
2551 this.sequenceFeatures.setState(true);
2552 viewport.setShowSequenceFeatures(true);
2553 if (alignPanel != null
2554 && (fr = alignPanel.getFeatureRenderer()) != null)
2557 fr.setGroupVisibility(Arrays.asList(groups), state);
2558 alignPanel.seqPanel.seqCanvas.repaint();
2559 if (alignPanel.overviewPanel != null)
2561 alignPanel.overviewPanel.updateOverviewImage();
2566 public void seqLimits_itemStateChanged()
2568 viewport.setShowJVSuffix(seqLimits.getState());
2569 alignPanel.fontChanged();
2570 alignPanel.paintAlignment(true);
2573 protected void colourTextMenuItem_actionPerformed()
2575 viewport.setColourText(colourTextMenuItem.getState());
2576 alignPanel.paintAlignment(true);
2579 protected void displayNonconservedMenuItem_actionPerformed()
2581 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2582 alignPanel.paintAlignment(true);
2585 protected void wrapMenuItem_actionPerformed()
2587 viewport.setWrapAlignment(wrapMenuItem.getState());
2588 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2589 scaleAbove.setEnabled(wrapMenuItem.getState());
2590 scaleLeft.setEnabled(wrapMenuItem.getState());
2591 scaleRight.setEnabled(wrapMenuItem.getState());
2592 alignPanel.paintAlignment(true);
2595 public void overviewMenuItem_actionPerformed()
2597 if (alignPanel.overviewPanel != null)
2602 Frame frame = new Frame();
2603 OverviewPanel overview = new OverviewPanel(alignPanel);
2604 frame.add(overview);
2605 // +50 must allow for applet frame window
2606 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2607 "label.overview_params", new String[] { this.getTitle() }),
2608 overview.getPreferredSize().width,
2609 overview.getPreferredSize().height + 50);
2612 final AlignmentPanel ap = alignPanel;
2613 frame.addWindowListener(new WindowAdapter()
2616 public void windowClosing(WindowEvent e)
2620 ap.setOverviewPanel(null);
2625 alignPanel.setOverviewPanel(overview);
2630 public void changeColour(ColourSchemeI cs)
2635 if (viewport.getAbovePIDThreshold())
2637 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2641 if (viewport.getConservationSelected())
2643 cs.setConservationApplied(true);
2644 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2649 cs.setConservationApplied(false);
2652 viewport.setGlobalColourScheme(cs);
2654 alignPanel.paintAlignment(true);
2657 protected void modifyPID_actionPerformed()
2659 if (viewport.getAbovePIDThreshold()
2660 && viewport.getGlobalColourScheme() != null)
2662 SliderPanel.setPIDSliderSource(alignPanel,
2663 viewport.getGlobalColourScheme(), "Background");
2664 SliderPanel.showPIDSlider();
2668 protected void modifyConservation_actionPerformed()
2670 if (viewport.getConservationSelected()
2671 && viewport.getGlobalColourScheme() != null)
2673 SliderPanel.setConservationSlider(alignPanel,
2674 viewport.getGlobalColourScheme(), "Background");
2675 SliderPanel.showConservationSlider();
2679 protected void conservationMenuItem_actionPerformed()
2681 boolean selected = conservationMenuItem.getState();
2682 modifyConservation.setEnabled(selected);
2683 viewport.setConservationSelected(selected);
2685 // viewport.setAbovePIDThreshold(false);
2686 // abovePIDThreshold.setState(false);
2688 changeColour(viewport.getGlobalColourScheme());
2692 modifyConservation_actionPerformed();
2696 SliderPanel.hideConservationSlider();
2700 public void abovePIDThreshold_actionPerformed()
2702 boolean selected = abovePIDThreshold.getState();
2703 modifyPID.setEnabled(selected);
2704 viewport.setAbovePIDThreshold(selected);
2705 // conservationMenuItem.setState(false);
2706 // viewport.setConservationSelected(false);
2708 changeColour(viewport.getGlobalColourScheme());
2712 modifyPID_actionPerformed();
2716 SliderPanel.hidePIDSlider();
2720 public void sortPairwiseMenuItem_actionPerformed()
2722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2724 .getAlignment().getSequenceAt(0), null);
2726 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2727 viewport.getAlignment()));
2728 alignPanel.paintAlignment(true);
2731 public void sortIDMenuItem_actionPerformed()
2733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734 AlignmentSorter.sortByID(viewport.getAlignment());
2735 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2736 viewport.getAlignment()));
2737 alignPanel.paintAlignment(true);
2740 public void sortLengthMenuItem_actionPerformed()
2742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2743 AlignmentSorter.sortByLength(viewport.getAlignment());
2744 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2745 viewport.getAlignment()));
2746 alignPanel.paintAlignment(true);
2749 public void sortGroupMenuItem_actionPerformed()
2751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752 AlignmentSorter.sortByGroup(viewport.getAlignment());
2753 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2754 viewport.getAlignment()));
2755 alignPanel.paintAlignment(true);
2759 public void removeRedundancyMenuItem_actionPerformed()
2761 new RedundancyPanel(alignPanel);
2764 public void pairwiseAlignmentMenuItem_actionPerformed()
2766 if (viewport.getSelectionGroup() != null
2767 && viewport.getSelectionGroup().getSize() > 1)
2769 Frame frame = new Frame();
2770 frame.add(new PairwiseAlignPanel(alignPanel));
2771 jalview.bin.JalviewLite.addFrame(frame,
2772 MessageManager.getString("action.pairwise_alignment"), 600,
2777 public void PCAMenuItem_actionPerformed()
2779 // are the sequences aligned?
