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 viewport.setConservationSelected(conservationMenuItem.getState());
2683 viewport.setAbovePIDThreshold(false);
2684 abovePIDThreshold.setState(false);
2686 changeColour(viewport.getGlobalColourScheme());
2688 modifyConservation_actionPerformed();
2691 public void abovePIDThreshold_actionPerformed()
2693 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2695 conservationMenuItem.setState(false);
2696 viewport.setConservationSelected(false);
2698 changeColour(viewport.getGlobalColourScheme());
2700 modifyPID_actionPerformed();
2703 public void sortPairwiseMenuItem_actionPerformed()
2705 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2706 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2707 .getAlignment().getSequenceAt(0), null);
2709 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2710 viewport.getAlignment()));
2711 alignPanel.paintAlignment(true);
2714 public void sortIDMenuItem_actionPerformed()
2716 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2717 AlignmentSorter.sortByID(viewport.getAlignment());
2718 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2719 viewport.getAlignment()));
2720 alignPanel.paintAlignment(true);
2723 public void sortLengthMenuItem_actionPerformed()
2725 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2726 AlignmentSorter.sortByLength(viewport.getAlignment());
2727 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2728 viewport.getAlignment()));
2729 alignPanel.paintAlignment(true);
2732 public void sortGroupMenuItem_actionPerformed()
2734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735 AlignmentSorter.sortByGroup(viewport.getAlignment());
2736 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2737 viewport.getAlignment()));
2738 alignPanel.paintAlignment(true);
2742 public void removeRedundancyMenuItem_actionPerformed()
2744 new RedundancyPanel(alignPanel);
2747 public void pairwiseAlignmentMenuItem_actionPerformed()
2749 if (viewport.getSelectionGroup() != null
2750 && viewport.getSelectionGroup().getSize() > 1)
2752 Frame frame = new Frame();
2753 frame.add(new PairwiseAlignPanel(alignPanel));
2754 jalview.bin.JalviewLite.addFrame(frame,
2755 MessageManager.getString("action.pairwise_alignment"), 600,
2760 public void PCAMenuItem_actionPerformed()
2762 // are the sequences aligned?
2763 if (!viewport.getAlignment().isAligned(false))
2766 int Width = viewport.getAlignment().getWidth();
2768 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2770 current = viewport.getAlignment().getSequenceAt(i);
2772 if (current.getLength() < Width)
2774 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2777 alignPanel.paintAlignment(true);
2780 if ((viewport.getSelectionGroup() != null
2781 && viewport.getSelectionGroup().getSize() < 4 && viewport
2782 .getSelectionGroup().getSize() > 0)
2783 || viewport.getAlignment().getHeight() < 4)
2790 new PCAPanel(viewport);
2791 } catch (java.lang.OutOfMemoryError ex)
2797 public void averageDistanceTreeMenuItem_actionPerformed()
2799 NewTreePanel("AV", "PID", "Average distance tree using PID");
2802 public void neighbourTreeMenuItem_actionPerformed()
2804 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2807 protected void njTreeBlosumMenuItem_actionPerformed()
2809 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2812 protected void avTreeBlosumMenuItem_actionPerformed()
2814 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2817 void NewTreePanel(String type, String pwType, String title)
2819 // are the sequences aligned?
2820 if (!viewport.getAlignment().isAligned(false))
2823 int Width = viewport.getAlignment().getWidth();
2825 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2827 current = viewport.getAlignment().getSequenceAt(i);
2829 if (current.getLength() < Width)
2831 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2834 alignPanel.paintAlignment(true);
2838 if ((viewport.getSelectionGroup() != null && viewport
2839 .getSelectionGroup().getSize() > 1)
2840 || (viewport.getAlignment().getHeight() > 1))
2842 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2844 addTreeMenuItem(tp, title);
2846 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2850 void loadTree_actionPerformed()
2852 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2853 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2854 cap.setTreeImport();
2855 Frame frame = new Frame();
2857 jalview.bin.JalviewLite.addFrame(frame,
2858 MessageManager.getString("label.paste_newick_file"), 400, 300);
2861 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2863 TreePanel tp = new TreePanel(alignPanel, treeFile,
2864 MessageManager.getString("label.load_tree_from_file"), tree);
2865 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2866 addTreeMenuItem(tp, treeFile);
2870 * sort the alignment using the given treePanel
2873 * tree used to sort view
2875 * string used for undo event name
2877 public void sortByTree(TreePanel treePanel, String title)
2879 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2881 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2882 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2883 // HistoryItem.SORT));
2884 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2885 "label.order_by_params", new String[] { title }), oldOrder,
2886 viewport.getAlignment()));
2887 alignPanel.paintAlignment(true);
2891 * Do any automatic reordering of the alignment and add the necessary bits to
2892 * the menu structure for the new tree
2897 protected void addTreeMenuItem(final TreePanel treePanel,
2900 final MenuItem item = new MenuItem(title);
2901 sortByTreeMenu.add(item);
