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.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
110 import java.net.URLEncoder;
111 import java.util.Arrays;
112 import java.util.Deque;
113 import java.util.HashMap;
114 import java.util.List;
115 import java.util.Map;
116 import java.util.StringTokenizer;
117 import java.util.Vector;
119 import org.jmol.viewer.Viewer;
121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
122 ItemListener, KeyListener, AlignViewControllerGuiI
124 public AlignViewControllerI avc;
126 public AlignmentPanel alignPanel;
128 public AlignViewport viewport;
130 // width and height may be overridden by applet parameters
131 int frameWidth = 700;
133 int frameHeight = 500;
135 String jalviewServletURL;
138 * Flag for showing autocalculated consensus above or below other consensus
141 private boolean showAutoCalculatedAbove;
143 private SequenceAnnotationOrder annotationSortOrder;
146 * Constructor that creates the frame and adds it to the display.
153 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156 this(al, applet, title, embedded, true);
160 * Constructor that optionally allows the frame to be displayed or only
167 * @param addToDisplay
169 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
170 boolean embedded, boolean addToDisplay)
172 this(al, null, null, applet, title, embedded, addToDisplay);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 HiddenColumns hidden, JalviewLite applet, String title,
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet, String title,
184 boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
238 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
239 followMouseOverFlag.setState(viewport.isFollowHighlight());
240 showGroupConsensus.setState(viewport.isShowGroupConsensus());
241 showGroupConservation.setState(viewport.isShowGroupConservation());
242 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
243 showSequenceLogo.setState(viewport.isShowSequenceLogo());
244 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
245 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
246 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
247 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
248 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showAlignmentAnnotations.setState(true);
250 showSequenceAnnotations.setState(false);
252 seqLimits.setState(viewport.getShowJVSuffix());
256 String param = applet.getParameter("sortBy");
259 if (param.equalsIgnoreCase("Id"))
261 sortIDMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Pairwise Identity"))
265 sortPairwiseMenuItem_actionPerformed();
267 else if (param.equalsIgnoreCase("Length"))
269 sortLengthMenuItem_actionPerformed();
273 param = applet.getParameter("wrap");
276 if (param.equalsIgnoreCase("true"))
278 wrapMenuItem.setState(true);
279 wrapMenuItem_actionPerformed();
282 param = applet.getParameter("centrecolumnlabels");
285 centreColumnLabelFlag.setState(true);
286 centreColumnLabelFlag_stateChanged();
290 if (viewport.getAlignment().isNucleotide())
292 conservationMenuItem.setEnabled(false);
293 clustalColour.setEnabled(false);
294 BLOSUM62Colour.setEnabled(false);
295 zappoColour.setEnabled(false);
296 taylorColour.setEnabled(false);
297 hydrophobicityColour.setEnabled(false);
298 helixColour.setEnabled(false);
299 strandColour.setEnabled(false);
300 turnColour.setEnabled(false);
301 buriedColour.setEnabled(false);
302 viewport.updateStrucConsensus(alignPanel);
303 if (viewport.getAlignment().hasRNAStructure())
305 RNAHelixColour.setEnabled(true);
309 RNAHelixColour.setEnabled(false);
314 RNAHelixColour.setEnabled(false);
315 purinePyrimidineColour.setEnabled(false);
316 nucleotideColour.setEnabled(false);
318 // Some JVMS send keyevents to Top frame or lowest panel,
319 // Havent worked out why yet. So add to both this frame and seqCanvas for
321 this.addKeyListener(this);
322 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
323 alignPanel.idPanel.idCanvas.addKeyListener(this);
324 alignPanel.scalePanel.addKeyListener(this);
325 alignPanel.annotationPanel.addKeyListener(this);
326 alignPanel.annotationPanelHolder.addKeyListener(this);
327 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
328 alignPanel.alabels.addKeyListener(this);
330 setAnnotationsVisibility();
334 addToDisplay(embedded);
341 public void addToDisplay(boolean embedded)
343 createAlignFrameWindow(embedded);
345 alignPanel.adjustAnnotationHeight();
346 alignPanel.paintAlignment(true);
349 public AlignViewport getAlignViewport()
354 public SeqCanvas getSeqcanvas()
356 return alignPanel.seqPanel.seqCanvas;
360 * Load a features file onto the alignment
363 * file URL, content, or other resolvable path
365 * is protocol for accessing data referred to by file
368 public boolean parseFeaturesFile(String file, DataSourceType type)
370 return parseFeaturesFile(file, type, true);
374 * Load a features file onto the alignment
377 * file URL, content, or other resolvable path
379 * is protocol for accessing data referred to by file
380 * @param autoenabledisplay
381 * when true, display features flag will be automatically enabled if
382 * features are loaded
383 * @return true if data parsed as a features file
385 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
386 boolean autoenabledisplay)
388 boolean featuresFile = false;
391 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
392 .getFeatureRenderer().getFeatureColours();
393 boolean relaxedIdMatching = viewport.applet
394 .getDefaultParameter("relaxedidmatch", false);
395 featuresFile = new FeaturesFile(file, sourceType).parse(
396 viewport.getAlignment(), colours, true, relaxedIdMatching);
397 } catch (Exception ex)
399 ex.printStackTrace();
404 if (autoenabledisplay)
406 viewport.setShowSequenceFeatures(true);
407 sequenceFeatures.setState(true);
409 if (alignPanel.seqPanel.seqCanvas.fr != null)
411 // update the min/max ranges where necessary
412 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
414 if (viewport.featureSettings != null)
416 viewport.featureSettings.refreshTable();
418 alignPanel.paintAlignment(true);
419 statusBar.setText(MessageManager
420 .getString("label.successfully_added_features_alignment"));
426 public void keyPressed(KeyEvent evt)
428 ViewportRanges ranges = viewport.getRanges();
430 if (viewport.cursorMode
431 && ((evt.getKeyCode() >= KeyEvent.VK_0
432 && evt.getKeyCode() <= KeyEvent.VK_9)
433 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
434 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
435 && Character.isDigit(evt.getKeyChar()))
437 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
440 switch (evt.getKeyCode())
442 case 27: // escape key
443 deselectAllSequenceMenuItem_actionPerformed();
445 alignPanel.alabels.cancelDrag();
448 if (evt.isControlDown() || evt.isMetaDown())
450 cut_actionPerformed();
454 if (viewport.cursorMode && !evt.isControlDown())
456 alignPanel.seqPanel.setCursorColumn();
458 if (evt.isControlDown() || evt.isMetaDown())
460 copy_actionPerformed();
464 if (evt.isControlDown())
466 paste(evt.isShiftDown());
470 if (evt.isControlDown() || evt.isMetaDown())
472 selectAllSequenceMenuItem_actionPerformed();
475 case KeyEvent.VK_DOWN:
476 if (viewport.cursorMode)
478 alignPanel.seqPanel.moveCursor(0, 1);
482 moveSelectedSequences(false);
487 if (viewport.cursorMode)
489 alignPanel.seqPanel.moveCursor(0, -1);
493 moveSelectedSequences(true);
497 case KeyEvent.VK_LEFT:
498 if (evt.isAltDown() || !viewport.cursorMode)
500 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
504 alignPanel.seqPanel.moveCursor(-1, 0);
508 case KeyEvent.VK_RIGHT:
509 if (evt.isAltDown() || !viewport.cursorMode)
511 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
515 alignPanel.seqPanel.moveCursor(1, 0);
519 case KeyEvent.VK_SPACE:
520 if (viewport.cursorMode)
522 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
523 || evt.isShiftDown() || evt.isAltDown());
527 case KeyEvent.VK_DELETE:
528 case KeyEvent.VK_BACK_SPACE:
529 if (viewport.cursorMode)
531 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
532 || evt.isShiftDown() || evt.isAltDown());
536 cut_actionPerformed();
537 alignPanel.seqPanel.seqCanvas.repaint();
542 if (viewport.cursorMode)
544 alignPanel.seqPanel.setCursorRow();
548 if (viewport.cursorMode)
550 alignPanel.seqPanel.setCursorPosition();
554 case KeyEvent.VK_ENTER:
555 case KeyEvent.VK_COMMA:
556 if (viewport.cursorMode)
558 alignPanel.seqPanel.setCursorRowAndColumn();
563 if (viewport.cursorMode)
565 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
569 if (viewport.cursorMode)
571 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
576 viewport.cursorMode = !viewport.cursorMode;
577 statusBar.setText(MessageManager
578 .formatMessage("label.keyboard_editing_mode", new String[]
579 { (viewport.cursorMode ? "on" : "off") }));
580 if (viewport.cursorMode)
582 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
583 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
588 if (evt.isControlDown())
590 findMenuItem_actionPerformed();
596 boolean toggleSeqs = !evt.isControlDown();
597 boolean toggleCols = !evt.isShiftDown();
598 toggleHiddenRegions(toggleSeqs, toggleCols);
602 case KeyEvent.VK_PAGE_UP:
606 case KeyEvent.VK_PAGE_DOWN:
611 if (evt.isControlDown())
613 undoMenuItem_actionPerformed();
618 if (evt.isControlDown())
620 redoMenuItem_actionPerformed();
625 if (evt.isControlDown())
632 if (evt.isControlDown())
634 trimAlignment(false);
639 if (evt.isControlDown())
641 if (evt.isShiftDown())
643 this.removeAllGapsMenuItem_actionPerformed();
647 removeGappedColumnMenuItem_actionPerformed();
652 if (evt.isControlDown())
656 invertColSel_actionPerformed();
660 invertSequenceMenuItem_actionPerformed();
666 if (evt.isControlDown())
668 if (evt.isShiftDown())
670 this.unGroup_actionPerformed();
674 this.createGroup_actionPerformed();
680 if (evt.isControlDown())
682 this.deleteGroups_actionPerformed();
687 if (evt.isControlDown())
694 alignPanel.paintAlignment(true);
698 * called by key handler and the hide all/show all menu items
703 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
705 boolean hide = false;
706 SequenceGroup sg = viewport.getSelectionGroup();
707 if (!toggleSeqs && !toggleCols)
709 // Hide everything by the current selection - this is a hack - we do the
710 // invert and then hide
711 // first check that there will be visible columns after the invert.
712 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
713 && sg.getStartRes() <= sg.getEndRes()))
715 // now invert the sequence set, if required - empty selection implies
716 // that no hiding is required.
719 invertSequenceMenuItem_actionPerformed();
720 sg = viewport.getSelectionGroup();
724 viewport.expandColSelection(sg, true);
725 // finally invert the column selection and get the new sequence
726 // selection and indicate it should be hidden.