2780 if (!viewport.getAlignment().isAligned(false))
2783 int Width = viewport.getAlignment().getWidth();
2785 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2787 current = viewport.getAlignment().getSequenceAt(i);
2789 if (current.getLength() < Width)
2791 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2794 alignPanel.paintAlignment(true);
2797 if ((viewport.getSelectionGroup() != null
2798 && viewport.getSelectionGroup().getSize() < 4 && viewport
2799 .getSelectionGroup().getSize() > 0)
2800 || viewport.getAlignment().getHeight() < 4)
2807 new PCAPanel(viewport);
2808 } catch (java.lang.OutOfMemoryError ex)
2814 public void averageDistanceTreeMenuItem_actionPerformed()
2816 NewTreePanel("AV", "PID", "Average distance tree using PID");
2819 public void neighbourTreeMenuItem_actionPerformed()
2821 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2824 protected void njTreeBlosumMenuItem_actionPerformed()
2826 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2829 protected void avTreeBlosumMenuItem_actionPerformed()
2831 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2834 void NewTreePanel(String type, String pwType, String title)
2836 // are the sequences aligned?
2837 if (!viewport.getAlignment().isAligned(false))
2840 int Width = viewport.getAlignment().getWidth();
2842 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2844 current = viewport.getAlignment().getSequenceAt(i);
2846 if (current.getLength() < Width)
2848 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2851 alignPanel.paintAlignment(true);
2855 if ((viewport.getSelectionGroup() != null && viewport
2856 .getSelectionGroup().getSize() > 1)
2857 || (viewport.getAlignment().getHeight() > 1))
2859 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2861 addTreeMenuItem(tp, title);
2863 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2867 void loadTree_actionPerformed()
2869 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2870 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2871 cap.setTreeImport();
2872 Frame frame = new Frame();
2874 jalview.bin.JalviewLite.addFrame(frame,
2875 MessageManager.getString("label.paste_newick_file"), 400, 300);
2878 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2880 TreePanel tp = new TreePanel(alignPanel, treeFile,
2881 MessageManager.getString("label.load_tree_from_file"), tree);
2882 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2883 addTreeMenuItem(tp, treeFile);
2887 * sort the alignment using the given treePanel
2890 * tree used to sort view
2892 * string used for undo event name
2894 public void sortByTree(TreePanel treePanel, String title)
2896 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2898 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2899 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2900 // HistoryItem.SORT));
2901 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2902 "label.order_by_params", new String[] { title }), oldOrder,
2903 viewport.getAlignment()));
2904 alignPanel.paintAlignment(true);
2908 * Do any automatic reordering of the alignment and add the necessary bits to
2909 * the menu structure for the new tree
2914 protected void addTreeMenuItem(final TreePanel treePanel,
2917 final MenuItem item = new MenuItem(title);
2918 sortByTreeMenu.add(item);
2919 item.addActionListener(new java.awt.event.ActionListener()
2922 public void actionPerformed(ActionEvent evt)
2924 sortByTree(treePanel, title); // treePanel.getTitle());
2928 treePanel.addWindowListener(new WindowAdapter()
2931 public void windowOpened(WindowEvent e)
2933 if (viewport.sortByTree)
2935 sortByTree(treePanel, title);
2937 super.windowOpened(e);
2941 public void windowClosing(WindowEvent e)
2943 sortByTreeMenu.remove(item);
2948 public boolean sortBy(AlignmentOrder alorder, String undoname)
2950 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2951 if (viewport.applet.debug)
2953 System.err.println("Sorting " + alorder.getOrder().size()
2954 + " in alignment '" + getTitle() + "'");
2956 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2957 if (undoname != null)
2959 addHistoryItem(new OrderCommand(undoname, oldOrder,
2960 viewport.getAlignment()));
2962 alignPanel.paintAlignment(true);
2966 protected void documentation_actionPerformed()
2968 alignPanel.av.applet.openJalviewHelpUrl();
2971 protected void about_actionPerformed()
2974 class AboutPanel extends Canvas
2980 public AboutPanel(String version, String builddate)
2982 this.version = version;
2983 this.builddate = builddate;
2987 public void paint(Graphics g)
2989 g.setColor(Color.white);
2990 g.fillRect(0, 0, getSize().width, getSize().height);
2991 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2992 FontMetrics fm = g.getFontMetrics();
2993 int fh = fm.getHeight();
2995 g.setColor(Color.black);
2996 // TODO: update this text for each release or centrally store it for
2997 // lite and application
2998 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2999 g.drawString(MessageManager.formatMessage(
3000 "label.jalviewLite_release", new String[] { version }), x,
3002 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3003 g.drawString(MessageManager.formatMessage(
3004 "label.jaview_build_date", new String[] { builddate }), x,
3006 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3007 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3009 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3010 x + 50, y += fh + 8);
3012 MessageManager.getString("label.jalview_dev_managers"), x,
3014 g.drawString(MessageManager
3015 .getString("label.jalview_distribution_lists"), x, y += fh);
3016 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3019 MessageManager.getString("label.jalview_cite_1_authors"),
3022 MessageManager.getString("label.jalview_cite_1_title"), x,
3024 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3029 Frame frame = new Frame();
3030 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3032 jalview.bin.JalviewLite.addFrame(frame,
3033 MessageManager.getString("label.jalview"), 580, 220);
3037 public void showURL(String url, String target)
3039 if (viewport.applet == null)
3041 System.out.println("Not running as applet - no browser available.");