2902 item.addActionListener(new java.awt.event.ActionListener()
2905 public void actionPerformed(ActionEvent evt)
2907 sortByTree(treePanel, title); // treePanel.getTitle());
2911 treePanel.addWindowListener(new WindowAdapter()
2914 public void windowOpened(WindowEvent e)
2916 if (viewport.sortByTree)
2918 sortByTree(treePanel, title);
2920 super.windowOpened(e);
2924 public void windowClosing(WindowEvent e)
2926 sortByTreeMenu.remove(item);
2931 public boolean sortBy(AlignmentOrder alorder, String undoname)
2933 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2934 if (viewport.applet.debug)
2936 System.err.println("Sorting " + alorder.getOrder().size()
2937 + " in alignment '" + getTitle() + "'");
2939 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2940 if (undoname != null)
2942 addHistoryItem(new OrderCommand(undoname, oldOrder,
2943 viewport.getAlignment()));
2945 alignPanel.paintAlignment(true);
2949 protected void documentation_actionPerformed()
2951 alignPanel.av.applet.openJalviewHelpUrl();
2954 protected void about_actionPerformed()
2957 class AboutPanel extends Canvas
2963 public AboutPanel(String version, String builddate)
2965 this.version = version;
2966 this.builddate = builddate;
2970 public void paint(Graphics g)
2972 g.setColor(Color.white);
2973 g.fillRect(0, 0, getSize().width, getSize().height);
2974 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2975 FontMetrics fm = g.getFontMetrics();
2976 int fh = fm.getHeight();
2978 g.setColor(Color.black);
2979 // TODO: update this text for each release or centrally store it for
2980 // lite and application
2981 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2982 g.drawString(MessageManager.formatMessage(
2983 "label.jalviewLite_release", new String[] { version }), x,
2985 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2986 g.drawString(MessageManager.formatMessage(
2987 "label.jaview_build_date", new String[] { builddate }), x,
2989 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2990 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2992 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2993 x + 50, y += fh + 8);
2995 MessageManager.getString("label.jalview_dev_managers"), x,
2997 g.drawString(MessageManager
2998 .getString("label.jalview_distribution_lists"), x, y += fh);
2999 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3002 MessageManager.getString("label.jalview_cite_1_authors"),
3005 MessageManager.getString("label.jalview_cite_1_title"), x,
3007 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3012 Frame frame = new Frame();
3013 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3015 jalview.bin.JalviewLite.addFrame(frame,
3016 MessageManager.getString("label.jalview"), 580, 220);
3020 public void showURL(String url, String target)
3022 if (viewport.applet == null)
3024 System.out.println("Not running as applet - no browser available.");
3028 viewport.applet.showURL(url, target);
3032 // ////////////////////////////////////////////////////////////////////////////////
3033 // JBuilder Graphics here
3035 MenuBar alignFrameMenuBar = new MenuBar();
3037 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3039 MenuItem loadApplication = new MenuItem(
3040 MessageManager.getString("label.view_full_application"));
3042 MenuItem loadTree = new MenuItem(
3043 MessageManager.getString("label.load_associated_tree"));
3045 MenuItem loadAnnotations = new MenuItem(
3046 MessageManager.getString("label.load_features_annotations"));
3048 MenuItem outputFeatures = new MenuItem(
3049 MessageManager.getString("label.export_features"));
3051 MenuItem outputAnnotations = new MenuItem(
3052 MessageManager.getString("label.export_annotations"));
3054 MenuItem closeMenuItem = new MenuItem(
3055 MessageManager.getString("action.close"));
3057 MenuItem selectAllSequenceMenuItem = new MenuItem(
3058 MessageManager.getString("action.select_all"));
3060 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3061 MessageManager.getString("action.deselect_all"));
3063 MenuItem invertSequenceMenuItem = new MenuItem(
3064 MessageManager.getString("action.invert_selection"));
3066 MenuItem remove2LeftMenuItem = new MenuItem();
3068 MenuItem remove2RightMenuItem = new MenuItem();
3070 MenuItem removeGappedColumnMenuItem = new MenuItem();
3072 MenuItem removeAllGapsMenuItem = new MenuItem();
3074 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3076 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3078 MenuItem sortPairwiseMenuItem = new MenuItem();
3080 MenuItem sortIDMenuItem = new MenuItem();
3082 MenuItem sortLengthMenuItem = new MenuItem();
3084 MenuItem sortGroupMenuItem = new MenuItem();
3086 MenuItem removeRedundancyMenuItem = new MenuItem();
3088 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3090 MenuItem PCAMenuItem = new MenuItem();
3092 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3094 MenuItem neighbourTreeMenuItem = new MenuItem();
3096 BorderLayout borderLayout1 = new BorderLayout();
3098 public Label statusBar = new Label();
3100 MenuItem clustalColour = new MenuItem();
3102 MenuItem zappoColour = new MenuItem();
3104 MenuItem taylorColour = new MenuItem();
3106 MenuItem hydrophobicityColour = new MenuItem();
3108 MenuItem helixColour = new MenuItem();
3110 MenuItem strandColour = new MenuItem();
3112 MenuItem turnColour = new MenuItem();
3114 MenuItem buriedColour = new MenuItem();
3116 MenuItem purinePyrimidineColour = new MenuItem();
3118 // MenuItem RNAInteractionColour = new MenuItem();
3120 MenuItem RNAHelixColour = new MenuItem();
3122 MenuItem userDefinedColour = new MenuItem();
3124 MenuItem PIDColour = new MenuItem();