727 invertColSel_actionPerformed();
734 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
737 viewport.hideAllSelectedSeqs();
739 else if (!(toggleCols && viewport.hasSelectedColumns()))
741 viewport.showAllHiddenSeqs();
747 if (viewport.hasSelectedColumns())
749 viewport.hideSelectedColumns();
752 viewport.setSelectionGroup(sg);
757 viewport.showAllHiddenColumns();
759 viewport.sendSelection();
764 public void keyReleased(KeyEvent evt)
769 public void keyTyped(KeyEvent evt)
774 public void itemStateChanged(ItemEvent evt)
776 final Object source = evt.getSource();
777 if (source == displayNonconservedMenuItem)
779 displayNonconservedMenuItem_actionPerformed();
781 else if (source == colourTextMenuItem)
783 colourTextMenuItem_actionPerformed();
785 else if (source == wrapMenuItem)
787 wrapMenuItem_actionPerformed();
789 else if (source == scaleAbove)
791 viewport.setScaleAboveWrapped(scaleAbove.getState());
793 else if (source == scaleLeft)
795 viewport.setScaleLeftWrapped(scaleLeft.getState());
797 else if (source == scaleRight)
799 viewport.setScaleRightWrapped(scaleRight.getState());
801 else if (source == seqLimits)
803 seqLimits_itemStateChanged();
805 else if (source == viewBoxesMenuItem)
807 viewport.setShowBoxes(viewBoxesMenuItem.getState());
809 else if (source == viewTextMenuItem)
811 viewport.setShowText(viewTextMenuItem.getState());
813 else if (source == renderGapsMenuItem)
815 viewport.setRenderGaps(renderGapsMenuItem.getState());
817 else if (source == annotationPanelMenuItem)
819 boolean showAnnotations = annotationPanelMenuItem.getState();
820 showAlignmentAnnotations.setEnabled(showAnnotations);
821 showSequenceAnnotations.setEnabled(showAnnotations);
822 viewport.setShowAnnotation(showAnnotations);
823 alignPanel.setAnnotationVisible(showAnnotations);
825 else if (source == sequenceFeatures)
827 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
828 alignPanel.seqPanel.seqCanvas.repaint();
830 else if (source == showAlignmentAnnotations)
832 setAnnotationsVisibility();
834 else if (source == showSequenceAnnotations)
836 setAnnotationsVisibility();
838 else if (source == sortAnnBySequence)
840 boolean newState = sortAnnBySequence.getState();
841 sortAnnByLabel.setState(false);
842 setAnnotationSortOrder(
843 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
844 : SequenceAnnotationOrder.NONE);
845 setViewportAnnotationOrder();
847 else if (source == sortAnnByLabel)
849 boolean newState = sortAnnByLabel.getState();
850 sortAnnBySequence.setState(false);
851 setAnnotationSortOrder(
852 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
853 : SequenceAnnotationOrder.NONE);
854 setViewportAnnotationOrder();
856 else if (source == showAutoFirst)
858 showAutoLast.setState(!showAutoFirst.getState());
859 setShowAutoCalculatedAbove(showAutoFirst.getState());
860 setViewportAnnotationOrder();
862 else if (source == showAutoLast)
864 showAutoFirst.setState(!showAutoLast.getState());
865 setShowAutoCalculatedAbove(showAutoFirst.getState());
866 setViewportAnnotationOrder();
868 else if (source == conservationMenuItem)
870 conservationMenuItem_actionPerformed();
872 else if (source == abovePIDThreshold)
874 abovePIDThreshold_actionPerformed();
876 else if (source == applyToAllGroups)
878 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
880 else if (source == autoCalculate)
882 viewport.autoCalculateConsensus = autoCalculate.getState();
884 else if (source == sortByTree)
886 viewport.sortByTree = sortByTree.getState();
888 else if (source == this.centreColumnLabelFlag)
890 centreColumnLabelFlag_stateChanged();
892 else if (source == this.followMouseOverFlag)
894 mouseOverFlag_stateChanged();
896 else if (source == showGroupConsensus)
898 showGroupConsensus_actionPerformed();
900 else if (source == showGroupConservation)
902 showGroupConservation_actionPerformed();
904 else if (source == showSequenceLogo)
906 showSequenceLogo_actionPerformed();
908 else if (source == normSequenceLogo)
910 normSequenceLogo_actionPerformed();
912 else if (source == showConsensusHistogram)
914 showConsensusHistogram_actionPerformed();
916 else if (source == applyAutoAnnotationSettings)
918 applyAutoAnnotationSettings_actionPerformed();
920 alignPanel.paintAlignment(true);
924 * Set the visibility state of sequence-related and/or alignment-related
925 * annotations depending on checkbox selections, and repaint.
929 private void setAnnotationsVisibility()
931 boolean showForAlignment = showAlignmentAnnotations.getState();
932 boolean showForSequences = showSequenceAnnotations.getState();
933 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
935 for (AlignmentAnnotation aa : alignPanel.getAlignment()
936 .getAlignmentAnnotation())
938 boolean visible = (aa.sequenceRef == null ? showForAlignment
940 aa.visible = visible;
943 alignPanel.validateAnnotationDimensions(true);
948 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
950 this.annotationSortOrder = order;
954 * Set flags on the viewport that control annotation ordering
956 private void setViewportAnnotationOrder()
958 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
960 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
963 private void setShowAutoCalculatedAbove(boolean showAbove)
965 this.showAutoCalculatedAbove = showAbove;
968 private void mouseOverFlag_stateChanged()
970 viewport.setFollowHighlight(followMouseOverFlag.getState());
971 // TODO: could kick the scrollTo mechanism to reset view for current
975 private void centreColumnLabelFlag_stateChanged()
977 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
978 this.alignPanel.annotationPanel.repaint();
982 public void actionPerformed(ActionEvent evt)
984 viewport.applet.currentAlignFrame = this;
986 Object source = evt.getSource();
988 if (source == inputText)
990 inputText_actionPerformed();
992 else if (source == loadTree)
994 loadTree_actionPerformed();
996 else if (source == loadApplication)
998 launchFullApplication();
1000 else if (source == loadAnnotations)
1004 else if (source == outputAnnotations)
1006 outputAnnotations(true);
1008 else if (source == outputFeatures)
1010 outputFeatures(true, "Jalview");
1012 else if (source == closeMenuItem)
1014 closeMenuItem_actionPerformed();
1016 else if (source == copy)
1018 copy_actionPerformed();
1020 else if (source == undoMenuItem)
1022 undoMenuItem_actionPerformed();
1024 else if (source == redoMenuItem)
1026 redoMenuItem_actionPerformed();
1028 else if (source == inputText)
1030 inputText_actionPerformed();
1032 else if (source == closeMenuItem)
1034 closeMenuItem_actionPerformed();
1036 else if (source == undoMenuItem)
1038 undoMenuItem_actionPerformed();
1040 else if (source == redoMenuItem)
1042 redoMenuItem_actionPerformed();
1044 else if (source == copy)
1046 copy_actionPerformed();
1048 else if (source == pasteNew)
1050 pasteNew_actionPerformed();
1052 else if (source == pasteThis)
1054 pasteThis_actionPerformed();
1056 else if (source == cut)
1058 cut_actionPerformed();
1060 else if (source == delete)
1062 delete_actionPerformed();
1064 else if (source == createGroup)
1066 createGroup_actionPerformed();
1068 else if (source == unGroup)
1070 unGroup_actionPerformed();
1072 else if (source == grpsFromSelection)
1074 makeGrpsFromSelection_actionPerformed();
1076 else if (source == deleteGroups)
1078 deleteGroups_actionPerformed();
1080 else if (source == selectAllSequenceMenuItem)
1082 selectAllSequenceMenuItem_actionPerformed();
1084 else if (source == deselectAllSequenceMenuItem)
1086 deselectAllSequenceMenuItem_actionPerformed();
1088 else if (source == invertSequenceMenuItem)
1090 invertSequenceMenuItem_actionPerformed();
1091 // uncomment to slave sequence selections in split frame
1092 // viewport.sendSelection();
1094 else if (source == invertColSel)
1096 viewport.invertColumnSelection();
1097 alignPanel.paintAlignment(true);
1098 viewport.sendSelection();
1100 else if (source == remove2LeftMenuItem)
1102 trimAlignment(true);
1104 else if (source == remove2RightMenuItem)
1106 trimAlignment(false);
1108 else if (source == removeGappedColumnMenuItem)
1110 removeGappedColumnMenuItem_actionPerformed();
1112 else if (source == removeAllGapsMenuItem)
1114 removeAllGapsMenuItem_actionPerformed();
1116 else if (source == findMenuItem)
1118 findMenuItem_actionPerformed();
1120 else if (source == font)
1122 new FontChooser(alignPanel);
1124 else if (source == newView)
1128 else if (source == showColumns)
1130 viewport.showAllHiddenColumns();
1131 alignPanel.paintAlignment(true);
1132 viewport.sendSelection();
1134 else if (source == showSeqs)
1136 viewport.showAllHiddenSeqs();
1137 alignPanel.paintAlignment(true);
1138 // uncomment if we want to slave sequence selections in split frame
1139 // viewport.sendSelection();
1141 else if (source == hideColumns)
1143 viewport.hideSelectedColumns();
1144 alignPanel.paintAlignment(true);
1145 viewport.sendSelection();
1147 else if (source == hideSequences
1148 && viewport.getSelectionGroup() != null)
1150 viewport.hideAllSelectedSeqs();
1151 alignPanel.paintAlignment(true);
1152 // uncomment if we want to slave sequence selections in split frame
1153 // viewport.sendSelection();
1155 else if (source == hideAllButSelection)
1157 toggleHiddenRegions(false, false);
1158 alignPanel.paintAlignment(true);
1159 viewport.sendSelection();
1161 else if (source == hideAllSelection)
1163 SequenceGroup sg = viewport.getSelectionGroup();
1164 viewport.expandColSelection(sg, false);
1165 viewport.hideAllSelectedSeqs();
1166 viewport.hideSelectedColumns();
1167 alignPanel.paintAlignment(true);
1168 viewport.sendSelection();
1170 else if (source == showAllHidden)
1172 viewport.showAllHiddenColumns();
1173 viewport.showAllHiddenSeqs();
1174 alignPanel.paintAlignment(true);
1175 viewport.sendSelection();
1177 else if (source == showGroupConsensus)
1179 showGroupConsensus_actionPerformed();
1181 else if (source == showGroupConservation)
1183 showGroupConservation_actionPerformed();
1185 else if (source == showSequenceLogo)
1187 showSequenceLogo_actionPerformed();
1189 else if (source == normSequenceLogo)
1191 normSequenceLogo_actionPerformed();
1193 else if (source == showConsensusHistogram)
1195 showConsensusHistogram_actionPerformed();
1197 else if (source == applyAutoAnnotationSettings)
1199 applyAutoAnnotationSettings_actionPerformed();
1201 else if (source == featureSettings)
1203 new FeatureSettings(alignPanel);
1205 else if (source == alProperties)
1207 StringBuffer contents = new jalview.io.AlignmentProperties(