3045 viewport.applet.showURL(url, target);
3049 // ////////////////////////////////////////////////////////////////////////////////
3050 // JBuilder Graphics here
3052 MenuBar alignFrameMenuBar = new MenuBar();
3054 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3056 MenuItem loadApplication = new MenuItem(
3057 MessageManager.getString("label.view_full_application"));
3059 MenuItem loadTree = new MenuItem(
3060 MessageManager.getString("label.load_associated_tree"));
3062 MenuItem loadAnnotations = new MenuItem(
3063 MessageManager.getString("label.load_features_annotations"));
3065 MenuItem outputFeatures = new MenuItem(
3066 MessageManager.getString("label.export_features"));
3068 MenuItem outputAnnotations = new MenuItem(
3069 MessageManager.getString("label.export_annotations"));
3071 MenuItem closeMenuItem = new MenuItem(
3072 MessageManager.getString("action.close"));
3074 MenuItem selectAllSequenceMenuItem = new MenuItem(
3075 MessageManager.getString("action.select_all"));
3077 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3078 MessageManager.getString("action.deselect_all"));
3080 MenuItem invertSequenceMenuItem = new MenuItem(
3081 MessageManager.getString("action.invert_selection"));
3083 MenuItem remove2LeftMenuItem = new MenuItem();
3085 MenuItem remove2RightMenuItem = new MenuItem();
3087 MenuItem removeGappedColumnMenuItem = new MenuItem();
3089 MenuItem removeAllGapsMenuItem = new MenuItem();
3091 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3093 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3095 MenuItem sortPairwiseMenuItem = new MenuItem();
3097 MenuItem sortIDMenuItem = new MenuItem();
3099 MenuItem sortLengthMenuItem = new MenuItem();
3101 MenuItem sortGroupMenuItem = new MenuItem();
3103 MenuItem removeRedundancyMenuItem = new MenuItem();
3105 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3107 MenuItem PCAMenuItem = new MenuItem();
3109 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3111 MenuItem neighbourTreeMenuItem = new MenuItem();
3113 BorderLayout borderLayout1 = new BorderLayout();
3115 public Label statusBar = new Label();
3117 MenuItem clustalColour = new MenuItem();
3119 MenuItem zappoColour = new MenuItem();
3121 MenuItem taylorColour = new MenuItem();
3123 MenuItem hydrophobicityColour = new MenuItem();
3125 MenuItem helixColour = new MenuItem();
3127 MenuItem strandColour = new MenuItem();
3129 MenuItem turnColour = new MenuItem();
3131 MenuItem buriedColour = new MenuItem();
3133 MenuItem purinePyrimidineColour = new MenuItem();
3135 // MenuItem RNAInteractionColour = new MenuItem();
3137 MenuItem RNAHelixColour = new MenuItem();
3139 MenuItem userDefinedColour = new MenuItem();
3141 MenuItem PIDColour = new MenuItem();
3143 MenuItem BLOSUM62Colour = new MenuItem();
3145 MenuItem tcoffeeColour = new MenuItem();
3147 MenuItem njTreeBlosumMenuItem = new MenuItem();
3149 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3151 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3153 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3155 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3157 MenuItem alProperties = new MenuItem(
3158 MessageManager.getString("label.alignment_props"));
3160 MenuItem overviewMenuItem = new MenuItem();
3162 MenuItem undoMenuItem = new MenuItem();
3164 MenuItem redoMenuItem = new MenuItem();
3166 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3168 MenuItem noColourmenuItem = new MenuItem();
3170 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3172 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3174 MenuItem findMenuItem = new MenuItem();
3176 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3178 MenuItem nucleotideColour = new MenuItem();
3180 MenuItem deleteGroups = new MenuItem();
3182 MenuItem grpsFromSelection = new MenuItem();
3184 MenuItem createGroup = new MenuItem();
3186 MenuItem unGroup = new MenuItem();
3188 MenuItem delete = new MenuItem();
3190 MenuItem copy = new MenuItem();
3192 MenuItem cut = new MenuItem();
3194 Menu pasteMenu = new Menu();
3196 MenuItem pasteNew = new MenuItem();
3198 MenuItem pasteThis = new MenuItem();
3200 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3202 MenuItem font = new MenuItem();
3204 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3206 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3208 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3210 MenuItem modifyPID = new MenuItem();
3212 MenuItem modifyConservation = new MenuItem();
3214 CheckboxMenuItem autoCalculate = null;
3216 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3217 "Sort Alignment With New Tree", true);
3219 Menu sortByTreeMenu = new Menu();
3221 MenuItem inputText = new MenuItem();
3223 MenuItem documentation = new MenuItem();
3225 MenuItem about = new MenuItem();
3227 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3229 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3231 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3233 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3235 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3237 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3239 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3241 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3243 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3246 * Initialise menus and other items
3250 private void jbInit() throws Exception
3252 setMenuBar(alignFrameMenuBar);
3255 * Configure File menu items and actions
3258 .setLabel(MessageManager.getString("label.input_from_textbox"));
3259 inputText.addActionListener(this);
3260 Menu outputTextboxMenu = new Menu(
3261 MessageManager.getString("label.out_to_textbox"));
3262 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3264 MenuItem item = new MenuItem(ff);
3266 item.addActionListener(new java.awt.event.ActionListener()
3269 public void actionPerformed(ActionEvent e)
3271 outputText_actionPerformed(e);
3275 outputTextboxMenu.add(item);
3277 closeMenuItem.addActionListener(this);
3278 loadApplication.addActionListener(this);
3279 loadTree.addActionListener(this);
3280 loadAnnotations.addActionListener(this);
3281 outputFeatures.addActionListener(this);