3126 MenuItem BLOSUM62Colour = new MenuItem();
3128 MenuItem tcoffeeColour = new MenuItem();
3130 MenuItem njTreeBlosumMenuItem = new MenuItem();
3132 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3134 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3136 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3138 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3140 MenuItem alProperties = new MenuItem(
3141 MessageManager.getString("label.alignment_props"));
3143 MenuItem overviewMenuItem = new MenuItem();
3145 MenuItem undoMenuItem = new MenuItem();
3147 MenuItem redoMenuItem = new MenuItem();
3149 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3151 MenuItem noColourmenuItem = new MenuItem();
3153 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3155 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3157 MenuItem findMenuItem = new MenuItem();
3159 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3161 MenuItem nucleotideColour = new MenuItem();
3163 MenuItem deleteGroups = new MenuItem();
3165 MenuItem grpsFromSelection = new MenuItem();
3167 MenuItem createGroup = new MenuItem();
3169 MenuItem unGroup = new MenuItem();
3171 MenuItem delete = new MenuItem();
3173 MenuItem copy = new MenuItem();
3175 MenuItem cut = new MenuItem();
3177 Menu pasteMenu = new Menu();
3179 MenuItem pasteNew = new MenuItem();
3181 MenuItem pasteThis = new MenuItem();
3183 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3185 MenuItem font = new MenuItem();
3187 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3189 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3191 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3193 MenuItem modifyPID = new MenuItem();
3195 MenuItem modifyConservation = new MenuItem();
3197 CheckboxMenuItem autoCalculate = null;
3199 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3200 "Sort Alignment With New Tree", true);
3202 Menu sortByTreeMenu = new Menu();
3204 MenuItem inputText = new MenuItem();
3206 MenuItem documentation = new MenuItem();
3208 MenuItem about = new MenuItem();
3210 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3212 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3214 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3216 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3218 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3220 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3222 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3224 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3226 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3229 * Initialise menus and other items
3233 private void jbInit() throws Exception
3235 setMenuBar(alignFrameMenuBar);
3238 * Configure File menu items and actions
3241 .setLabel(MessageManager.getString("label.input_from_textbox"));
3242 inputText.addActionListener(this);
3243 Menu outputTextboxMenu = new Menu(
3244 MessageManager.getString("label.out_to_textbox"));
3245 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3247 MenuItem item = new MenuItem(ff);
3249 item.addActionListener(new java.awt.event.ActionListener()
3252 public void actionPerformed(ActionEvent e)
3254 outputText_actionPerformed(e);
3258 outputTextboxMenu.add(item);
3260 closeMenuItem.addActionListener(this);
3261 loadApplication.addActionListener(this);
3262 loadTree.addActionListener(this);
3263 loadAnnotations.addActionListener(this);
3264 outputFeatures.addActionListener(this);
3265 outputAnnotations.addActionListener(this);
3268 * Configure Edit menu items and actions
3270 undoMenuItem.setEnabled(false);
3271 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3272 undoMenuItem.addActionListener(this);
3273 redoMenuItem.setEnabled(false);
3274 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3275 redoMenuItem.addActionListener(this);
3276 copy.setLabel(MessageManager.getString("action.copy"));
3277 copy.addActionListener(this);
3278 cut.setLabel(MessageManager.getString("action.cut"));
3279 cut.addActionListener(this);
3280 delete.setLabel(MessageManager.getString("action.delete"));
3281 delete.addActionListener(this);
3282 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3283 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3284 pasteNew.addActionListener(this);
3285 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3286 pasteThis.addActionListener(this);
3287 remove2LeftMenuItem.setLabel(MessageManager
3288 .getString("action.remove_left"));
3289 remove2LeftMenuItem.addActionListener(this);
3290 remove2RightMenuItem.setLabel(MessageManager
3291 .getString("action.remove_right"));
3292 remove2RightMenuItem.addActionListener(this);
3293 removeGappedColumnMenuItem.setLabel(MessageManager
3294 .getString("action.remove_empty_columns"));
3295 removeGappedColumnMenuItem.addActionListener(this);
3296 removeAllGapsMenuItem.setLabel(MessageManager
3297 .getString("action.remove_all_gaps"));
3298 removeAllGapsMenuItem.addActionListener(this);
3299 removeRedundancyMenuItem.setLabel(MessageManager
3300 .getString("action.remove_redundancy"));
3301 removeRedundancyMenuItem.addActionListener(this);
3304 * Configure Select menu items and actions
3306 findMenuItem.setLabel(MessageManager.getString("action.find"));
3307 findMenuItem.addActionListener(this);
3308 selectAllSequenceMenuItem.addActionListener(this);
3309 deselectAllSequenceMenuItem.addActionListener(this);
3310 invertSequenceMenuItem.setLabel(MessageManager
3311 .getString("action.invert_sequence_selection"));
3312 invertSequenceMenuItem.addActionListener(this);
3313 invertColSel.setLabel(MessageManager
3314 .getString("action.invert_column_selection"));