1208 viewport.getAlignment()).formatAsString();
1209 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1210 cap.setText(contents.toString());
1211 Frame frame = new Frame();
1213 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1214 .formatMessage("label.alignment_properties", new String[]
1215 { getTitle() }), 400, 250);
1217 else if (source == overviewMenuItem)
1219 overviewMenuItem_actionPerformed();
1221 else if (source == noColourmenuItem)
1225 else if (source == clustalColour)
1227 abovePIDThreshold.setState(false);
1228 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1230 else if (source == zappoColour)
1232 changeColour(new ZappoColourScheme());
1234 else if (source == taylorColour)
1236 changeColour(new TaylorColourScheme());
1238 else if (source == hydrophobicityColour)
1240 changeColour(new HydrophobicColourScheme());
1242 else if (source == helixColour)
1244 changeColour(new HelixColourScheme());
1246 else if (source == strandColour)
1248 changeColour(new StrandColourScheme());
1250 else if (source == turnColour)
1252 changeColour(new TurnColourScheme());
1254 else if (source == buriedColour)
1256 changeColour(new BuriedColourScheme());
1258 else if (source == nucleotideColour)
1260 changeColour(new NucleotideColourScheme());
1262 else if (source == purinePyrimidineColour)
1264 changeColour(new PurinePyrimidineColourScheme());
1266 // else if (source == RNAInteractionColour)
1268 // changeColour(new RNAInteractionColourScheme());
1270 else if (source == RNAHelixColour)
1272 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1273 // new RNAHelicesColourChooser(viewport, alignPanel);
1275 else if (source == modifyPID)
1277 modifyPID_actionPerformed();
1279 else if (source == modifyConservation)
1281 modifyConservation_actionPerformed();
1283 else if (source == userDefinedColour)
1285 new UserDefinedColours(alignPanel, null);
1287 else if (source == PIDColour)
1289 changeColour(new PIDColourScheme());
1291 else if (source == BLOSUM62Colour)
1293 changeColour(new Blosum62ColourScheme());
1295 else if (source == tcoffeeColour)
1297 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1299 else if (source == annotationColour)
1301 new AnnotationColourChooser(viewport, alignPanel);
1303 else if (source == annotationColumnSelection)
1305 new AnnotationColumnChooser(viewport, alignPanel);
1307 else if (source == sortPairwiseMenuItem)
1309 sortPairwiseMenuItem_actionPerformed();
1311 else if (source == sortIDMenuItem)
1313 sortIDMenuItem_actionPerformed();
1315 else if (source == sortLengthMenuItem)
1317 sortLengthMenuItem_actionPerformed();
1319 else if (source == sortGroupMenuItem)
1321 sortGroupMenuItem_actionPerformed();
1323 else if (source == removeRedundancyMenuItem)
1325 removeRedundancyMenuItem_actionPerformed();
1327 else if (source == pairwiseAlignmentMenuItem)
1329 pairwiseAlignmentMenuItem_actionPerformed();
1331 else if (source == PCAMenuItem)
1333 PCAMenuItem_actionPerformed();
1335 else if (source == averageDistanceTreeMenuItem)
1337 averageDistanceTreeMenuItem_actionPerformed();
1339 else if (source == neighbourTreeMenuItem)
1341 neighbourTreeMenuItem_actionPerformed();
1343 else if (source == njTreeBlosumMenuItem)
1345 njTreeBlosumMenuItem_actionPerformed();
1347 else if (source == avDistanceTreeBlosumMenuItem)
1349 avTreeBlosumMenuItem_actionPerformed();
1351 else if (source == documentation)
1353 documentation_actionPerformed();
1355 else if (source == about)
1357 about_actionPerformed();
1362 public void inputText_actionPerformed()
1364 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1365 Frame frame = new Frame();
1367 jalview.bin.JalviewLite.addFrame(frame,
1368 MessageManager.getString("label.input_cut_paste"), 500, 500);
1371 protected void outputText_actionPerformed(ActionEvent e)
1373 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1374 Frame frame = new Frame();
1376 JalviewLite.addFrame(frame, MessageManager
1377 .formatMessage("label.alignment_output_command", new Object[]
1378 { e.getActionCommand() }), 600, 500);
1380 FileFormatI fileFormat = FileFormats.getInstance()
1381 .forName(e.getActionCommand());
1383 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1384 viewport.getAlignment(), viewport.getShowJVSuffix()));
1387 public void loadAnnotations()
1389 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1390 cap.setText(MessageManager
1391 .getString("label.paste_features_annotations_Tcoffee_here"));
1392 cap.setAnnotationImport();
1393 Frame frame = new Frame();
1395 jalview.bin.JalviewLite.addFrame(frame,
1396 MessageManager.getString("action.paste_annotations"), 400, 300);
1400 public String outputAnnotations(boolean displayTextbox)
1402 String annotation = new AnnotationFile()
1403 .printAnnotationsForView(viewport);
1407 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1408 Frame frame = new Frame();
1410 jalview.bin.JalviewLite.addFrame(frame,
1411 MessageManager.getString("label.annotations"), 600, 500);
1412 cap.setText(annotation);
1418 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1420 if (alignPanel.getFeatureRenderer() != null
1421 && viewport.getFeaturesDisplayed() != null)
1423 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1429 public String outputFeatures(boolean displayTextbox, String format)
1432 FeaturesFile formatter = new FeaturesFile();
1433 if (format.equalsIgnoreCase("Jalview"))
1435 features = formatter.printJalviewFormat(
1436 viewport.getAlignment().getSequencesArray(),
1437 getDisplayedFeatureCols());
1441 features = formatter.printGffFormat(
1442 viewport.getAlignment().getSequencesArray(),
1443 getDisplayedFeatureCols());
1448 boolean frimport = false;
1449 if (features == null || features.equals("No Features Visible"))
1451 features = "# No features visible - paste some and import them here.";
1455 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1458 cap.setAnnotationImport();
1460 Frame frame = new Frame();
1462 jalview.bin.JalviewLite.addFrame(frame,
1463 MessageManager.getString("label.features"), 600, 500);
1464 cap.setText(features);
1468 if (features == null)
1477 void launchFullApplication()
1479 StringBuffer url = new StringBuffer(jalviewServletURL);
1481 // allow servlet parameters to be passed in applet parameter
1482 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1484 url.append(firstSep);
1487 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1489 if (viewport.applet.getParameter("features") != null)
1491 url.append("&features=");
1492 url.append(appendProtocol(viewport.applet.getParameter("features")));
1495 if (viewport.applet.getParameter("annotations") != null)
1497 url.append("&annotations=");
1499 appendProtocol(viewport.applet.getParameter("annotations")));
1502 if (viewport.applet.getParameter("jnetfile") != null
1503 || viewport.applet.getParameter("jpredfile") != null)
1505 url.append("&annotations=");
1506 url.append(appendProtocol(
1507 viewport.applet.getParameter("jnetfile") != null
1508 ? viewport.applet.getParameter("jnetfile")
1509 : viewport.applet.getParameter("jpredfile")));
1512 if (viewport.applet.getParameter("defaultColour") != null)
1514 url.append("&colour=" + removeWhiteSpace(
1515 viewport.applet.getParameter("defaultColour")));
1518 if (viewport.applet.getParameter("userDefinedColour") != null)
1520 url.append("&colour=" + removeWhiteSpace(
1521 viewport.applet.getParameter("userDefinedColour")));
1523 if (viewport.applet.getParameter("tree") != null)
1526 + appendProtocol(viewport.applet.getParameter("tree")));
1528 if (viewport.applet.getParameter("treeFile") != null)
1531 + appendProtocol(viewport.applet.getParameter("treeFile")));
1534 showURL(url.toString(), "FULL_APP");
1537 String removeWhiteSpace(String colour)
1539 StringBuffer sb = new StringBuffer();
1540 for (int i = 0; i < colour.length(); i++)
1542 if (Character.isWhitespace(colour.charAt(i)))
1548 sb.append(colour.charAt(i));
1552 return sb.toString();
1555 String appendProtocol(String url)
1560 url = URLEncoder.encode(url);
1563 * When we finally deprecate 1.1 compatibility, we can start to use
1564 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1565 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1566 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1567 * ex.printStackTrace(); }
1569 catch (java.net.MalformedURLException ex)
1571 url = viewport.applet.getCodeBase() + url;
1576 public void closeMenuItem_actionPerformed()
1578 PaintRefresher.RemoveComponent(alignPanel);
1579 if (alignPanel.seqPanel != null
1580 && alignPanel.seqPanel.seqCanvas != null)
1582 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1584 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1586 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1589 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1604 void updateEditMenuBar()
1607 if (viewport.getHistoryList().size() > 0)
1609 undoMenuItem.setEnabled(true);
1610 CommandI command = viewport.getHistoryList().peek();
1611 undoMenuItem.setLabel(MessageManager
1612 .formatMessage("label.undo_command", new Object[]
1613 { command.getDescription() }));
1617 undoMenuItem.setEnabled(false);
1618 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1621 if (viewport.getRedoList().size() > 0)
1623 redoMenuItem.setEnabled(true);
1625 CommandI command = viewport.getRedoList().peek();
1626 redoMenuItem.setLabel(MessageManager
1627 .formatMessage("label.redo_command", new Object[]
1628 { command.getDescription() }));
1632 redoMenuItem.setEnabled(false);
1633 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1641 public void addHistoryItem(CommandI command)
1643 if (command.getSize() > 0)
1645 viewport.addToHistoryList(command);
1646 viewport.clearRedoList();
1647 updateEditMenuBar();
1648 viewport.updateHiddenColumns();
1653 * TODO: JAL-1104 DOCUMENT ME!
1658 protected void undoMenuItem_actionPerformed()
1660 if (viewport.getHistoryList().isEmpty())
1665 CommandI command = viewport.getHistoryList().pop();
1666 viewport.addToRedoList(command);
1667 command.undoCommand(null);
1669 AlignmentViewport originalSource = getOriginatingSource(command);
1671 if (originalSource != viewport)
1674 .println("Warning: Viewport object mismatch whilst undoing");
1676 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1677 // viewport.getColumnSelection().getHiddenColumns()
1679 updateEditMenuBar();
1680 originalSource.firePropertyChange("alignment", null,
1681 originalSource.getAlignment().getSequences());
1685 * TODO: JAL-1104 DOCUMENT ME!