3282 outputAnnotations.addActionListener(this);
3285 * Configure Edit menu items and actions
3287 undoMenuItem.setEnabled(false);
3288 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3289 undoMenuItem.addActionListener(this);
3290 redoMenuItem.setEnabled(false);
3291 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3292 redoMenuItem.addActionListener(this);
3293 copy.setLabel(MessageManager.getString("action.copy"));
3294 copy.addActionListener(this);
3295 cut.setLabel(MessageManager.getString("action.cut"));
3296 cut.addActionListener(this);
3297 delete.setLabel(MessageManager.getString("action.delete"));
3298 delete.addActionListener(this);
3299 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3300 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3301 pasteNew.addActionListener(this);
3302 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3303 pasteThis.addActionListener(this);
3304 remove2LeftMenuItem.setLabel(MessageManager
3305 .getString("action.remove_left"));
3306 remove2LeftMenuItem.addActionListener(this);
3307 remove2RightMenuItem.setLabel(MessageManager
3308 .getString("action.remove_right"));
3309 remove2RightMenuItem.addActionListener(this);
3310 removeGappedColumnMenuItem.setLabel(MessageManager
3311 .getString("action.remove_empty_columns"));
3312 removeGappedColumnMenuItem.addActionListener(this);
3313 removeAllGapsMenuItem.setLabel(MessageManager
3314 .getString("action.remove_all_gaps"));
3315 removeAllGapsMenuItem.addActionListener(this);
3316 removeRedundancyMenuItem.setLabel(MessageManager
3317 .getString("action.remove_redundancy"));
3318 removeRedundancyMenuItem.addActionListener(this);
3321 * Configure Select menu items and actions
3323 findMenuItem.setLabel(MessageManager.getString("action.find"));
3324 findMenuItem.addActionListener(this);
3325 selectAllSequenceMenuItem.addActionListener(this);
3326 deselectAllSequenceMenuItem.addActionListener(this);
3327 invertSequenceMenuItem.setLabel(MessageManager
3328 .getString("action.invert_sequence_selection"));
3329 invertSequenceMenuItem.addActionListener(this);
3330 invertColSel.setLabel(MessageManager
3331 .getString("action.invert_column_selection"));
3332 invertColSel.addActionListener(this);
3333 deleteGroups.setLabel(MessageManager
3334 .getString("action.undefine_groups"));
3335 deleteGroups.addActionListener(this);
3336 grpsFromSelection.setLabel(MessageManager
3337 .getString("action.make_groups_selection"));
3338 grpsFromSelection.addActionListener(this);
3339 createGroup.setLabel(MessageManager.getString("action.create_group"));
3340 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3341 annotationColumnSelection.setLabel(MessageManager
3342 .getString("action.select_by_annotation"));
3343 annotationColumnSelection.addActionListener(this);
3346 * Configure View menu items and actions
3348 newView.setLabel(MessageManager.getString("action.new_view"));
3349 newView.addActionListener(this);
3350 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3351 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3352 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3353 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3355 .setLabel(MessageManager.getString("label.selected_columns"));
3356 hideSequences.setLabel(MessageManager
3357 .getString("label.selected_sequences"));
3358 hideAllButSelection.setLabel(MessageManager
3359 .getString("label.all_but_selected_region"));
3360 hideAllSelection.setLabel(MessageManager
3361 .getString("label.selected_region"));
3362 showAllHidden.setLabel(MessageManager
3363 .getString("label.all_sequences_columns"));
3364 showColumns.addActionListener(this);
3365 showSeqs.addActionListener(this);
3366 hideColumns.addActionListener(this);
3367 hideSequences.addActionListener(this);
3368 hideAllButSelection.addActionListener(this);
3369 hideAllSelection.addActionListener(this);
3370 showAllHidden.addActionListener(this);
3371 featureSettings.setLabel(MessageManager
3372 .getString("action.feature_settings"));
3373 featureSettings.addActionListener(this);
3374 sequenceFeatures.setLabel(MessageManager
3375 .getString("label.show_sequence_features"));
3376 sequenceFeatures.addItemListener(this);
3377 sequenceFeatures.setState(false);
3378 followMouseOverFlag.setLabel(MessageManager
3379 .getString("label.automatic_scrolling"));
3380 followMouseOverFlag.addItemListener(this);
3381 alProperties.addActionListener(this);
3382 overviewMenuItem.setLabel(MessageManager
3383 .getString("label.overview_window"));
3384 overviewMenuItem.addActionListener(this);
3387 * Configure Annotations menu items and actions
3389 annotationPanelMenuItem.setLabel(MessageManager
3390 .getString("label.show_annotations"));
3391 annotationPanelMenuItem.addItemListener(this);
3392 showGroupConsensus.setLabel(MessageManager
3393 .getString("label.group_consensus"));
3394 showGroupConservation.setLabel(MessageManager
3395 .getString("label.group_conservation"));
3396 showConsensusHistogram.setLabel(MessageManager
3397 .getString("label.show_consensus_histogram"));
3398 showSequenceLogo.setLabel(MessageManager
3399 .getString("label.show_consensus_logo"));
3400 normSequenceLogo.setLabel(MessageManager
3401 .getString("label.norm_consensus_logo"));
3402 applyAutoAnnotationSettings.setLabel(MessageManager
3403 .getString("label.apply_all_groups"));
3404 applyAutoAnnotationSettings.setState(true);
3405 Menu autoAnnMenu = new Menu(
3406 MessageManager.getString("label.autocalculated_annotation"));
3407 showGroupConsensus.addItemListener(this);
3408 showGroupConservation.addItemListener(this);
3409 showConsensusHistogram.addItemListener(this);
3410 showSequenceLogo.addItemListener(this);
3411 normSequenceLogo.addItemListener(this);
3412 applyAutoAnnotationSettings.addItemListener(this);
3413 showAlignmentAnnotations = new CheckboxMenuItem(
3414 MessageManager.getString("label.show_all_al_annotations"));
3415 showSequenceAnnotations = new CheckboxMenuItem(
3416 MessageManager.getString("label.show_all_seq_annotations"));
3417 sortAnnBySequence = new CheckboxMenuItem(
3418 MessageManager.getString("label.sort_annotations_by_sequence"));
3419 sortAnnByLabel = new CheckboxMenuItem(