3315 invertColSel.addActionListener(this);
3316 deleteGroups.setLabel(MessageManager
3317 .getString("action.undefine_groups"));
3318 deleteGroups.addActionListener(this);
3319 grpsFromSelection.setLabel(MessageManager
3320 .getString("action.make_groups_selection"));
3321 grpsFromSelection.addActionListener(this);
3322 createGroup.setLabel(MessageManager.getString("action.create_group"));
3323 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3324 annotationColumnSelection.setLabel(MessageManager
3325 .getString("action.select_by_annotation"));
3326 annotationColumnSelection.addActionListener(this);
3329 * Configure View menu items and actions
3331 newView.setLabel(MessageManager.getString("action.new_view"));
3332 newView.addActionListener(this);
3333 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3334 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3335 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3336 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3338 .setLabel(MessageManager.getString("label.selected_columns"));
3339 hideSequences.setLabel(MessageManager
3340 .getString("label.selected_sequences"));
3341 hideAllButSelection.setLabel(MessageManager
3342 .getString("label.all_but_selected_region"));
3343 hideAllSelection.setLabel(MessageManager
3344 .getString("label.selected_region"));
3345 showAllHidden.setLabel(MessageManager
3346 .getString("label.all_sequences_columns"));
3347 showColumns.addActionListener(this);
3348 showSeqs.addActionListener(this);
3349 hideColumns.addActionListener(this);
3350 hideSequences.addActionListener(this);
3351 hideAllButSelection.addActionListener(this);
3352 hideAllSelection.addActionListener(this);
3353 showAllHidden.addActionListener(this);
3354 featureSettings.setLabel(MessageManager
3355 .getString("action.feature_settings"));
3356 featureSettings.addActionListener(this);
3357 sequenceFeatures.setLabel(MessageManager
3358 .getString("label.show_sequence_features"));
3359 sequenceFeatures.addItemListener(this);
3360 sequenceFeatures.setState(false);
3361 followMouseOverFlag.setLabel(MessageManager
3362 .getString("label.automatic_scrolling"));
3363 followMouseOverFlag.addItemListener(this);
3364 alProperties.addActionListener(this);
3365 overviewMenuItem.setLabel(MessageManager
3366 .getString("label.overview_window"));
3367 overviewMenuItem.addActionListener(this);
3370 * Configure Annotations menu items and actions
3372 annotationPanelMenuItem.setLabel(MessageManager
3373 .getString("label.show_annotations"));
3374 annotationPanelMenuItem.addItemListener(this);
3375 showGroupConsensus.setLabel(MessageManager
3376 .getString("label.group_consensus"));
3377 showGroupConservation.setLabel(MessageManager
3378 .getString("label.group_conservation"));
3379 showConsensusHistogram.setLabel(MessageManager
3380 .getString("label.show_consensus_histogram"));
3381 showSequenceLogo.setLabel(MessageManager
3382 .getString("label.show_consensus_logo"));
3383 normSequenceLogo.setLabel(MessageManager
3384 .getString("label.norm_consensus_logo"));
3385 applyAutoAnnotationSettings.setLabel(MessageManager
3386 .getString("label.apply_all_groups"));
3387 applyAutoAnnotationSettings.setState(true);
3388 Menu autoAnnMenu = new Menu(
3389 MessageManager.getString("label.autocalculated_annotation"));
3390 showGroupConsensus.addItemListener(this);
3391 showGroupConservation.addItemListener(this);
3392 showConsensusHistogram.addItemListener(this);
3393 showSequenceLogo.addItemListener(this);
3394 normSequenceLogo.addItemListener(this);
3395 applyAutoAnnotationSettings.addItemListener(this);
3396 showAlignmentAnnotations = new CheckboxMenuItem(
3397 MessageManager.getString("label.show_all_al_annotations"));
3398 showSequenceAnnotations = new CheckboxMenuItem(
3399 MessageManager.getString("label.show_all_seq_annotations"));
3400 sortAnnBySequence = new CheckboxMenuItem(
3401 MessageManager.getString("label.sort_annotations_by_sequence"));
3402 sortAnnByLabel = new CheckboxMenuItem(
3403 MessageManager.getString("label.sort_annotations_by_label"));
3404 showAutoFirst = new CheckboxMenuItem(
3405 MessageManager.getString("label.show_first"));
3406 showAutoFirst.setState(false); // pending applet parameter
3407 setShowAutoCalculatedAbove(showAutoFirst.getState());
3408 showAutoLast = new CheckboxMenuItem(
3409 MessageManager.getString("label.show_last"));
3410 showAutoLast.setState(!showAutoFirst.getState());
3411 showAlignmentAnnotations.addItemListener(this);
3412 showSequenceAnnotations.addItemListener(this);
3413 sortAnnBySequence.addItemListener(this);
3414 sortAnnByLabel.addItemListener(this);
3415 showAutoFirst.addItemListener(this);
3416 showAutoLast.addItemListener(this);
3419 * Configure Format menu items and actions
3421 font.setLabel(MessageManager.getString("action.font"));
3422 font.addActionListener(this);
3423 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3424 scaleAbove.setState(true);
3425 scaleAbove.setEnabled(false);
3426 scaleAbove.addItemListener(this);
3427 scaleLeft.setEnabled(false);
3428 scaleLeft.setState(true);
3429 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3430 scaleLeft.addItemListener(this);
3431 scaleRight.setEnabled(false);
3432 scaleRight.setState(true);
3433 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3434 scaleRight.addItemListener(this);
3435 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3436 viewBoxesMenuItem.setState(true);
3437 viewBoxesMenuItem.addItemListener(this);
3438 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3439 viewTextMenuItem.setState(true);
3440 viewTextMenuItem.addItemListener(this);
3441 colourTextMenuItem.setLabel(MessageManager