1690 protected void redoMenuItem_actionPerformed()
1692 if (viewport.getRedoList().isEmpty())
1697 CommandI command = viewport.getRedoList().pop();
1698 viewport.addToHistoryList(command);
1699 command.doCommand(null);
1701 AlignmentViewport originalSource = getOriginatingSource(command);
1703 if (originalSource != viewport)
1706 .println("Warning: Viewport object mismatch whilst re-doing");
1708 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1709 // viewport.getColumnSelection().getHiddenColumns()
1712 updateEditMenuBar();
1713 originalSource.firePropertyChange("alignment", null,
1714 originalSource.getAlignment().getSequences());
1717 AlignmentViewport getOriginatingSource(CommandI command)
1719 AlignmentViewport originalSource = null;
1720 // For sequence removal and addition, we need to fire
1721 // the property change event FROM the viewport where the
1722 // original alignment was altered
1723 AlignmentI al = null;
1724 if (command instanceof EditCommand)
1726 EditCommand editCommand = (EditCommand) command;
1727 al = editCommand.getAlignment();
1728 Vector comps = (Vector) PaintRefresher.components
1729 .get(viewport.getSequenceSetId());
1730 for (int i = 0; i < comps.size(); i++)
1732 if (comps.elementAt(i) instanceof AlignmentPanel)
1734 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1736 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1743 if (originalSource == null)
1745 // The original view is closed, we must validate
1746 // the current view against the closed view first
1749 PaintRefresher.validateSequences(al, viewport.getAlignment());
1752 originalSource = viewport;
1755 return originalSource;
1759 * Move the currently selected sequences up or down one position in the
1764 public void moveSelectedSequences(boolean up)
1766 SequenceGroup sg = viewport.getSelectionGroup();
1771 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1772 up ? null : viewport.getHiddenRepSequences(), up);
1773 alignPanel.paintAlignment(true);
1776 * Also move cDNA/protein complement sequences
1778 AlignViewportI complement = viewport.getCodingComplement();
1779 if (complement != null)
1781 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1782 viewport, complement);
1783 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1784 up ? null : complement.getHiddenRepSequences(), up);
1785 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1789 synchronized void slideSequences(boolean right, int size)
1791 List<SequenceI> sg = new Vector<>();
1792 if (viewport.cursorMode)
1794 sg.add(viewport.getAlignment()
1795 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1797 else if (viewport.getSelectionGroup() != null
1798 && viewport.getSelectionGroup().getSize() != viewport
1799 .getAlignment().getHeight())
1801 sg = viewport.getSelectionGroup()
1802 .getSequences(viewport.getHiddenRepSequences());
1810 Vector<SequenceI> invertGroup = new Vector();
1812 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1814 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1816 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1820 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1822 SequenceI[] seqs2 = invertGroup
1823 .toArray(new SequenceI[invertGroup.size()]);
1824 for (int i = 0; i < invertGroup.size(); i++)
1826 seqs2[i] = invertGroup.elementAt(i);
1829 SlideSequencesCommand ssc;
1832 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1833 viewport.getGapCharacter());
1837 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1838 viewport.getGapCharacter());
1841 int groupAdjustment = 0;
1842 if (ssc.getGapsInsertedBegin() && right)
1844 if (viewport.cursorMode)
1846 alignPanel.seqPanel.moveCursor(size, 0);
1850 groupAdjustment = size;
1853 else if (!ssc.getGapsInsertedBegin() && !right)
1855 if (viewport.cursorMode)
1857 alignPanel.seqPanel.moveCursor(-size, 0);
1861 groupAdjustment = -size;
1865 if (groupAdjustment != 0)
1867 viewport.getSelectionGroup().setStartRes(
1868 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1869 viewport.getSelectionGroup().setEndRes(
1870 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1873 boolean appendHistoryItem = false;
1874 Deque<CommandI> historyList = viewport.getHistoryList();
1875 if (historyList != null && historyList.size() > 0
1876 && historyList.peek() instanceof SlideSequencesCommand)
1878 appendHistoryItem = ssc.appendSlideCommand(
1879 (SlideSequencesCommand) historyList.peek());
1882 if (!appendHistoryItem)
1884 addHistoryItem(ssc);
1890 static StringBuffer copiedSequences;
1892 static Vector<int[]> copiedHiddenColumns;
1894 protected void copy_actionPerformed()
1896 if (viewport.getSelectionGroup() == null)
1901 SequenceGroup sg = viewport.getSelectionGroup();
1902 copiedSequences = new StringBuffer();
1903 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1904 for (int i = 0; i < sg.getSize(); i++)
1906 SequenceI seq = sg.getSequenceAt(i);
1907 int index = viewport.getAlignment().findIndex(seq);
1908 orderedSeqs.put(index, seq);
1911 int index = 0, startRes, endRes;
1914 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1916 copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1917 .getHiddenColumns().getHiddenColumnsCopy());
1918 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1919 for (int[] region : copiedHiddenColumns)
1921 region[0] = region[0] - hiddenOffset;
1922 region[1] = region[1] - hiddenOffset;
1927 copiedHiddenColumns = null;
1930 for (int i = 0; i < sg.getSize(); i++)
1932 SequenceI seq = null;
1936 if (orderedSeqs.containsKey(index))
1938 seq = orderedSeqs.get(index);
1949 // Returns residue following index if gap
1950 startRes = seq.findPosition(sg.getStartRes());
1953 // Need to find the residue preceeding index if gap
1956 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1958 ch = seq.getCharAt(j);
1959 if (!jalview.util.Comparison.isGap((ch)))
1967 endRes += seq.getStart() - 1;
1970 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1971 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1978 protected void pasteNew_actionPerformed()
1983 protected void pasteThis_actionPerformed()
1988 void paste(boolean newAlignment)
1993 if (copiedSequences == null)
1998 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1999 Vector seqs = new Vector();
2000 while (st.hasMoreElements())
2002 String name = st.nextToken();
2003 int start = Integer.parseInt(st.nextToken());
2004 int end = Integer.parseInt(st.nextToken());
2005 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2007 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2008 for (int i = 0; i < seqs.size(); i++)
2010 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2015 String newtitle = MessageManager
2016 .getString("label.copied_sequences");
2017 if (getTitle().startsWith(
2018 MessageManager.getString("label.copied_sequences")))
2020 newtitle = getTitle();
2024 newtitle = newtitle.concat(MessageManager
2025 .formatMessage("label.from_msname", new String[]
2028 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2029 viewport.applet, newtitle, false);
2030 if (copiedHiddenColumns != null)
2032 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2034 int[] region = copiedHiddenColumns.elementAt(i);
2035 af.viewport.hideColumns(region[0], region[1]);
2039 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2044 addSequences(newSeqs);
2047 } catch (Exception ex)
2049 } // could be anything being pasted in here
2053 void addSequences(SequenceI[] seqs)
2055 for (int i = 0; i < seqs.length; i++)
2057 viewport.getAlignment().addSequence(seqs[i]);
2061 addHistoryItem(new EditCommand(
2062 MessageManager.getString("label.add_sequences"), Action.PASTE,
2063 seqs, 0, viewport.getAlignment().getWidth(),
2064 viewport.getAlignment()));
2066 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2067 viewport.getAlignment().getWidth();
2068 viewport.firePropertyChange("alignment", null,
2069 viewport.getAlignment().getSequences());
2073 protected void cut_actionPerformed()
2075 copy_actionPerformed();
2076 delete_actionPerformed();
2079 protected void delete_actionPerformed()
2082 SequenceGroup sg = viewport.getSelectionGroup();
2088 Vector seqs = new Vector();
2090 for (int i = 0; i < sg.getSize(); i++)
2092 seq = sg.getSequenceAt(i);
2093 seqs.addElement(seq);
2097 * If the cut affects all sequences, warn, remove highlighted columns
2099 if (sg.getSize() == viewport.getAlignment().getHeight())
2101 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2102 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2103 if (isEntireAlignWidth)
2105 String title = MessageManager.getString("label.delete_all");
2106 Panel infoPanel = new Panel();
2107 infoPanel.setLayout(new FlowLayout());
2109 new Label(MessageManager.getString("warn.delete_all")));
2111 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2112 dialog.setMainPanel(infoPanel);
2113 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2114 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2115 dialog.setVisible(true);
2122 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2123 sg.getEndRes() + 1);
2126 SequenceI[] cut = new SequenceI[seqs.size()];
2127 for (int i = 0; i < seqs.size(); i++)
2129 cut[i] = (SequenceI) seqs.elementAt(i);
2133 * //ADD HISTORY ITEM
2135 addHistoryItem(new EditCommand(
2136 MessageManager.getString("label.cut_sequences"), Action.CUT,
2137 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2138 viewport.getAlignment()));
2140 viewport.setSelectionGroup(null);
2141 viewport.getAlignment().deleteGroup(sg);
2143 viewport.firePropertyChange("alignment", null,
2144 viewport.getAlignment().getSequences());
2146 if (viewport.getAlignment().getHeight() < 1)
2148 this.setVisible(false);
2150 viewport.sendSelection();
2154 * group consensus toggled
2157 protected void showGroupConsensus_actionPerformed()
2159 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2160 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2165 * group conservation toggled.
2167 protected void showGroupConservation_actionPerformed()
2169 viewport.setShowGroupConservation(showGroupConservation.getState());
2170 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2178 * .event.ActionEvent)
2180 protected void showConsensusHistogram_actionPerformed()
2182 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2183 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2191 * .event.ActionEvent)
2193 protected void showSequenceLogo_actionPerformed()
2195 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2196 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2199 protected void normSequenceLogo_actionPerformed()
2201 showSequenceLogo.setState(true);
2202 viewport.setShowSequenceLogo(true);
2203 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2204 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2207 protected void applyAutoAnnotationSettings_actionPerformed()
2209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2212 protected void makeGrpsFromSelection_actionPerformed()
2214 if (avc.makeGroupsFromSelection())
2216 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2217 alignPanel.updateAnnotation();
2218 alignPanel.paintAlignment(true);
2222 protected void createGroup_actionPerformed()
2227 protected void unGroup_actionPerformed()
2231 alignPanel.alignmentChanged();
2235 protected void deleteGroups_actionPerformed()
2237 if (avc.deleteGroups())
2239 alignPanel.alignmentChanged();
2243 public void selectAllSequenceMenuItem_actionPerformed()
2245 SequenceGroup sg = new SequenceGroup();
2246 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2248 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2250 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2251 viewport.setSelectionGroup(sg);
2252 // JAL-2034 - should delegate to
2253 // alignPanel to decide if overview needs
2255 alignPanel.paintAlignment(false);
2256 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257 viewport.sendSelection();
2260 public void deselectAllSequenceMenuItem_actionPerformed()
2262 if (viewport.cursorMode)
2264 alignPanel.seqPanel.keyboardNo1 = null;
2265 alignPanel.seqPanel.keyboardNo2 = null;
2267 viewport.setSelectionGroup(null);
2268 viewport.getColumnSelection().clear();
2269 viewport.setSelectionGroup(null);
2270 alignPanel.idPanel.idCanvas.searchResults = null;
2271 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2272 // JAL-2034 - should delegate to
2273 // alignPanel to decide if overview needs
2275 alignPanel.paintAlignment(false);
2276 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277 viewport.sendSelection();
2280 public void invertSequenceMenuItem_actionPerformed()
2282 SequenceGroup sg = viewport.getSelectionGroup();
2283 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2285 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2288 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289 viewport.sendSelection();
2292 public void invertColSel_actionPerformed()