3420 MessageManager.getString("label.sort_annotations_by_label"));
3421 showAutoFirst = new CheckboxMenuItem(
3422 MessageManager.getString("label.show_first"));
3423 showAutoFirst.setState(false); // pending applet parameter
3424 setShowAutoCalculatedAbove(showAutoFirst.getState());
3425 showAutoLast = new CheckboxMenuItem(
3426 MessageManager.getString("label.show_last"));
3427 showAutoLast.setState(!showAutoFirst.getState());
3428 showAlignmentAnnotations.addItemListener(this);
3429 showSequenceAnnotations.addItemListener(this);
3430 sortAnnBySequence.addItemListener(this);
3431 sortAnnByLabel.addItemListener(this);
3432 showAutoFirst.addItemListener(this);
3433 showAutoLast.addItemListener(this);
3436 * Configure Format menu items and actions
3438 font.setLabel(MessageManager.getString("action.font"));
3439 font.addActionListener(this);
3440 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3441 scaleAbove.setState(true);
3442 scaleAbove.setEnabled(false);
3443 scaleAbove.addItemListener(this);
3444 scaleLeft.setEnabled(false);
3445 scaleLeft.setState(true);
3446 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3447 scaleLeft.addItemListener(this);
3448 scaleRight.setEnabled(false);
3449 scaleRight.setState(true);
3450 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3451 scaleRight.addItemListener(this);
3452 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3453 viewBoxesMenuItem.setState(true);
3454 viewBoxesMenuItem.addItemListener(this);
3455 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3456 viewTextMenuItem.setState(true);
3457 viewTextMenuItem.addItemListener(this);
3458 colourTextMenuItem.setLabel(MessageManager
3459 .getString("label.colour_text"));
3460 colourTextMenuItem.addItemListener(this);
3461 displayNonconservedMenuItem.setLabel(MessageManager
3462 .getString("label.show_non_conversed"));
3463 displayNonconservedMenuItem.addItemListener(this);
3464 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3465 wrapMenuItem.addItemListener(this);
3466 renderGapsMenuItem.setLabel(MessageManager
3467 .getString("action.show_gaps"));
3468 renderGapsMenuItem.setState(true);
3469 renderGapsMenuItem.addItemListener(this);
3470 centreColumnLabelFlag.setLabel(MessageManager
3471 .getString("label.centre_column_labels"));
3472 centreColumnLabelFlag.addItemListener(this);
3473 seqLimits.setState(true);
3474 seqLimits.setLabel(MessageManager
3475 .getString("label.show_sequence_limits"));
3476 seqLimits.addItemListener(this);
3479 * Configure Colour menu items and actions
3481 applyToAllGroups.setLabel(MessageManager
3482 .getString("label.apply_colour_to_all_groups"));
3483 applyToAllGroups.setState(true);
3484 applyToAllGroups.addItemListener(this);
3485 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3486 clustalColour.addActionListener(this);
3487 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3488 zappoColour.addActionListener(this);
3489 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3490 taylorColour.addActionListener(this);
3491 hydrophobicityColour.setLabel(MessageManager
3492 .getString("label.hydrophobicity"));
3493 hydrophobicityColour.addActionListener(this);
3495 .setLabel(MessageManager.getString("label.helix_propensity"));
3496 helixColour.addActionListener(this);
3497 strandColour.setLabel(MessageManager
3498 .getString("label.strand_propensity"));
3499 strandColour.addActionListener(this);
3500 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3501 turnColour.addActionListener(this);
3502 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3503 buriedColour.addActionListener(this);
3504 purinePyrimidineColour.setLabel(MessageManager
3505 .getString("label.purine_pyrimidine"));
3506 purinePyrimidineColour.addActionListener(this);
3507 // RNAInteractionColour.setLabel(MessageManager
3508 // .getString("label.rna_interaction"));
3509 // RNAInteractionColour.addActionListener(this);
3510 RNAHelixColour.setLabel(MessageManager
3511 .getString("action.by_rna_helixes"));
3512 RNAHelixColour.addActionListener(this);
3513 userDefinedColour.setLabel(MessageManager
3514 .getString("action.user_defined"));
3515 userDefinedColour.addActionListener(this);
3516 PIDColour.setLabel(MessageManager
3517 .getString("label.percentage_identity"));
3518 PIDColour.addActionListener(this);
3519 BLOSUM62Colour.setLabel(MessageManager
3520 .getString("label.blosum62_score"));
3521 BLOSUM62Colour.addActionListener(this);
3523 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3524 // it will be enabled only if a score file is provided
3525 tcoffeeColour.setEnabled(false);
3526 tcoffeeColour.addActionListener(this);
3527 conservationMenuItem.setLabel(MessageManager
3528 .getString("action.by_conservation"));
3529 conservationMenuItem.addItemListener(this);
3530 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3531 noColourmenuItem.addActionListener(this);
3532 abovePIDThreshold.setLabel(MessageManager
3533 .getString("label.above_identity_threshold"));
3534 abovePIDThreshold.addItemListener(this);
3535 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3536 nucleotideColour.addActionListener(this);
3537 modifyPID.setLabel(MessageManager
3538 .getString("label.modify_identity_threshold"));
3539 modifyPID.setEnabled(abovePIDThreshold.getState());
3540 modifyPID.addActionListener(this);
3541 modifyConservation.setLabel(MessageManager
3542 .getString("label.modify_conservation_threshold"));
3543 modifyConservation.setEnabled(conservationMenuItem.getState());
3544 modifyConservation.addActionListener(this);
3545 annotationColour.setLabel(MessageManager
3546 .getString("action.by_annotation"));
3547 annotationColour.addActionListener(this);
3550 * Configure Calculate menu items and actions
3552 sortPairwiseMenuItem.setLabel(MessageManager
3553 .getString("action.by_pairwise_id"));
3554 sortPairwiseMenuItem.addActionListener(this);
3555 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3556 sortIDMenuItem.addActionListener(this);
3557 sortLengthMenuItem.setLabel(MessageManager
3558 .getString("action.by_length"));
3559 sortLengthMenuItem.addActionListener(this);
3560 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3561 sortGroupMenuItem.addActionListener(this);