3442 .getString("label.colour_text"));
3443 colourTextMenuItem.addItemListener(this);
3444 displayNonconservedMenuItem.setLabel(MessageManager
3445 .getString("label.show_non_conversed"));
3446 displayNonconservedMenuItem.addItemListener(this);
3447 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3448 wrapMenuItem.addItemListener(this);
3449 renderGapsMenuItem.setLabel(MessageManager
3450 .getString("action.show_gaps"));
3451 renderGapsMenuItem.setState(true);
3452 renderGapsMenuItem.addItemListener(this);
3453 centreColumnLabelFlag.setLabel(MessageManager
3454 .getString("label.centre_column_labels"));
3455 centreColumnLabelFlag.addItemListener(this);
3456 seqLimits.setState(true);
3457 seqLimits.setLabel(MessageManager
3458 .getString("label.show_sequence_limits"));
3459 seqLimits.addItemListener(this);
3462 * Configure Colour menu items and actions
3464 applyToAllGroups.setLabel(MessageManager
3465 .getString("label.apply_colour_to_all_groups"));
3466 applyToAllGroups.setState(true);
3467 applyToAllGroups.addItemListener(this);
3468 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3469 clustalColour.addActionListener(this);
3470 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3471 zappoColour.addActionListener(this);
3472 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3473 taylorColour.addActionListener(this);
3474 hydrophobicityColour.setLabel(MessageManager
3475 .getString("label.hydrophobicity"));
3476 hydrophobicityColour.addActionListener(this);
3478 .setLabel(MessageManager.getString("label.helix_propensity"));
3479 helixColour.addActionListener(this);
3480 strandColour.setLabel(MessageManager
3481 .getString("label.strand_propensity"));
3482 strandColour.addActionListener(this);
3483 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3484 turnColour.addActionListener(this);
3485 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3486 buriedColour.addActionListener(this);
3487 purinePyrimidineColour.setLabel(MessageManager
3488 .getString("label.purine_pyrimidine"));
3489 purinePyrimidineColour.addActionListener(this);
3490 // RNAInteractionColour.setLabel(MessageManager
3491 // .getString("label.rna_interaction"));
3492 // RNAInteractionColour.addActionListener(this);
3493 RNAHelixColour.setLabel(MessageManager
3494 .getString("action.by_rna_helixes"));
3495 RNAHelixColour.addActionListener(this);
3496 userDefinedColour.setLabel(MessageManager
3497 .getString("action.user_defined"));
3498 userDefinedColour.addActionListener(this);
3499 PIDColour.setLabel(MessageManager
3500 .getString("label.percentage_identity"));
3501 PIDColour.addActionListener(this);
3502 BLOSUM62Colour.setLabel(MessageManager
3503 .getString("label.blosum62_score"));
3504 BLOSUM62Colour.addActionListener(this);
3506 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3507 // it will be enabled only if a score file is provided
3508 tcoffeeColour.setEnabled(false);
3509 tcoffeeColour.addActionListener(this);
3510 conservationMenuItem.setLabel(MessageManager
3511 .getString("action.by_conservation"));
3512 conservationMenuItem.addItemListener(this);
3513 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3514 noColourmenuItem.addActionListener(this);
3515 abovePIDThreshold.setLabel(MessageManager
3516 .getString("label.above_identity_threshold"));
3517 abovePIDThreshold.addItemListener(this);
3518 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3519 nucleotideColour.addActionListener(this);
3520 modifyPID.setLabel(MessageManager
3521 .getString("label.modify_identity_threshold"));
3522 modifyPID.addActionListener(this);
3523 modifyConservation.setLabel(MessageManager
3524 .getString("label.modify_conservation_threshold"));
3525 modifyConservation.addActionListener(this);
3526 annotationColour.setLabel(MessageManager
3527 .getString("action.by_annotation"));
3528 annotationColour.addActionListener(this);
3531 * Configure Calculate menu items and actions
3533 sortPairwiseMenuItem.setLabel(MessageManager
3534 .getString("action.by_pairwise_id"));
3535 sortPairwiseMenuItem.addActionListener(this);
3536 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3537 sortIDMenuItem.addActionListener(this);
3538 sortLengthMenuItem.setLabel(MessageManager
3539 .getString("action.by_length"));
3540 sortLengthMenuItem.addActionListener(this);
3541 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3542 sortGroupMenuItem.addActionListener(this);
3543 pairwiseAlignmentMenuItem.setLabel(MessageManager
3544 .getString("action.pairwise_alignment"));
3545 pairwiseAlignmentMenuItem.addActionListener(this);
3546 PCAMenuItem.setLabel(MessageManager
3547 .getString("label.principal_component_analysis"));
3548 PCAMenuItem.addActionListener(this);
3549 autoCalculate = new CheckboxMenuItem(
3550 MessageManager.getString("label.autocalculate_consensus"), true);
3551 averageDistanceTreeMenuItem.setLabel(MessageManager
3552 .getString("label.average_distance_identity"));
3553 averageDistanceTreeMenuItem.addActionListener(this);
3554 neighbourTreeMenuItem.setLabel(MessageManager
3555 .getString("label.neighbour_joining_identity"));
3556 neighbourTreeMenuItem.addActionListener(this);
3557 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3558 .getString("label.average_distance_bloslum62"));
3559 avDistanceTreeBlosumMenuItem.addActionListener(this);
3560 njTreeBlosumMenuItem.setLabel(MessageManager
3561 .getString("label.neighbour_blosum62"));
3562 njTreeBlosumMenuItem.addActionListener(this);
3563 sortByTreeMenu.setLabel(MessageManager
3564 .getString("action.by_tree_order"));
3565 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3566 Menu calculateTreeMenu = new Menu(