2294 viewport.invertColumnSelection();
2295 alignPanel.paintAlignment(true);
2296 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297 viewport.sendSelection();
2300 void trimAlignment(boolean trimLeft)
2302 AlignmentI al = viewport.getAlignment();
2303 ViewportRanges ranges = viewport.getRanges();
2304 ColumnSelection colSel = viewport.getColumnSelection();
2307 if (!colSel.isEmpty())
2311 column = colSel.getMin();
2315 column = colSel.getMax();
2319 if (viewport.getSelectionGroup() != null)
2321 seqs = viewport.getSelectionGroup()
2322 .getSequencesAsArray(viewport.getHiddenRepSequences());
2326 seqs = al.getSequencesArray();
2329 TrimRegionCommand trimRegion;
2332 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2334 ranges.setStartRes(0);
2338 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2342 statusBar.setText(MessageManager
2343 .formatMessage("label.removed_columns", new String[]
2344 { Integer.valueOf(trimRegion.getSize()).toString() }));
2345 addHistoryItem(trimRegion);
2347 for (SequenceGroup sg : al.getGroups())
2349 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2350 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2356 viewport.firePropertyChange("alignment", null, al.getSequences());
2360 public void removeGappedColumnMenuItem_actionPerformed()
2362 AlignmentI al = viewport.getAlignment();
2363 ViewportRanges ranges = viewport.getRanges();
2365 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2368 if (viewport.getSelectionGroup() != null)
2370 seqs = viewport.getSelectionGroup()
2371 .getSequencesAsArray(viewport.getHiddenRepSequences());
2372 start = viewport.getSelectionGroup().getStartRes();
2373 end = viewport.getSelectionGroup().getEndRes();
2377 seqs = viewport.getAlignment().getSequencesArray();
2380 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2381 "Remove Gapped Columns", seqs, start, end,
2382 viewport.getAlignment());
2384 addHistoryItem(removeGapCols);
2386 statusBar.setText(MessageManager
2387 .formatMessage("label.removed_empty_columns", new String[]
2388 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2390 // This is to maintain viewport position on first residue
2391 // of first sequence
2392 SequenceI seq = al.getSequenceAt(0);
2393 int startRes = seq.findPosition(ranges.getStartRes());
2394 // ShiftList shifts;
2395 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2396 // edit.alColumnChanges=shifts.getInverse();
2397 // if (viewport.hasHiddenColumns)
2398 // viewport.getColumnSelection().compensateForEdits(shifts);
2399 ranges.setStartRes(seq.findIndex(startRes) - 1);
2400 viewport.firePropertyChange("alignment", null, al.getSequences());
2404 public void removeAllGapsMenuItem_actionPerformed()
2406 AlignmentI al = viewport.getAlignment();
2407 ViewportRanges ranges = viewport.getRanges();
2409 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2412 if (viewport.getSelectionGroup() != null)
2414 seqs = viewport.getSelectionGroup()
2415 .getSequencesAsArray(viewport.getHiddenRepSequences());
2416 start = viewport.getSelectionGroup().getStartRes();
2417 end = viewport.getSelectionGroup().getEndRes();
2421 seqs = viewport.getAlignment().getSequencesArray();
2424 // This is to maintain viewport position on first residue
2425 // of first sequence
2426 SequenceI seq = al.getSequenceAt(0);
2427 int startRes = seq.findPosition(ranges.getStartRes());
2430 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2432 ranges.setStartRes(seq.findIndex(startRes) - 1);
2434 viewport.firePropertyChange("alignment", null, al.getSequences());
2438 public void findMenuItem_actionPerformed()
2440 new Finder(alignPanel);
2444 * create a new view derived from the current view
2447 * @return frame for the new view
2449 public AlignFrame newView(String viewtitle)
2452 if (viewport.hasHiddenRows())
2454 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2455 .getFullAlignment().getSequencesArray());
2459 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2462 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2464 for (int i = 0; i < viewport.getAlignment()
2465 .getAlignmentAnnotation().length; i++)
2467 if (!viewport.getAlignment()
2468 .getAlignmentAnnotation()[i].autoCalculated)
2470 newal.addAnnotation(
2471 viewport.getAlignment().getAlignmentAnnotation()[i]);
2476 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2478 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2479 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2480 PaintRefresher.Register(newaf.alignPanel,
2481 newaf.alignPanel.av.getSequenceSetId());
2483 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2484 newaf.alignPanel.av.getSequenceSetId());
2485 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2486 newaf.alignPanel.av.getSequenceSetId());
2488 Vector comps = (Vector) PaintRefresher.components
2489 .get(viewport.getSequenceSetId());
2491 for (int i = 0; i < comps.size(); i++)
2493 if (comps.elementAt(i) instanceof AlignmentPanel)
2499 String title = new String(this.getTitle());
2500 if (viewtitle != null)
2502 title = viewtitle + " ( " + title + ")";
2506 if (title.indexOf("(View") > -1)
2508 title = title.substring(0, title.indexOf("(View"));
2510 title += "(View " + viewSize + ")";
2513 newaf.setTitle(title.toString());
2515 newaf.viewport.setHistoryList(viewport.getHistoryList());
2516 newaf.viewport.setRedoList(viewport.getRedoList());
2522 * @return list of feature groups on the view
2524 public String[] getFeatureGroups()
2526 FeatureRenderer fr = null;
2527 if (alignPanel != null
2528 && (fr = alignPanel.getFeatureRenderer()) != null)
2530 List<String> gps = fr.getFeatureGroups();
2531 String[] _gps = gps.toArray(new String[gps.size()]);
2538 * get sequence feature groups that are hidden or shown
2544 public String[] getFeatureGroupsOfState(boolean visible)
2546 FeatureRenderer fr = null;
2547 if (alignPanel != null
2548 && (fr = alignPanel.getFeatureRenderer()) != null)
2550 List<String> gps = fr.getGroups(visible);
2551 String[] _gps = gps.toArray(new String[gps.size()]);
2558 * Change the display state for the given feature groups
2561 * list of group strings
2563 * visible or invisible
2565 public void setFeatureGroupState(String[] groups, boolean state)
2567 FeatureRenderer fr = null;
2568 this.sequenceFeatures.setState(true);
2569 viewport.setShowSequenceFeatures(true);
2570 if (alignPanel != null
2571 && (fr = alignPanel.getFeatureRenderer()) != null)
2574 fr.setGroupVisibility(Arrays.asList(groups), state);
2575 alignPanel.seqPanel.seqCanvas.repaint();
2576 if (alignPanel.overviewPanel != null)
2578 alignPanel.overviewPanel.updateOverviewImage();
2583 public void seqLimits_itemStateChanged()
2585 viewport.setShowJVSuffix(seqLimits.getState());
2586 alignPanel.fontChanged();
2587 alignPanel.paintAlignment(true);
2590 protected void colourTextMenuItem_actionPerformed()
2592 viewport.setColourText(colourTextMenuItem.getState());
2593 alignPanel.paintAlignment(true);
2596 protected void displayNonconservedMenuItem_actionPerformed()
2598 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2599 alignPanel.paintAlignment(true);
2602 protected void wrapMenuItem_actionPerformed()
2604 viewport.setWrapAlignment(wrapMenuItem.getState());
2605 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2606 scaleAbove.setEnabled(wrapMenuItem.getState());
2607 scaleLeft.setEnabled(wrapMenuItem.getState());
2608 scaleRight.setEnabled(wrapMenuItem.getState());
2609 alignPanel.paintAlignment(true);
2612 public void overviewMenuItem_actionPerformed()
2614 if (alignPanel.overviewPanel != null)
2619 Frame frame = new Frame();
2620 final OverviewPanel overview = new OverviewPanel(alignPanel);
2621 frame.add(overview);
2622 // +50 must allow for applet frame window
2623 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2624 .formatMessage("label.overview_params", new String[]
2625 { this.getTitle() }), overview.getPreferredSize().width,
2626 overview.getPreferredSize().height + 50);
2629 final AlignmentPanel ap = alignPanel;
2630 frame.addWindowListener(new WindowAdapter()
2633 public void windowClosing(WindowEvent e)
2638 ap.setOverviewPanel(null);
2643 alignPanel.setOverviewPanel(overview);
2648 public void changeColour(ColourSchemeI cs)
2650 viewport.setGlobalColourScheme(cs);
2652 alignPanel.paintAlignment(true);
2655 protected void modifyPID_actionPerformed()
2657 if (viewport.getAbovePIDThreshold()
2658 && viewport.getGlobalColourScheme() != null)
2660 SliderPanel.setPIDSliderSource(alignPanel,
2661 viewport.getResidueShading(), alignPanel.getViewName());
2662 SliderPanel.showPIDSlider();
2666 protected void modifyConservation_actionPerformed()
2668 if (viewport.getConservationSelected()
2669 && viewport.getGlobalColourScheme() != null)
2671 SliderPanel.setConservationSlider(alignPanel,
2672 viewport.getResidueShading(), alignPanel.getViewName());
2673 SliderPanel.showConservationSlider();
2677 protected void conservationMenuItem_actionPerformed()
2679 boolean selected = conservationMenuItem.getState();
2680 modifyConservation.setEnabled(selected);
2681 viewport.setConservationSelected(selected);
2682 viewport.getResidueShading().setConservationApplied(selected);
2684 changeColour(viewport.getGlobalColourScheme());
2688 modifyConservation_actionPerformed();
2692 SliderPanel.hideConservationSlider();
2696 public void abovePIDThreshold_actionPerformed()
2698 boolean selected = abovePIDThreshold.getState();
2699 modifyPID.setEnabled(selected);
2700 viewport.setAbovePIDThreshold(selected);
2703 viewport.getResidueShading().setThreshold(0,
2704 viewport.isIgnoreGapsConsensus());
2707 changeColour(viewport.getGlobalColourScheme());
2711 modifyPID_actionPerformed();
2715 SliderPanel.hidePIDSlider();
2719 public void sortPairwiseMenuItem_actionPerformed()
2721 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2722 AlignmentSorter.sortByPID(viewport.getAlignment(),
2723 viewport.getAlignment().getSequenceAt(0));
2725 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2726 viewport.getAlignment()));
2727 alignPanel.paintAlignment(true);
2730 public void sortIDMenuItem_actionPerformed()
2732 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2733 AlignmentSorter.sortByID(viewport.getAlignment());
2735 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2736 alignPanel.paintAlignment(true);
2739 public void sortLengthMenuItem_actionPerformed()
2741 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2742 AlignmentSorter.sortByLength(viewport.getAlignment());
2743 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2744 viewport.getAlignment()));
2745 alignPanel.paintAlignment(true);
2748 public void sortGroupMenuItem_actionPerformed()
2750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2751 AlignmentSorter.sortByGroup(viewport.getAlignment());
2752 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2753 viewport.getAlignment()));
2754 alignPanel.paintAlignment(true);
2758 public void removeRedundancyMenuItem_actionPerformed()
2760 new RedundancyPanel(alignPanel);
2763 public void pairwiseAlignmentMenuItem_actionPerformed()
2765 if (viewport.getSelectionGroup() != null
2766 && viewport.getSelectionGroup().getSize() > 1)
2768 Frame frame = new Frame();
2769 frame.add(new PairwiseAlignPanel(alignPanel));
2770 jalview.bin.JalviewLite.addFrame(frame,
2771 MessageManager.getString("action.pairwise_alignment"), 600,
2776 public void PCAMenuItem_actionPerformed()
2778 // are the sequences aligned?
2779 if (!viewport.getAlignment().isAligned(false))
2782 int Width = viewport.getAlignment().getWidth();
2784 for (int i = 0; i < viewport.getAlignment().getSequences()
2787 current = viewport.getAlignment().getSequenceAt(i);
2789 if (current.getLength() < Width)
2791 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2794 alignPanel.paintAlignment(true);
2797 if ((viewport.getSelectionGroup() != null
2798 && viewport.getSelectionGroup().getSize() < 4
2799 && viewport.getSelectionGroup().getSize() > 0)
2800 || viewport.getAlignment().getHeight() < 4)
2807 new PCAPanel(viewport);
2808 } catch (java.lang.OutOfMemoryError ex)
2814 public void averageDistanceTreeMenuItem_actionPerformed()
2816 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2817 "Average distance tree using PID");
2820 public void neighbourTreeMenuItem_actionPerformed()
2822 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2823 "Neighbour joining tree using PID");
2826 protected void njTreeBlosumMenuItem_actionPerformed()
2828 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2829 ScoreModels.getInstance().getBlosum62().getName(),
2830 "Neighbour joining tree using BLOSUM62");
2833 protected void avTreeBlosumMenuItem_actionPerformed()
2835 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2836 ScoreModels.getInstance().getBlosum62().getName(),
2837 "Average distance tree using BLOSUM62");
2840 void newTreePanel(String type, String pwType, String title)
2842 // are the sequences aligned?