3562 pairwiseAlignmentMenuItem.setLabel(MessageManager
3563 .getString("action.pairwise_alignment"));
3564 pairwiseAlignmentMenuItem.addActionListener(this);
3565 PCAMenuItem.setLabel(MessageManager
3566 .getString("label.principal_component_analysis"));
3567 PCAMenuItem.addActionListener(this);
3568 autoCalculate = new CheckboxMenuItem(
3569 MessageManager.getString("label.autocalculate_consensus"), true);
3570 averageDistanceTreeMenuItem.setLabel(MessageManager
3571 .getString("label.average_distance_identity"));
3572 averageDistanceTreeMenuItem.addActionListener(this);
3573 neighbourTreeMenuItem.setLabel(MessageManager
3574 .getString("label.neighbour_joining_identity"));
3575 neighbourTreeMenuItem.addActionListener(this);
3576 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3577 .getString("label.average_distance_bloslum62"));
3578 avDistanceTreeBlosumMenuItem.addActionListener(this);
3579 njTreeBlosumMenuItem.setLabel(MessageManager
3580 .getString("label.neighbour_blosum62"));
3581 njTreeBlosumMenuItem.addActionListener(this);
3582 sortByTreeMenu.setLabel(MessageManager
3583 .getString("action.by_tree_order"));
3584 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3585 Menu calculateTreeMenu = new Menu(
3586 MessageManager.getString("action.calculate_tree"));
3587 autoCalculate.addItemListener(this);
3588 sortByTree.addItemListener(this);
3591 * Configure Help menu items and actions
3593 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3594 documentation.setLabel(MessageManager.getString("label.documentation"));
3595 documentation.addActionListener(this);
3596 about.setLabel(MessageManager.getString("label.about"));
3597 about.addActionListener(this);
3600 * Add top level menus to frame
3602 alignFrameMenuBar.add(fileMenu);
3603 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3604 alignFrameMenuBar.add(editMenu);
3605 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3606 alignFrameMenuBar.add(selectMenu);
3607 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3608 alignFrameMenuBar.add(viewMenu);
3609 Menu annotationsMenu = new Menu(
3610 MessageManager.getString("action.annotations"));
3611 alignFrameMenuBar.add(annotationsMenu);
3612 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3613 alignFrameMenuBar.add(formatMenu);
3614 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3615 alignFrameMenuBar.add(colourMenu);
3616 Menu calculateMenu = new Menu(
3617 MessageManager.getString("action.calculate"));
3618 alignFrameMenuBar.add(calculateMenu);
3619 alignFrameMenuBar.add(helpMenu);
3624 fileMenu.add(inputText);
3625 fileMenu.add(loadTree);
3626 fileMenu.add(loadAnnotations);
3627 fileMenu.addSeparator();
3628 fileMenu.add(outputTextboxMenu);
3629 fileMenu.add(outputFeatures);
3630 fileMenu.add(outputAnnotations);
3631 if (jalviewServletURL != null)
3633 fileMenu.add(loadApplication);
3635 fileMenu.addSeparator();
3636 fileMenu.add(closeMenuItem);
3641 editMenu.add(undoMenuItem);
3642 editMenu.add(redoMenuItem);
3645 pasteMenu.add(pasteNew);
3646 pasteMenu.add(pasteThis);
3647 editMenu.add(pasteMenu);
3648 editMenu.add(delete);
3649 editMenu.addSeparator();
3650 editMenu.add(remove2LeftMenuItem);
3651 editMenu.add(remove2RightMenuItem);
3652 editMenu.add(removeGappedColumnMenuItem);
3653 editMenu.add(removeAllGapsMenuItem);
3654 editMenu.add(removeRedundancyMenuItem);
3659 selectMenu.add(findMenuItem);
3660 selectMenu.addSeparator();
3661 selectMenu.add(selectAllSequenceMenuItem);
3662 selectMenu.add(deselectAllSequenceMenuItem);
3663 selectMenu.add(invertSequenceMenuItem);
3664 selectMenu.add(invertColSel);
3665 selectMenu.add(createGroup);
3666 selectMenu.add(unGroup);
3667 selectMenu.add(grpsFromSelection);
3668 selectMenu.add(deleteGroups);
3669 selectMenu.add(annotationColumnSelection);
3674 viewMenu.add(newView);
3675 viewMenu.addSeparator();
3676 showMenu.add(showColumns);
3677 showMenu.add(showSeqs);
3678 showMenu.add(showAllHidden);
3679 viewMenu.add(showMenu);
3680 hideMenu.add(hideColumns);
3681 hideMenu.add(hideSequences);
3682 hideMenu.add(hideAllSelection);
3683 hideMenu.add(hideAllButSelection);
3684 viewMenu.add(hideMenu);
3685 viewMenu.addSeparator();
3686 viewMenu.add(followMouseOverFlag);
3687 viewMenu.addSeparator();
3688 viewMenu.add(sequenceFeatures);
3689 viewMenu.add(featureSettings);
3690 viewMenu.addSeparator();
3691 viewMenu.add(alProperties);
3692 viewMenu.addSeparator();
3693 viewMenu.add(overviewMenuItem);
3698 annotationsMenu.add(annotationPanelMenuItem);
3699 annotationsMenu.addSeparator();
3700 annotationsMenu.add(showAlignmentAnnotations);
3701 annotationsMenu.add(showSequenceAnnotations);
3702 annotationsMenu.add(sortAnnBySequence);
3703 annotationsMenu.add(sortAnnByLabel);
3704 annotationsMenu.addSeparator();
3705 autoAnnMenu.add(showAutoFirst);
3706 autoAnnMenu.add(showAutoLast);
3707 autoAnnMenu.addSeparator();
3708 autoAnnMenu.add(applyAutoAnnotationSettings);
3709 autoAnnMenu.add(showConsensusHistogram);
3710 autoAnnMenu.add(showSequenceLogo);
3711 autoAnnMenu.add(normSequenceLogo);
3712 autoAnnMenu.addSeparator();
3713 autoAnnMenu.add(showGroupConservation);
3714 autoAnnMenu.add(showGroupConsensus);
3715 annotationsMenu.add(autoAnnMenu);
3720 formatMenu.add(font);
3721 formatMenu.add(seqLimits);
3722 formatMenu.add(wrapMenuItem);
3723 formatMenu.add(scaleAbove);
3724 formatMenu.add(scaleLeft);
3725 formatMenu.add(scaleRight);
3726 formatMenu.add(viewBoxesMenuItem);
3727 formatMenu.add(viewTextMenuItem);
3728 formatMenu.add(colourTextMenuItem);
3729 formatMenu.add(displayNonconservedMenuItem);
3730 formatMenu.add(renderGapsMenuItem);
3731 formatMenu.add(centreColumnLabelFlag);
3736 colourMenu.add(applyToAllGroups);
3737 colourMenu.addSeparator();
3738 colourMenu.add(noColourmenuItem);
3739 colourMenu.add(clustalColour);
3740 colourMenu.add(BLOSUM62Colour);
3741 colourMenu.add(PIDColour);
3742 colourMenu.add(zappoColour);
3743 colourMenu.add(taylorColour);
3744 colourMenu.add(hydrophobicityColour);
3745 colourMenu.add(helixColour);
3746 colourMenu.add(strandColour);
3747 colourMenu.add(turnColour);
3748 colourMenu.add(buriedColour);
3749 colourMenu.add(nucleotideColour);
3750 colourMenu.add(purinePyrimidineColour);