3567 MessageManager.getString("action.calculate_tree"));
3568 autoCalculate.addItemListener(this);
3569 sortByTree.addItemListener(this);
3572 * Configure Help menu items and actions
3574 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3575 documentation.setLabel(MessageManager.getString("label.documentation"));
3576 documentation.addActionListener(this);
3577 about.setLabel(MessageManager.getString("label.about"));
3578 about.addActionListener(this);
3581 * Add top level menus to frame
3583 alignFrameMenuBar.add(fileMenu);
3584 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3585 alignFrameMenuBar.add(editMenu);
3586 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3587 alignFrameMenuBar.add(selectMenu);
3588 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3589 alignFrameMenuBar.add(viewMenu);
3590 Menu annotationsMenu = new Menu(
3591 MessageManager.getString("action.annotations"));
3592 alignFrameMenuBar.add(annotationsMenu);
3593 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3594 alignFrameMenuBar.add(formatMenu);
3595 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3596 alignFrameMenuBar.add(colourMenu);
3597 Menu calculateMenu = new Menu(
3598 MessageManager.getString("action.calculate"));
3599 alignFrameMenuBar.add(calculateMenu);
3600 alignFrameMenuBar.add(helpMenu);
3605 fileMenu.add(inputText);
3606 fileMenu.add(loadTree);
3607 fileMenu.add(loadAnnotations);
3608 fileMenu.addSeparator();
3609 fileMenu.add(outputTextboxMenu);
3610 fileMenu.add(outputFeatures);
3611 fileMenu.add(outputAnnotations);
3612 if (jalviewServletURL != null)
3614 fileMenu.add(loadApplication);
3616 fileMenu.addSeparator();
3617 fileMenu.add(closeMenuItem);
3622 editMenu.add(undoMenuItem);
3623 editMenu.add(redoMenuItem);
3626 pasteMenu.add(pasteNew);
3627 pasteMenu.add(pasteThis);
3628 editMenu.add(pasteMenu);
3629 editMenu.add(delete);
3630 editMenu.addSeparator();
3631 editMenu.add(remove2LeftMenuItem);
3632 editMenu.add(remove2RightMenuItem);
3633 editMenu.add(removeGappedColumnMenuItem);
3634 editMenu.add(removeAllGapsMenuItem);
3635 editMenu.add(removeRedundancyMenuItem);
3640 selectMenu.add(findMenuItem);
3641 selectMenu.addSeparator();
3642 selectMenu.add(selectAllSequenceMenuItem);
3643 selectMenu.add(deselectAllSequenceMenuItem);
3644 selectMenu.add(invertSequenceMenuItem);
3645 selectMenu.add(invertColSel);
3646 selectMenu.add(createGroup);
3647 selectMenu.add(unGroup);
3648 selectMenu.add(grpsFromSelection);
3649 selectMenu.add(deleteGroups);
3650 selectMenu.add(annotationColumnSelection);
3655 viewMenu.add(newView);
3656 viewMenu.addSeparator();
3657 showMenu.add(showColumns);
3658 showMenu.add(showSeqs);
3659 showMenu.add(showAllHidden);
3660 viewMenu.add(showMenu);
3661 hideMenu.add(hideColumns);
3662 hideMenu.add(hideSequences);
3663 hideMenu.add(hideAllSelection);
3664 hideMenu.add(hideAllButSelection);
3665 viewMenu.add(hideMenu);
3666 viewMenu.addSeparator();
3667 viewMenu.add(followMouseOverFlag);
3668 viewMenu.addSeparator();
3669 viewMenu.add(sequenceFeatures);
3670 viewMenu.add(featureSettings);
3671 viewMenu.addSeparator();
3672 viewMenu.add(alProperties);
3673 viewMenu.addSeparator();
3674 viewMenu.add(overviewMenuItem);
3679 annotationsMenu.add(annotationPanelMenuItem);
3680 annotationsMenu.addSeparator();
3681 annotationsMenu.add(showAlignmentAnnotations);
3682 annotationsMenu.add(showSequenceAnnotations);
3683 annotationsMenu.add(sortAnnBySequence);
3684 annotationsMenu.add(sortAnnByLabel);
3685 annotationsMenu.addSeparator();
3686 autoAnnMenu.add(showAutoFirst);
3687 autoAnnMenu.add(showAutoLast);
3688 autoAnnMenu.addSeparator();
3689 autoAnnMenu.add(applyAutoAnnotationSettings);
3690 autoAnnMenu.add(showConsensusHistogram);
3691 autoAnnMenu.add(showSequenceLogo);
3692 autoAnnMenu.add(normSequenceLogo);
3693 autoAnnMenu.addSeparator();
3694 autoAnnMenu.add(showGroupConservation);
3695 autoAnnMenu.add(showGroupConsensus);
3696 annotationsMenu.add(autoAnnMenu);
3701 formatMenu.add(font);
3702 formatMenu.add(seqLimits);
3703 formatMenu.add(wrapMenuItem);
3704 formatMenu.add(scaleAbove);
3705 formatMenu.add(scaleLeft);
3706 formatMenu.add(scaleRight);
3707 formatMenu.add(viewBoxesMenuItem);
3708 formatMenu.add(viewTextMenuItem);
3709 formatMenu.add(colourTextMenuItem);
3710 formatMenu.add(displayNonconservedMenuItem);
3711 formatMenu.add(renderGapsMenuItem);
3712 formatMenu.add(centreColumnLabelFlag);
3717 colourMenu.add(applyToAllGroups);
3718 colourMenu.addSeparator();
3719 colourMenu.add(noColourmenuItem);
3720 colourMenu.add(clustalColour);
3721 colourMenu.add(BLOSUM62Colour);
3722 colourMenu.add(PIDColour);
3723 colourMenu.add(zappoColour);
3724 colourMenu.add(taylorColour);
3725 colourMenu.add(hydrophobicityColour);
3726 colourMenu.add(helixColour);
3727 colourMenu.add(strandColour);
3728 colourMenu.add(turnColour);
3729 colourMenu.add(buriedColour);
3730 colourMenu.add(nucleotideColour);
3731 colourMenu.add(purinePyrimidineColour);
3732 // colourMenu.add(RNAInteractionColour);
3733 colourMenu.add(tcoffeeColour);
3734 colourMenu.add(userDefinedColour);
3735 colourMenu.addSeparator();
3736 colourMenu.add(conservationMenuItem);
3737 colourMenu.add(modifyConservation);
3738 colourMenu.add(abovePIDThreshold);
3739 colourMenu.add(modifyPID);
3740 colourMenu.add(annotationColour);
3741 colourMenu.add(RNAHelixColour);
3746 sortMenu.add(sortIDMenuItem);
3747 sortMenu.add(sortLengthMenuItem);
3748 sortMenu.add(sortByTreeMenu);
3749 sortMenu.add(sortGroupMenuItem);
3750 sortMenu.add(sortPairwiseMenuItem);
3751 calculateMenu.add(sortMenu);
3752 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3753 calculateTreeMenu.add(neighbourTreeMenuItem);