2843 if (!viewport.getAlignment().isAligned(false))
2846 int Width = viewport.getAlignment().getWidth();
2848 for (int i = 0; i < viewport.getAlignment().getSequences()
2851 current = viewport.getAlignment().getSequenceAt(i);
2853 if (current.getLength() < Width)
2855 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2858 alignPanel.paintAlignment(true);
2862 if ((viewport.getSelectionGroup() != null
2863 && viewport.getSelectionGroup().getSize() > 1)
2864 || (viewport.getAlignment().getHeight() > 1))
2866 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2868 addTreeMenuItem(tp, title);
2870 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2874 void loadTree_actionPerformed()
2876 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2877 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2878 cap.setTreeImport();
2879 Frame frame = new Frame();
2881 jalview.bin.JalviewLite.addFrame(frame,
2882 MessageManager.getString("label.paste_newick_file"), 400, 300);
2885 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2887 TreePanel tp = new TreePanel(alignPanel, treeFile,
2888 MessageManager.getString("label.load_tree_from_file"), tree);
2889 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2890 addTreeMenuItem(tp, treeFile);
2894 * sort the alignment using the given treePanel
2897 * tree used to sort view
2899 * string used for undo event name
2901 public void sortByTree(TreePanel treePanel, String title)
2903 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2904 AlignmentSorter.sortByTree(viewport.getAlignment(),
2905 treePanel.getTree());
2906 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2907 // HistoryItem.SORT));
2908 addHistoryItem(new OrderCommand(MessageManager
2909 .formatMessage("label.order_by_params", new String[]
2910 { title }), oldOrder, viewport.getAlignment()));
2911 alignPanel.paintAlignment(true);
2915 * Do any automatic reordering of the alignment and add the necessary bits to
2916 * the menu structure for the new tree
2921 protected void addTreeMenuItem(final TreePanel treePanel,
2924 final MenuItem item = new MenuItem(title);
2925 sortByTreeMenu.add(item);
2926 item.addActionListener(new java.awt.event.ActionListener()
2929 public void actionPerformed(ActionEvent evt)
2931 sortByTree(treePanel, title); // treePanel.getTitle());
2935 treePanel.addWindowListener(new WindowAdapter()
2938 public void windowOpened(WindowEvent e)
2940 if (viewport.sortByTree)
2942 sortByTree(treePanel, title);
2944 super.windowOpened(e);
2948 public void windowClosing(WindowEvent e)
2950 sortByTreeMenu.remove(item);
2955 public boolean sortBy(AlignmentOrder alorder, String undoname)
2957 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2958 if (viewport.applet.debug)
2960 System.err.println("Sorting " + alorder.getOrder().size()
2961 + " in alignment '" + getTitle() + "'");
2963 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2964 if (undoname != null)
2966 addHistoryItem(new OrderCommand(undoname, oldOrder,
2967 viewport.getAlignment()));
2969 alignPanel.paintAlignment(true);
2973 protected void documentation_actionPerformed()
2975 alignPanel.av.applet.openJalviewHelpUrl();
2978 protected void about_actionPerformed()
2981 class AboutPanel extends Canvas
2987 public AboutPanel(String version, String builddate)
2989 this.version = version;
2990 this.builddate = builddate;
2994 public void paint(Graphics g)
2996 g.setColor(Color.white);
2997 g.fillRect(0, 0, getSize().width, getSize().height);
2998 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2999 FontMetrics fm = g.getFontMetrics();
3000 int fh = fm.getHeight();
3002 g.setColor(Color.black);
3003 // TODO: update this text for each release or centrally store it for
3004 // lite and application
3005 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3006 g.drawString(MessageManager
3007 .formatMessage("label.jalviewLite_release", new String[]
3008 { version }), x, y += fh);
3009 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3010 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3012 { builddate }), x, y += fh);
3013 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3014 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3016 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3017 x + 50, y += fh + 8);
3018 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3020 g.drawString(MessageManager
3021 .getString("label.jalview_distribution_lists"), x, y += fh);
3022 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3025 MessageManager.getString("label.jalview_cite_1_authors"), x,
3027 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3029 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3034 Frame frame = new Frame();
3035 frame.add(new AboutPanel(JalviewLite.getVersion(),
3036 JalviewLite.getBuildDate()));
3037 jalview.bin.JalviewLite.addFrame(frame,
3038 MessageManager.getString("label.jalview"), 580, 220);
3042 public void showURL(String url, String target)
3044 if (viewport.applet == null)
3046 System.out.println("Not running as applet - no browser available.");
3050 viewport.applet.showURL(url, target);
3054 // ////////////////////////////////////////////////////////////////////////////////
3055 // JBuilder Graphics here
3057 MenuBar alignFrameMenuBar = new MenuBar();
3059 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3061 MenuItem loadApplication = new MenuItem(
3062 MessageManager.getString("label.view_full_application"));
3064 MenuItem loadTree = new MenuItem(
3065 MessageManager.getString("label.load_associated_tree"));
3067 MenuItem loadAnnotations = new MenuItem(
3068 MessageManager.getString("label.load_features_annotations"));
3070 MenuItem outputFeatures = new MenuItem(
3071 MessageManager.getString("label.export_features"));
3073 MenuItem outputAnnotations = new MenuItem(
3074 MessageManager.getString("label.export_annotations"));
3076 MenuItem closeMenuItem = new MenuItem(
3077 MessageManager.getString("action.close"));
3079 MenuItem selectAllSequenceMenuItem = new MenuItem(
3080 MessageManager.getString("action.select_all"));
3082 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3083 MessageManager.getString("action.deselect_all"));
3085 MenuItem invertSequenceMenuItem = new MenuItem(
3086 MessageManager.getString("action.invert_selection"));
3088 MenuItem remove2LeftMenuItem = new MenuItem();
3090 MenuItem remove2RightMenuItem = new MenuItem();
3092 MenuItem removeGappedColumnMenuItem = new MenuItem();
3094 MenuItem removeAllGapsMenuItem = new MenuItem();
3096 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3098 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3100 MenuItem sortPairwiseMenuItem = new MenuItem();
3102 MenuItem sortIDMenuItem = new MenuItem();
3104 MenuItem sortLengthMenuItem = new MenuItem();
3106 MenuItem sortGroupMenuItem = new MenuItem();
3108 MenuItem removeRedundancyMenuItem = new MenuItem();
3110 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3112 MenuItem PCAMenuItem = new MenuItem();
3114 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3116 MenuItem neighbourTreeMenuItem = new MenuItem();
3118 BorderLayout borderLayout1 = new BorderLayout();
3120 public Label statusBar = new Label();
3122 MenuItem clustalColour = new MenuItem();
3124 MenuItem zappoColour = new MenuItem();
3126 MenuItem taylorColour = new MenuItem();
3128 MenuItem hydrophobicityColour = new MenuItem();
3130 MenuItem helixColour = new MenuItem();
3132 MenuItem strandColour = new MenuItem();
3134 MenuItem turnColour = new MenuItem();
3136 MenuItem buriedColour = new MenuItem();
3138 MenuItem purinePyrimidineColour = new MenuItem();
3140 // MenuItem RNAInteractionColour = new MenuItem();
3142 MenuItem RNAHelixColour = new MenuItem();
3144 MenuItem userDefinedColour = new MenuItem();
3146 MenuItem PIDColour = new MenuItem();
3148 MenuItem BLOSUM62Colour = new MenuItem();
3150 MenuItem tcoffeeColour = new MenuItem();
3152 MenuItem njTreeBlosumMenuItem = new MenuItem();
3154 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3156 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3158 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3160 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3162 MenuItem alProperties = new MenuItem(
3163 MessageManager.getString("label.alignment_props"));
3165 MenuItem overviewMenuItem = new MenuItem();
3167 MenuItem undoMenuItem = new MenuItem();
3169 MenuItem redoMenuItem = new MenuItem();
3171 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3173 MenuItem noColourmenuItem = new MenuItem();
3175 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3177 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3179 MenuItem findMenuItem = new MenuItem();
3181 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3183 MenuItem nucleotideColour = new MenuItem();
3185 MenuItem deleteGroups = new MenuItem();
3187 MenuItem grpsFromSelection = new MenuItem();
3189 MenuItem createGroup = new MenuItem();
3191 MenuItem unGroup = new MenuItem();
3193 MenuItem delete = new MenuItem();
3195 MenuItem copy = new MenuItem();
3197 MenuItem cut = new MenuItem();
3199 Menu pasteMenu = new Menu();
3201 MenuItem pasteNew = new MenuItem();
3203 MenuItem pasteThis = new MenuItem();
3205 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3207 MenuItem font = new MenuItem();
3209 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3211 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3213 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3215 MenuItem modifyPID = new MenuItem();
3217 MenuItem modifyConservation = new MenuItem();
3219 CheckboxMenuItem autoCalculate = null;
3221 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3222 "Sort Alignment With New Tree", true);
3224 Menu sortByTreeMenu = new Menu();
3226 MenuItem inputText = new MenuItem();
3228 MenuItem documentation = new MenuItem();
3230 MenuItem about = new MenuItem();
3232 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3234 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3236 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3238 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3240 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3242 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3244 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3246 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3248 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3251 * Initialise menus and other items
3255 private void jbInit() throws Exception
3257 setMenuBar(alignFrameMenuBar);
3260 * Configure File menu items and actions
3263 .setLabel(MessageManager.getString("label.input_from_textbox"));
3264 inputText.addActionListener(this);
3265 Menu outputTextboxMenu = new Menu(
3266 MessageManager.getString("label.out_to_textbox"));
3267 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3269 MenuItem item = new MenuItem(ff);
3271 item.addActionListener(new java.awt.event.ActionListener()
3274 public void actionPerformed(ActionEvent e)
3276 outputText_actionPerformed(e);
3280 outputTextboxMenu.add(item);
3282 closeMenuItem.addActionListener(this);
3283 loadApplication.addActionListener(this);
3284 loadTree.addActionListener(this);
3285 loadAnnotations.addActionListener(this);
3286 outputFeatures.addActionListener(this);
3287 outputAnnotations.addActionListener(this);
3290 * Configure Edit menu items and actions
3292 undoMenuItem.setEnabled(false);
3293 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3294 undoMenuItem.addActionListener(this);
3295 redoMenuItem.setEnabled(false);
3296 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3297 redoMenuItem.addActionListener(this);
3298 copy.setLabel(MessageManager.getString("action.copy"));
3299 copy.addActionListener(this);
3300 cut.setLabel(MessageManager.getString("action.cut"));
3301 cut.addActionListener(this);
3302 delete.setLabel(MessageManager.getString("action.delete"));
3303 delete.addActionListener(this);
3304 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3305 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3306 pasteNew.addActionListener(this);
3307 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3308 pasteThis.addActionListener(this);
3310 .setLabel(MessageManager.getString("action.remove_left"));
3311 remove2LeftMenuItem.addActionListener(this);
3312 remove2RightMenuItem