3751 // colourMenu.add(RNAInteractionColour);
3752 colourMenu.add(tcoffeeColour);
3753 colourMenu.add(userDefinedColour);
3754 colourMenu.addSeparator();
3755 colourMenu.add(conservationMenuItem);
3756 colourMenu.add(modifyConservation);
3757 colourMenu.add(abovePIDThreshold);
3758 colourMenu.add(modifyPID);
3759 colourMenu.add(annotationColour);
3760 colourMenu.add(RNAHelixColour);
3765 sortMenu.add(sortIDMenuItem);
3766 sortMenu.add(sortLengthMenuItem);
3767 sortMenu.add(sortByTreeMenu);
3768 sortMenu.add(sortGroupMenuItem);
3769 sortMenu.add(sortPairwiseMenuItem);
3770 calculateMenu.add(sortMenu);
3771 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3772 calculateTreeMenu.add(neighbourTreeMenuItem);
3773 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3774 calculateTreeMenu.add(njTreeBlosumMenuItem);
3775 calculateMenu.add(calculateTreeMenu);
3776 calculateMenu.addSeparator();
3777 calculateMenu.add(pairwiseAlignmentMenuItem);
3778 calculateMenu.add(PCAMenuItem);
3779 calculateMenu.add(autoCalculate);
3780 calculateMenu.add(sortByTree);
3785 helpMenu.add(documentation);
3786 helpMenu.add(about);
3791 statusBar.setBackground(Color.white);
3792 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3793 statusBar.setText(MessageManager.getString("label.status_bar"));
3794 this.add(statusBar, BorderLayout.SOUTH);
3798 public void setStatus(String string)
3800 statusBar.setText(string);
3803 MenuItem featureSettings = new MenuItem();
3805 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3807 MenuItem annotationColour = new MenuItem();
3809 MenuItem annotationColumnSelection = new MenuItem();
3811 MenuItem invertColSel = new MenuItem();
3813 MenuItem showColumns = new MenuItem();
3815 MenuItem showSeqs = new MenuItem();
3817 MenuItem hideColumns = new MenuItem();
3819 MenuItem hideSequences = new MenuItem();
3821 MenuItem hideAllButSelection = new MenuItem();
3823 MenuItem hideAllSelection = new MenuItem();
3825 MenuItem showAllHidden = new MenuItem();
3827 MenuItem newView = new MenuItem();
3829 private CheckboxMenuItem showAlignmentAnnotations;
3831 private CheckboxMenuItem showSequenceAnnotations;
3833 private CheckboxMenuItem sortAnnBySequence;
3835 private CheckboxMenuItem sortAnnByLabel;
3837 private CheckboxMenuItem showAutoFirst;
3839 private CheckboxMenuItem showAutoLast;
3841 private SplitFrame splitFrame;
3844 * Attach the alignFrame panels after embedding menus, if necessary. This used
3845 * to be called setEmbedded, but is now creates the dropdown menus in a
3846 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3848 * @param reallyEmbedded
3849 * true to attach the view to the applet area on the page rather than
3852 public void createAlignFrameWindow(boolean reallyEmbedded)
3856 embedAlignFrameInApplet(viewport.applet);
3861 // test and embed menu bar if necessary.
3863 if (embedMenuIfNeeded(alignPanel))
3866 * adjust for status bar height too. ? pointless as overridden by layout
3869 alignPanel.setSize(getSize().width,
3870 getSize().height - statusBar.getHeight());
3872 add(statusBar, BorderLayout.SOUTH);
3873 add(alignPanel, BorderLayout.CENTER);
3874 // and register with the applet so it can pass external API calls to us
3875 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3881 * Add the components of this AlignFrame to the applet container.
3885 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3888 // Explicitly build the embedded menu panel for the on-page applet
3890 // view cannot be closed if its actually on the page
3891 fileMenu.remove(closeMenuItem);
3892 fileMenu.remove(3); // Remove Separator
3893 // construct embedded menu, using default font
3894 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3895 // and actually add the components to the applet area
3896 theApplet.setLayout(new BorderLayout());
3897 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3898 theApplet.add(statusBar, BorderLayout.SOUTH);
3899 // TODO should size be left to the layout manager?
3900 alignPanel.setSize(theApplet.getSize().width,
3901 theApplet.getSize().height - embeddedMenu.getHeight()
3902 - statusBar.getHeight());
3903 theApplet.add(alignPanel, BorderLayout.CENTER);
3904 final AlignFrame me = this;
3905 theApplet.addFocusListener(new FocusListener()
3909 public void focusLost(FocusEvent e)
3911 if (theApplet.currentAlignFrame == me)
3913 theApplet.currentAlignFrame = null;
3918 public void focusGained(FocusEvent e)
3920 theApplet.currentAlignFrame = me;
3923 theApplet.validate();
3927 * create a new binding between structures in an existing jmol viewer instance
3928 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3929 * this does not open a new Jmol window, or modify the display of the
3930 * structures in the original jmol window. Note This method doesn't work
3931 * without an additional javascript library to exchange messages between the
3932 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3935 * JmolViewer instance
3936 * @param sequenceIds
3937 * - sequence Ids to search for associations
3939 public SequenceStructureBinding addStructureViewInstance(
3940 Object jmolviewer, String[] sequenceIds)
3942 Viewer viewer = null;
3945 viewer = (Viewer) jmolviewer;
3946 } catch (ClassCastException ex)
3948 System.err.println("Unsupported viewer object :"
3949 + jmolviewer.getClass());
3953 System.err.println("Can't use this object as a structure viewer:"
3954 + jmolviewer.getClass());
3957 SequenceI[] seqs = null;
3958 if (sequenceIds == null || sequenceIds.length == 0)
3960 seqs = viewport.getAlignment().getSequencesArray();
3964 Vector sqi = new Vector();
3965 AlignmentI al = viewport.getAlignment();
3966 for (int sid = 0; sid < sequenceIds.length; sid++)
3968 SequenceI sq = al.findName(sequenceIds[sid]);
3976 seqs = new SequenceI[sqi.size()];
3977 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3979 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3987 AAStructureBindingModel jmv = null;
3988 // TODO: search for a jmv that involves viewer
3990 { // create a new viewer/jalview binding.
3991 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3998 * bind a pdb file to a sequence in the current view
4001 * - sequenceId within the dataset.