3754 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3755 calculateTreeMenu.add(njTreeBlosumMenuItem);
3756 calculateMenu.add(calculateTreeMenu);
3757 calculateMenu.addSeparator();
3758 calculateMenu.add(pairwiseAlignmentMenuItem);
3759 calculateMenu.add(PCAMenuItem);
3760 calculateMenu.add(autoCalculate);
3761 calculateMenu.add(sortByTree);
3766 helpMenu.add(documentation);
3767 helpMenu.add(about);
3772 statusBar.setBackground(Color.white);
3773 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3774 statusBar.setText(MessageManager.getString("label.status_bar"));
3775 this.add(statusBar, BorderLayout.SOUTH);
3779 public void setStatus(String string)
3781 statusBar.setText(string);
3784 MenuItem featureSettings = new MenuItem();
3786 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3788 MenuItem annotationColour = new MenuItem();
3790 MenuItem annotationColumnSelection = new MenuItem();
3792 MenuItem invertColSel = new MenuItem();
3794 MenuItem showColumns = new MenuItem();
3796 MenuItem showSeqs = new MenuItem();
3798 MenuItem hideColumns = new MenuItem();
3800 MenuItem hideSequences = new MenuItem();
3802 MenuItem hideAllButSelection = new MenuItem();
3804 MenuItem hideAllSelection = new MenuItem();
3806 MenuItem showAllHidden = new MenuItem();
3808 MenuItem newView = new MenuItem();
3810 private CheckboxMenuItem showAlignmentAnnotations;
3812 private CheckboxMenuItem showSequenceAnnotations;
3814 private CheckboxMenuItem sortAnnBySequence;
3816 private CheckboxMenuItem sortAnnByLabel;
3818 private CheckboxMenuItem showAutoFirst;
3820 private CheckboxMenuItem showAutoLast;
3822 private SplitFrame splitFrame;
3825 * Attach the alignFrame panels after embedding menus, if necessary. This used
3826 * to be called setEmbedded, but is now creates the dropdown menus in a
3827 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3829 * @param reallyEmbedded
3830 * true to attach the view to the applet area on the page rather than
3833 public void createAlignFrameWindow(boolean reallyEmbedded)
3837 embedAlignFrameInApplet(viewport.applet);
3842 // test and embed menu bar if necessary.
3844 if (embedMenuIfNeeded(alignPanel))
3847 * adjust for status bar height too. ? pointless as overridden by layout
3850 alignPanel.setSize(getSize().width,
3851 getSize().height - statusBar.getHeight());
3853 add(statusBar, BorderLayout.SOUTH);
3854 add(alignPanel, BorderLayout.CENTER);
3855 // and register with the applet so it can pass external API calls to us
3856 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3862 * Add the components of this AlignFrame to the applet container.
3866 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3869 // Explicitly build the embedded menu panel for the on-page applet
3871 // view cannot be closed if its actually on the page
3872 fileMenu.remove(closeMenuItem);
3873 fileMenu.remove(3); // Remove Separator
3874 // construct embedded menu, using default font
3875 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3876 // and actually add the components to the applet area
3877 theApplet.setLayout(new BorderLayout());
3878 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3879 theApplet.add(statusBar, BorderLayout.SOUTH);
3880 // TODO should size be left to the layout manager?
3881 alignPanel.setSize(theApplet.getSize().width,
3882 theApplet.getSize().height - embeddedMenu.getHeight()
3883 - statusBar.getHeight());
3884 theApplet.add(alignPanel, BorderLayout.CENTER);
3885 final AlignFrame me = this;
3886 theApplet.addFocusListener(new FocusListener()
3890 public void focusLost(FocusEvent e)
3892 if (theApplet.currentAlignFrame == me)
3894 theApplet.currentAlignFrame = null;
3899 public void focusGained(FocusEvent e)
3901 theApplet.currentAlignFrame = me;
3904 theApplet.validate();
3908 * create a new binding between structures in an existing jmol viewer instance
3909 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3910 * this does not open a new Jmol window, or modify the display of the
3911 * structures in the original jmol window. Note This method doesn't work
3912 * without an additional javascript library to exchange messages between the
3913 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3916 * JmolViewer instance
3917 * @param sequenceIds
3918 * - sequence Ids to search for associations
3920 public SequenceStructureBinding addStructureViewInstance(
3921 Object jmolviewer, String[] sequenceIds)
3923 Viewer viewer = null;
3926 viewer = (Viewer) jmolviewer;
3927 } catch (ClassCastException ex)
3929 System.err.println("Unsupported viewer object :"
3930 + jmolviewer.getClass());
3934 System.err.println("Can't use this object as a structure viewer:"
3935 + jmolviewer.getClass());
3938 SequenceI[] seqs = null;
3939 if (sequenceIds == null || sequenceIds.length == 0)
3941 seqs = viewport.getAlignment().getSequencesArray();
3945 Vector sqi = new Vector();
3946 AlignmentI al = viewport.getAlignment();
3947 for (int sid = 0; sid < sequenceIds.length; sid++)
3949 SequenceI sq = al.findName(sequenceIds[sid]);
3957 seqs = new SequenceI[sqi.size()];
3958 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3960 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3968 AAStructureBindingModel jmv = null;
3969 // TODO: search for a jmv that involves viewer
3971 { // create a new viewer/jalview binding.
3972 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3979 * bind a pdb file to a sequence in the current view
3982 * - sequenceId within the dataset.
3983 * @param pdbEntryString
3984 * - the short name for the PDB file
3986 * - pdb file - either a URL or a valid PDB file.