3313 .setLabel(MessageManager.getString("action.remove_right"));
3314 remove2RightMenuItem.addActionListener(this);
3315 removeGappedColumnMenuItem.setLabel(
3316 MessageManager.getString("action.remove_empty_columns"));
3317 removeGappedColumnMenuItem.addActionListener(this);
3318 removeAllGapsMenuItem
3319 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3320 removeAllGapsMenuItem.addActionListener(this);
3321 removeRedundancyMenuItem
3322 .setLabel(MessageManager.getString("action.remove_redundancy"));
3323 removeRedundancyMenuItem.addActionListener(this);
3326 * Configure Select menu items and actions
3328 findMenuItem.setLabel(MessageManager.getString("action.find"));
3329 findMenuItem.addActionListener(this);
3330 selectAllSequenceMenuItem.addActionListener(this);
3331 deselectAllSequenceMenuItem.addActionListener(this);
3332 invertSequenceMenuItem.setLabel(
3333 MessageManager.getString("action.invert_sequence_selection"));
3334 invertSequenceMenuItem.addActionListener(this);
3335 invertColSel.setLabel(
3336 MessageManager.getString("action.invert_column_selection"));
3337 invertColSel.addActionListener(this);
3339 .setLabel(MessageManager.getString("action.undefine_groups"));
3340 deleteGroups.addActionListener(this);
3341 grpsFromSelection.setLabel(
3342 MessageManager.getString("action.make_groups_selection"));
3343 grpsFromSelection.addActionListener(this);
3344 createGroup.setLabel(MessageManager.getString("action.create_group"));
3345 createGroup.addActionListener(this);
3346 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3347 unGroup.addActionListener(this);
3349 annotationColumnSelection.setLabel(
3350 MessageManager.getString("action.select_by_annotation"));
3351 annotationColumnSelection.addActionListener(this);
3354 * Configure View menu items and actions
3356 newView.setLabel(MessageManager.getString("action.new_view"));
3357 newView.addActionListener(this);
3358 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3359 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3360 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3361 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3363 .setLabel(MessageManager.getString("label.selected_columns"));
3365 .setLabel(MessageManager.getString("label.selected_sequences"));
3366 hideAllButSelection.setLabel(
3367 MessageManager.getString("label.all_but_selected_region"));
3369 .setLabel(MessageManager.getString("label.selected_region"));
3370 showAllHidden.setLabel(
3371 MessageManager.getString("label.all_sequences_columns"));
3372 showColumns.addActionListener(this);
3373 showSeqs.addActionListener(this);
3374 hideColumns.addActionListener(this);
3375 hideSequences.addActionListener(this);
3376 hideAllButSelection.addActionListener(this);
3377 hideAllSelection.addActionListener(this);
3378 showAllHidden.addActionListener(this);
3380 .setLabel(MessageManager.getString("action.feature_settings"));
3381 featureSettings.addActionListener(this);
3382 sequenceFeatures.setLabel(
3383 MessageManager.getString("label.show_sequence_features"));
3384 sequenceFeatures.addItemListener(this);
3385 sequenceFeatures.setState(false);
3386 followMouseOverFlag.setLabel(
3387 MessageManager.getString("label.automatic_scrolling"));
3388 followMouseOverFlag.addItemListener(this);
3389 alProperties.addActionListener(this);
3391 .setLabel(MessageManager.getString("label.overview_window"));
3392 overviewMenuItem.addActionListener(this);
3395 * Configure Annotations menu items and actions
3397 annotationPanelMenuItem
3398 .setLabel(MessageManager.getString("label.show_annotations"));
3399 annotationPanelMenuItem.addItemListener(this);
3401 .setLabel(MessageManager.getString("label.group_consensus"));
3402 showGroupConservation
3403 .setLabel(MessageManager.getString("label.group_conservation"));
3404 showConsensusHistogram.setLabel(
3405 MessageManager.getString("label.show_consensus_histogram"));
3406 showSequenceLogo.setLabel(
3407 MessageManager.getString("label.show_consensus_logo"));
3408 normSequenceLogo.setLabel(
3409 MessageManager.getString("label.norm_consensus_logo"));
3410 applyAutoAnnotationSettings
3411 .setLabel(MessageManager.getString("label.apply_all_groups"));
3412 applyAutoAnnotationSettings.setState(true);
3413 Menu autoAnnMenu = new Menu(
3414 MessageManager.getString("label.autocalculated_annotation"));
3415 showGroupConsensus.addItemListener(this);
3416 showGroupConservation.addItemListener(this);
3417 showConsensusHistogram.addItemListener(this);
3418 showSequenceLogo.addItemListener(this);
3419 normSequenceLogo.addItemListener(this);
3420 applyAutoAnnotationSettings.addItemListener(this);
3421 showAlignmentAnnotations = new CheckboxMenuItem(
3422 MessageManager.getString("label.show_all_al_annotations"));
3423 showSequenceAnnotations = new CheckboxMenuItem(
3424 MessageManager.getString("label.show_all_seq_annotations"));
3425 sortAnnBySequence = new CheckboxMenuItem(
3426 MessageManager.getString("label.sort_annotations_by_sequence"));
3427 sortAnnByLabel = new CheckboxMenuItem(
3428 MessageManager.getString("label.sort_annotations_by_label"));
3429 showAutoFirst = new CheckboxMenuItem(
3430 MessageManager.getString("label.show_first"));
3431 showAutoFirst.setState(false); // pending applet parameter
3432 setShowAutoCalculatedAbove(showAutoFirst.getState());
3433 showAutoLast = new CheckboxMenuItem(
3434 MessageManager.getString("label.show_last"));
3435 showAutoLast.setState(!showAutoFirst.getState());
3436 showAlignmentAnnotations.addItemListener(this);
3437 showSequenceAnnotations.addItemListener(this);
3438 sortAnnBySequence.addItemListener(this);
3439 sortAnnByLabel.addItemListener(this);
3440 showAutoFirst.addItemListener(this);
3441 showAutoLast.addItemListener(this);
3444 * Configure Format menu items and actions
3446 font.setLabel(MessageManager.getString("action.font"));
3447 font.addActionListener(this);
3448 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3449 scaleAbove.setState(true);
3450 scaleAbove.setEnabled(false);
3451 scaleAbove.addItemListener(this);
3452 scaleLeft.setEnabled(false);
3453 scaleLeft.setState(true);
3454 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3455 scaleLeft.addItemListener(this);
3456 scaleRight.setEnabled(false);
3457 scaleRight.setState(true);
3458 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3459 scaleRight.addItemListener(this);
3460 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3461 viewBoxesMenuItem.setState(true);
3462 viewBoxesMenuItem.addItemListener(this);
3463 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3464 viewTextMenuItem.setState(true);
3465 viewTextMenuItem.addItemListener(this);
3467 .setLabel(MessageManager.getString("label.colour_text"));
3468 colourTextMenuItem.addItemListener(this);
3469 displayNonconservedMenuItem
3470 .setLabel(MessageManager.getString("label.show_non_conserved"));
3471 displayNonconservedMenuItem.addItemListener(this);
3472 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3473 wrapMenuItem.addItemListener(this);
3475 .setLabel(MessageManager.getString("action.show_gaps"));
3476 renderGapsMenuItem.setState(true);
3477 renderGapsMenuItem.addItemListener(this);
3478 centreColumnLabelFlag.setLabel(
3479 MessageManager.getString("label.centre_column_labels"));
3480 centreColumnLabelFlag.addItemListener(this);
3481 seqLimits.setState(true);
3483 MessageManager.getString("label.show_sequence_limits"));
3484 seqLimits.addItemListener(this);
3487 * Configure Colour menu items and actions
3489 applyToAllGroups.setLabel(
3490 MessageManager.getString("label.apply_colour_to_all_groups"));
3491 applyToAllGroups.setState(true);
3492 applyToAllGroups.addItemListener(this);
3493 clustalColour.setLabel(
3494 MessageManager.getString("label.colourScheme_clustal"));
3495 clustalColour.addActionListener(this);
3497 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3498 zappoColour.addActionListener(this);
3499 taylorColour.setLabel(
3500 MessageManager.getString("label.colourScheme_taylor"));
3501 taylorColour.addActionListener(this);
3502 hydrophobicityColour.setLabel(
3503 MessageManager.getString("label.colourScheme_hydrophobic"));
3504 hydrophobicityColour.addActionListener(this);
3505 helixColour.setLabel(MessageManager
3506 .getString("label.colourScheme_helix_propensity"));
3507 helixColour.addActionListener(this);
3508 strandColour.setLabel(MessageManager
3509 .getString("label.colourScheme_strand_propensity"));
3510 strandColour.addActionListener(this);
3511 turnColour.setLabel(
3512 MessageManager.getString("label.colourScheme_turn_propensity"));
3513 turnColour.addActionListener(this);
3514 buriedColour.setLabel(
3515 MessageManager.getString("label.colourScheme_buried_index"));
3516 buriedColour.addActionListener(this);
3517 purinePyrimidineColour.setLabel(MessageManager
3518 .getString("label.colourScheme_purine/pyrimidine"));
3519 purinePyrimidineColour.addActionListener(this);
3520 // RNAInteractionColour.setLabel(MessageManager
3521 // .getString("label.rna_interaction"));
3522 // RNAInteractionColour.addActionListener(this);
3523 RNAHelixColour.setLabel(
3524 MessageManager.getString("label.colourScheme_rna_helices"));
3525 RNAHelixColour.addActionListener(this);
3527 .setLabel(MessageManager.getString("action.user_defined"));
3528 userDefinedColour.addActionListener(this);
3530 MessageManager.getString("label.colourScheme_%_identity"));
3531 PIDColour.addActionListener(this);
3532 BLOSUM62Colour.setLabel(
3533 MessageManager.getString("label.colourScheme_blosum62"));
3534 BLOSUM62Colour.addActionListener(this);
3535 tcoffeeColour.setLabel(
3536 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3537 // it will be enabled only if a score file is provided
3538 tcoffeeColour.setEnabled(false);
3539 tcoffeeColour.addActionListener(this);
3540 conservationMenuItem
3541 .setLabel(MessageManager.getString("action.by_conservation"));
3542 conservationMenuItem.addItemListener(this);
3543 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3544 noColourmenuItem.addActionListener(this);
3545 abovePIDThreshold.setLabel(
3546 MessageManager.getString("label.above_identity_threshold"));
3547 abovePIDThreshold.addItemListener(this);
3548 nucleotideColour.setLabel(
3549 MessageManager.getString("label.colourScheme_nucleotide"));
3550 nucleotideColour.addActionListener(this);
3552 MessageManager.getString("label.modify_identity_threshold"));
3553 modifyPID.setEnabled(abovePIDThreshold.getState());
3554 modifyPID.addActionListener(this);
3555 modifyConservation.setLabel(MessageManager
3556 .getString("label.modify_conservation_threshold"));
3557 modifyConservation.setEnabled(conservationMenuItem.getState());
3558 modifyConservation.addActionListener(this);
3560 .setLabel(MessageManager.getString("action.by_annotation"));
3561 annotationColour.addActionListener(this);
3564 * Configure Calculate menu items and actions
3566 sortPairwiseMenuItem
3567 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3568 sortPairwiseMenuItem.addActionListener(this);
3569 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3570 sortIDMenuItem.addActionListener(this);
3572 .setLabel(MessageManager.getString("action.by_length"));
3573 sortLengthMenuItem.addActionListener(this);
3574 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3575 sortGroupMenuItem.addActionListener(this);
3576 pairwiseAlignmentMenuItem.setLabel(
3577 MessageManager.getString("action.pairwise_alignment"));
3578 pairwiseAlignmentMenuItem.addActionListener(this);
3579 PCAMenuItem.setLabel(
3580 MessageManager.getString("label.principal_component_analysis"));
3581 PCAMenuItem.addActionListener(this);
3582 autoCalculate = new CheckboxMenuItem(
3583 MessageManager.getString("label.autocalculate_consensus"),
3585 averageDistanceTreeMenuItem.setLabel(
3586 MessageManager.getString("label.average_distance_identity"));
3587 averageDistanceTreeMenuItem.addActionListener(this);
3588 neighbourTreeMenuItem.setLabel(
3589 MessageManager.getString("label.neighbour_joining_identity"));
3590 neighbourTreeMenuItem.addActionListener(this);
3591 avDistanceTreeBlosumMenuItem.setLabel(
3592 MessageManager.getString("label.average_distance_blosum62"));
3593 avDistanceTreeBlosumMenuItem.addActionListener(this);
3594 njTreeBlosumMenuItem