4002 * @param pdbEntryString
4003 * - the short name for the PDB file
4005 * - pdb file - either a URL or a valid PDB file.
4006 * @return true if binding was as success TODO: consider making an exception
4007 * structure for indicating when PDB parsing or sequenceId location
4010 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4013 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4014 boolean needtoadd = false;
4015 if (toaddpdb != null)
4017 Vector pdbe = toaddpdb.getAllPDBEntries();
4018 PDBEntry pdbentry = null;
4019 if (pdbe != null && pdbe.size() > 0)
4021 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4023 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4024 if (!pdbentry.getId().equals(pdbEntryString)
4025 && !pdbentry.getFile().equals(pdbFile))
4035 if (pdbentry == null)
4037 pdbentry = new PDBEntry();
4038 pdbentry.setId(pdbEntryString);
4039 pdbentry.setFile(pdbFile);
4040 needtoadd = true; // add this new entry to sequence.
4042 // resolve data source
4043 // TODO: this code should be a refactored to an io package
4044 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4045 pdbFile, FileFormat.PDB);
4046 if (protocol == null)
4052 pdbentry.setProperty("protocol", protocol);
4053 toaddpdb.addPDBId(pdbentry);
4054 alignPanel.getStructureSelectionManager()
4055 .registerPDBEntry(pdbentry);
4061 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4065 Vector sequences = new Vector();
4066 for (int i = 0; i < seqs.length; i++)
4068 if (seqs[i] != null)
4070 sequences.addElement(new Object[] { seqs[i],
4071 (chains != null) ? chains[i] : null });
4074 seqs = new SequenceI[sequences.size()];
4075 chains = new String[sequences.size()];
4076 for (int i = 0, isize = sequences.size(); i < isize; i++)
4078 Object[] oj = (Object[]) sequences.elementAt(i);
4080 seqs[i] = (SequenceI) oj[0];
4081 chains[i] = (String) oj[1];
4084 return new Object[] { seqs, chains };
4088 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4089 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4091 // Scrub any null sequences from the array
4092 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4093 seqs = (SequenceI[]) sqch[0];
4094 chains = (String[]) sqch[1];
4095 if (seqs == null || seqs.length == 0)
4098 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4100 if (protocol == null)
4102 String sourceType = (String) pdb.getProperty("protocol");
4105 protocol = DataSourceType.valueOf(sourceType);
4106 } catch (IllegalArgumentException e)
4110 if (protocol == null)
4112 System.err.println("Couldn't work out protocol to open structure: "
4117 if (applet.useXtrnalSviewer)
4119 // register the association(s) and quit, don't create any windows.
4120 if (StructureSelectionManager.getStructureSelectionManager(applet)
4121 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4123 System.err.println("Failed to map " + pdb.getFile() + " ("
4124 + protocol + ") to any sequences");
4128 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4130 // can only do alignments with Jmol
4131 // find the last jmol window assigned to this alignment
4132 AppletJmol ajm = null, tajm;
4133 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4134 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4136 tajm = (AppletJmol) jmols.elementAt(i);
4137 if (tajm.ap.alignFrame == this)
4146 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4147 // try and add the pdb structure
4152 // otherwise, create a new window
4153 if (applet.jmolAvailable)
4155 new AppletJmol(pdb, seqs, chains, alignPanel,
4157 applet.lastFrameX += 40;
4158 applet.lastFrameY += 40;
4162 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4167 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4168 SequenceI[][] seqs, String[][] chains, String[] protocols)
4170 // TODO Auto-generated method stub
4171 System.err.println("Aligned Structure View: Not yet implemented.");
4175 * modify the current selection, providing the user has not made a selection
4179 * - sequences from this alignment
4181 * - columns to be selected on the alignment
4183 public void select(SequenceGroup sel, ColumnSelection csel)
4185 alignPanel.seqPanel.selection(sel, csel, null);
4188 public void scrollTo(int row, int column)
4190 alignPanel.seqPanel.scrollTo(row, column);
4193 public void scrollToRow(int row)
4195 alignPanel.seqPanel.scrollToRow(row);
4198 public void scrollToColumn(int column)
4200 alignPanel.seqPanel.scrollToColumn(column);
4204 * @return the alignments unique ID.
4206 public String getSequenceSetId()
4208 return viewport.getSequenceSetId();
4212 * Load the (T-Coffee) score file from the specified url
4215 * File/URL/T-COFFEE score file contents
4216 * @throws IOException
4217 * @return true if alignment was annotated with data from source
4219 public boolean loadScoreFile(String source) throws IOException
4222 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4223 AppletFormatAdapter.checkProtocol(source));
4224 if (!file.isValid())
4226 // TODO: raise dialog for gui
4227 System.err.println("Problems parsing T-Coffee scores: "
4228 + file.getWarningMessage());
4229 System.err.println("Origin was:\n" + source);
4234 * check that the score matrix matches the alignment dimensions
4237 if ((aln = viewport.getAlignment()) != null
4238 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4241 // TODO: raise a dialog box here rather than bomb out.
4243 .println("The scores matrix does not match the alignment dimensions");
4247 // TODO add parameter to indicate if matching should be done
4248 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4250 alignPanel.fontChanged();
4251 tcoffeeColour.setEnabled(true);
4252 // switch to this color
4253 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4258 System.err.println("Problems resolving T-Coffee scores:");
4259 if (file.getWarningMessage() != null)
4261 System.err.println(file.getWarningMessage());
4267 public SplitFrame getSplitFrame()
4269 return this.splitFrame;
4272 public void setSplitFrame(SplitFrame sf)
4274 this.splitFrame = sf;
4277 // may not need this
4279 public void setShowSeqFeatures(boolean b)
4281 // showSeqFeatures.setSelected(b);
4282 viewport.setShowSequenceFeatures(b);
4287 public void setMenusForViewport()
4289 // setMenusFromViewport(viewport);
4294 public void refreshFeatureUI(boolean enableIfNecessary)
4296 if (enableIfNecessary)
4298 sequenceFeatures.setState(true);
4299 alignPanel.av.setShowSequenceFeatures(true);
4304 public FeatureSettingsControllerI getFeatureSettingsUI()
4306 return alignPanel.av.featureSettings;