3987 * @return true if binding was as success TODO: consider making an exception
3988 * structure for indicating when PDB parsing or sequenceId location
3991 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3994 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3995 boolean needtoadd = false;
3996 if (toaddpdb != null)
3998 Vector pdbe = toaddpdb.getAllPDBEntries();
3999 PDBEntry pdbentry = null;
4000 if (pdbe != null && pdbe.size() > 0)
4002 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4004 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4005 if (!pdbentry.getId().equals(pdbEntryString)
4006 && !pdbentry.getFile().equals(pdbFile))
4016 if (pdbentry == null)
4018 pdbentry = new PDBEntry();
4019 pdbentry.setId(pdbEntryString);
4020 pdbentry.setFile(pdbFile);
4021 needtoadd = true; // add this new entry to sequence.
4023 // resolve data source
4024 // TODO: this code should be a refactored to an io package
4025 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4026 pdbFile, FileFormat.PDB);
4027 if (protocol == null)
4033 pdbentry.setProperty("protocol", protocol);
4034 toaddpdb.addPDBId(pdbentry);
4035 alignPanel.getStructureSelectionManager()
4036 .registerPDBEntry(pdbentry);
4042 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4046 Vector sequences = new Vector();
4047 for (int i = 0; i < seqs.length; i++)
4049 if (seqs[i] != null)
4051 sequences.addElement(new Object[] { seqs[i],
4052 (chains != null) ? chains[i] : null });
4055 seqs = new SequenceI[sequences.size()];
4056 chains = new String[sequences.size()];
4057 for (int i = 0, isize = sequences.size(); i < isize; i++)
4059 Object[] oj = (Object[]) sequences.elementAt(i);
4061 seqs[i] = (SequenceI) oj[0];
4062 chains[i] = (String) oj[1];
4065 return new Object[] { seqs, chains };
4069 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4070 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4072 // Scrub any null sequences from the array
4073 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4074 seqs = (SequenceI[]) sqch[0];
4075 chains = (String[]) sqch[1];
4076 if (seqs == null || seqs.length == 0)
4079 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4081 if (protocol == null)
4083 String sourceType = (String) pdb.getProperty("protocol");
4086 protocol = DataSourceType.valueOf(sourceType);
4087 } catch (IllegalArgumentException e)
4091 if (protocol == null)
4093 System.err.println("Couldn't work out protocol to open structure: "
4098 if (applet.useXtrnalSviewer)
4100 // register the association(s) and quit, don't create any windows.
4101 if (StructureSelectionManager.getStructureSelectionManager(applet)
4102 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4104 System.err.println("Failed to map " + pdb.getFile() + " ("
4105 + protocol + ") to any sequences");
4109 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4111 // can only do alignments with Jmol
4112 // find the last jmol window assigned to this alignment
4113 AppletJmol ajm = null, tajm;
4114 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4115 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4117 tajm = (AppletJmol) jmols.elementAt(i);
4118 if (tajm.ap.alignFrame == this)
4127 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4128 // try and add the pdb structure
4133 // otherwise, create a new window
4134 if (applet.jmolAvailable)
4136 new AppletJmol(pdb, seqs, chains, alignPanel,
4138 applet.lastFrameX += 40;
4139 applet.lastFrameY += 40;
4143 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4148 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4149 SequenceI[][] seqs, String[][] chains, String[] protocols)
4151 // TODO Auto-generated method stub
4152 System.err.println("Aligned Structure View: Not yet implemented.");
4156 * modify the current selection, providing the user has not made a selection
4160 * - sequences from this alignment
4162 * - columns to be selected on the alignment
4164 public void select(SequenceGroup sel, ColumnSelection csel)
4166 alignPanel.seqPanel.selection(sel, csel, null);
4169 public void scrollTo(int row, int column)
4171 alignPanel.seqPanel.scrollTo(row, column);
4174 public void scrollToRow(int row)
4176 alignPanel.seqPanel.scrollToRow(row);
4179 public void scrollToColumn(int column)
4181 alignPanel.seqPanel.scrollToColumn(column);
4185 * @return the alignments unique ID.
4187 public String getSequenceSetId()
4189 return viewport.getSequenceSetId();
4193 * Load the (T-Coffee) score file from the specified url
4196 * File/URL/T-COFFEE score file contents
4197 * @throws IOException
4198 * @return true if alignment was annotated with data from source
4200 public boolean loadScoreFile(String source) throws IOException
4203 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4204 AppletFormatAdapter.checkProtocol(source));
4205 if (!file.isValid())
4207 // TODO: raise dialog for gui
4208 System.err.println("Problems parsing T-Coffee scores: "
4209 + file.getWarningMessage());
4210 System.err.println("Origin was:\n" + source);
4215 * check that the score matrix matches the alignment dimensions
4218 if ((aln = viewport.getAlignment()) != null
4219 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4222 // TODO: raise a dialog box here rather than bomb out.
4224 .println("The scores matrix does not match the alignment dimensions");
4228 // TODO add parameter to indicate if matching should be done
4229 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4231 alignPanel.fontChanged();
4232 tcoffeeColour.setEnabled(true);
4233 // switch to this color
4234 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4239 System.err.println("Problems resolving T-Coffee scores:");
4240 if (file.getWarningMessage() != null)
4242 System.err.println(file.getWarningMessage());
4248 public SplitFrame getSplitFrame()
4250 return this.splitFrame;
4253 public void setSplitFrame(SplitFrame sf)
4255 this.splitFrame = sf;
4258 // may not need this
4260 public void setShowSeqFeatures(boolean b)
4262 // showSeqFeatures.setSelected(b);
4263 viewport.setShowSequenceFeatures(b);
4268 public void setMenusForViewport()
4270 // setMenusFromViewport(viewport);
4275 public void refreshFeatureUI(boolean enableIfNecessary)
4277 if (enableIfNecessary)
4279 sequenceFeatures.setState(true);
4280 alignPanel.av.setShowSequenceFeatures(true);
4285 public FeatureSettingsControllerI getFeatureSettingsUI()
4287 return alignPanel.av.featureSettings;