3595 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3596 njTreeBlosumMenuItem.addActionListener(this);
3598 .setLabel(MessageManager.getString("action.by_tree_order"));
3599 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3600 Menu calculateTreeMenu = new Menu(
3601 MessageManager.getString("action.calculate_tree"));
3602 autoCalculate.addItemListener(this);
3603 sortByTree.addItemListener(this);
3606 * Configure Help menu items and actions
3608 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3609 documentation.setLabel(MessageManager.getString("label.documentation"));
3610 documentation.addActionListener(this);
3611 about.setLabel(MessageManager.getString("label.about"));
3612 about.addActionListener(this);
3615 * Add top level menus to frame
3617 alignFrameMenuBar.add(fileMenu);
3618 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3619 alignFrameMenuBar.add(editMenu);
3620 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3621 alignFrameMenuBar.add(selectMenu);
3622 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3623 alignFrameMenuBar.add(viewMenu);
3624 Menu annotationsMenu = new Menu(
3625 MessageManager.getString("action.annotations"));
3626 alignFrameMenuBar.add(annotationsMenu);
3627 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3628 alignFrameMenuBar.add(formatMenu);
3629 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3630 alignFrameMenuBar.add(colourMenu);
3631 Menu calculateMenu = new Menu(
3632 MessageManager.getString("action.calculate"));
3633 alignFrameMenuBar.add(calculateMenu);
3634 alignFrameMenuBar.add(helpMenu);
3639 fileMenu.add(inputText);
3640 fileMenu.add(loadTree);
3641 fileMenu.add(loadAnnotations);
3642 fileMenu.addSeparator();
3643 fileMenu.add(outputTextboxMenu);
3644 fileMenu.add(outputFeatures);
3645 fileMenu.add(outputAnnotations);
3646 if (jalviewServletURL != null)
3648 fileMenu.add(loadApplication);
3650 fileMenu.addSeparator();
3651 fileMenu.add(closeMenuItem);
3656 editMenu.add(undoMenuItem);
3657 editMenu.add(redoMenuItem);
3660 pasteMenu.add(pasteNew);
3661 pasteMenu.add(pasteThis);
3662 editMenu.add(pasteMenu);
3663 editMenu.add(delete);
3664 editMenu.addSeparator();
3665 editMenu.add(remove2LeftMenuItem);
3666 editMenu.add(remove2RightMenuItem);
3667 editMenu.add(removeGappedColumnMenuItem);
3668 editMenu.add(removeAllGapsMenuItem);
3669 editMenu.add(removeRedundancyMenuItem);
3674 selectMenu.add(findMenuItem);
3675 selectMenu.addSeparator();
3676 selectMenu.add(selectAllSequenceMenuItem);
3677 selectMenu.add(deselectAllSequenceMenuItem);
3678 selectMenu.add(invertSequenceMenuItem);
3679 selectMenu.add(invertColSel);
3680 selectMenu.add(createGroup);
3681 selectMenu.add(unGroup);
3682 selectMenu.add(grpsFromSelection);
3683 selectMenu.add(deleteGroups);
3684 selectMenu.add(annotationColumnSelection);
3689 viewMenu.add(newView);
3690 viewMenu.addSeparator();
3691 showMenu.add(showColumns);
3692 showMenu.add(showSeqs);
3693 showMenu.add(showAllHidden);
3694 viewMenu.add(showMenu);
3695 hideMenu.add(hideColumns);
3696 hideMenu.add(hideSequences);
3697 hideMenu.add(hideAllSelection);
3698 hideMenu.add(hideAllButSelection);
3699 viewMenu.add(hideMenu);
3700 viewMenu.addSeparator();
3701 viewMenu.add(followMouseOverFlag);
3702 viewMenu.addSeparator();
3703 viewMenu.add(sequenceFeatures);
3704 viewMenu.add(featureSettings);
3705 viewMenu.addSeparator();
3706 viewMenu.add(alProperties);
3707 viewMenu.addSeparator();
3708 viewMenu.add(overviewMenuItem);
3713 annotationsMenu.add(annotationPanelMenuItem);
3714 annotationsMenu.addSeparator();
3715 annotationsMenu.add(showAlignmentAnnotations);
3716 annotationsMenu.add(showSequenceAnnotations);
3717 annotationsMenu.add(sortAnnBySequence);
3718 annotationsMenu.add(sortAnnByLabel);
3719 annotationsMenu.addSeparator();
3720 autoAnnMenu.add(showAutoFirst);
3721 autoAnnMenu.add(showAutoLast);
3722 autoAnnMenu.addSeparator();
3723 autoAnnMenu.add(applyAutoAnnotationSettings);
3724 autoAnnMenu.add(showConsensusHistogram);
3725 autoAnnMenu.add(showSequenceLogo);
3726 autoAnnMenu.add(normSequenceLogo);
3727 autoAnnMenu.addSeparator();
3728 autoAnnMenu.add(showGroupConservation);
3729 autoAnnMenu.add(showGroupConsensus);
3730 annotationsMenu.add(autoAnnMenu);
3735 formatMenu.add(font);
3736 formatMenu.add(seqLimits);
3737 formatMenu.add(wrapMenuItem);
3738 formatMenu.add(scaleAbove);
3739 formatMenu.add(scaleLeft);
3740 formatMenu.add(scaleRight);
3741 formatMenu.add(viewBoxesMenuItem);
3742 formatMenu.add(viewTextMenuItem);
3743 formatMenu.add(colourTextMenuItem);
3744 formatMenu.add(displayNonconservedMenuItem);
3745 formatMenu.add(renderGapsMenuItem);
3746 formatMenu.add(centreColumnLabelFlag);
3751 colourMenu.add(applyToAllGroups);
3752 colourMenu.addSeparator();
3753 colourMenu.add(noColourmenuItem);
3754 colourMenu.add(clustalColour);
3755 colourMenu.add(BLOSUM62Colour);
3756 colourMenu.add(PIDColour);
3757 colourMenu.add(zappoColour);
3758 colourMenu.add(taylorColour);
3759 colourMenu.add(hydrophobicityColour);
3760 colourMenu.add(helixColour);
3761 colourMenu.add(strandColour);
3762 colourMenu.add(turnColour);
3763 colourMenu.add(buriedColour);
3764 colourMenu.add(nucleotideColour);
3765 colourMenu.add(purinePyrimidineColour);
3766 // colourMenu.add(RNAInteractionColour);
3767 colourMenu.add(tcoffeeColour);
3768 colourMenu.add(userDefinedColour);
3769 colourMenu.addSeparator();
3770 colourMenu.add(conservationMenuItem);
3771 colourMenu.add(modifyConservation);
3772 colourMenu.add(abovePIDThreshold);
3773 colourMenu.add(modifyPID);
3774 colourMenu.add(annotationColour);
3775 colourMenu.add(RNAHelixColour);
3780 sortMenu.add(sortIDMenuItem);
3781 sortMenu.add(sortLengthMenuItem);
3782 sortMenu.add(sortByTreeMenu);
3783 sortMenu.add(sortGroupMenuItem);
3784 sortMenu.add(sortPairwiseMenuItem);
3785 calculateMenu.add(sortMenu);
3786 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3787 calculateTreeMenu.add(neighbourTreeMenuItem);
3788 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3789 calculateTreeMenu.add(njTreeBlosumMenuItem);
3790 calculateMenu.add(calculateTreeMenu);
3791 calculateMenu.addSeparator();
3792 calculateMenu.add(pairwiseAlignmentMenuItem);
3793 calculateMenu.add(PCAMenuItem);
3794 calculateMenu.add(autoCalculate);
3795 calculateMenu.add(sortByTree);
3800 helpMenu.add(documentation);
3801 helpMenu.add(about);
3806 statusBar.setBackground(Color.white);
3807 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3808 statusBar.setText(MessageManager.getString("label.status_bar"));
3809 this.add(statusBar, BorderLayout.SOUTH);
3813 public void setStatus(String string)
3815 statusBar.setText(string);
3818 MenuItem featureSettings = new MenuItem();
3820 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3822 MenuItem annotationColour = new MenuItem();
3824 MenuItem annotationColumnSelection = new MenuItem();
3826 MenuItem invertColSel = new MenuItem();
3828 MenuItem showColumns = new MenuItem();
3830 MenuItem showSeqs = new MenuItem();
3832 MenuItem hideColumns = new MenuItem();
3834 MenuItem hideSequences = new MenuItem();
3836 MenuItem hideAllButSelection = new MenuItem();
3838 MenuItem hideAllSelection = new MenuItem();
3840 MenuItem showAllHidden = new MenuItem();
3842 MenuItem newView = new MenuItem();
3844 private CheckboxMenuItem showAlignmentAnnotations;
3846 private CheckboxMenuItem showSequenceAnnotations;
3848 private CheckboxMenuItem sortAnnBySequence;
3850 private CheckboxMenuItem sortAnnByLabel;
3852 private CheckboxMenuItem showAutoFirst;
3854 private CheckboxMenuItem showAutoLast;
3856 private SplitFrame splitFrame;
3859 * Attach the alignFrame panels after embedding menus, if necessary. This used
3860 * to be called setEmbedded, but is now creates the dropdown menus in a
3861 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3863 * @param reallyEmbedded
3864 * true to attach the view to the applet area on the page rather than
3867 public void createAlignFrameWindow(boolean reallyEmbedded)
3871 embedAlignFrameInApplet(viewport.applet);
3876 // test and embed menu bar if necessary.
3878 if (embedMenuIfNeeded(alignPanel))
3881 * adjust for status bar height too. ? pointless as overridden by layout
3884 alignPanel.setSize(getSize().width,
3885 getSize().height - statusBar.getHeight());
3887 add(statusBar, BorderLayout.SOUTH);
3888 add(alignPanel, BorderLayout.CENTER);
3889 // and register with the applet so it can pass external API calls to us
3890 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3896 * Add the components of this AlignFrame to the applet container.
3900 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3903 // Explicitly build the embedded menu panel for the on-page applet
3905 // view cannot be closed if its actually on the page
3906 fileMenu.remove(closeMenuItem);
3907 fileMenu.remove(3); // Remove Separator
3908 // construct embedded menu, using default font
3909 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3910 // and actually add the components to the applet area
3911 theApplet.setLayout(new BorderLayout());
3912 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3913 theApplet.add(statusBar, BorderLayout.SOUTH);
3914 // TODO should size be left to the layout manager?
3915 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3916 - embeddedMenu.getHeight() - statusBar.getHeight());
3917 theApplet.add(alignPanel, BorderLayout.CENTER);
3918 final AlignFrame me = this;
3919 theApplet.addFocusListener(new FocusListener()
3923 public void focusLost(FocusEvent e)
3925 if (theApplet.currentAlignFrame == me)
3927 theApplet.currentAlignFrame = null;
3932 public void focusGained(FocusEvent e)
3934 theApplet.currentAlignFrame = me;
3937 theApplet.validate();
3941 * create a new binding between structures in an existing jmol viewer instance
3942 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3943 * this does not open a new Jmol window, or modify the display of the
3944 * structures in the original jmol window. Note This method doesn't work
3945 * without an additional javascript library to exchange messages between the
3946 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3949 * JmolViewer instance
3950 * @param sequenceIds
3951 * - sequence Ids to search for associations
3953 public SequenceStructureBinding addStructureViewInstance(
3954 Object jmolviewer, String[] sequenceIds)
3956 Viewer viewer = null;
3959 viewer = (Viewer) jmolviewer;
3960 } catch (ClassCastException ex)
3963 "Unsupported viewer object :" + jmolviewer.getClass());
3967 System.err.println("Can't use this object as a structure viewer:"
3968 + jmolviewer.getClass());
3971 SequenceI[] seqs = null;
3972 if (sequenceIds == null || sequenceIds.length == 0)
3974 seqs = viewport.getAlignment().getSequencesArray();
3978 Vector sqi = new Vector();
3979 AlignmentI al = viewport.getAlignment();
3980 for (int sid = 0; sid < sequenceIds.length; sid++)
3982 SequenceI sq = al.findName(sequenceIds[sid]);
3990 seqs = new SequenceI[sqi.size()];
3991 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3993 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4001 AAStructureBindingModel jmv = null;
4002 // TODO: search for a jmv that involves viewer
4004 { // create a new viewer/jalview binding.
4005 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4012 * bind a pdb file to a sequence in the current view
4015 * - sequenceId within the dataset.
4016 * @param pdbEntryString
4017 * - the short name for the PDB file
4019 * - pdb file - either a URL or a valid PDB file.
4020 * @return true if binding was as success TODO: consider making an exception
4021 * structure for indicating when PDB parsing or sequenceId location
4024 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4027 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4028 boolean needtoadd = false;
4029 if (toaddpdb != null)
4031 Vector pdbe = toaddpdb.getAllPDBEntries();
4032 PDBEntry pdbentry = null;
4033 if (pdbe != null && pdbe.size() > 0)
4035 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4037 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4038 if (!pdbentry.getId().equals(pdbEntryString)
4039 && !pdbentry.getFile().equals(pdbFile))
4049 if (pdbentry == null)
4051 pdbentry = new PDBEntry();
4052 pdbentry.setId(pdbEntryString);
4053 pdbentry.setFile(pdbFile);
4054 needtoadd = true; // add this new entry to sequence.
4056 // resolve data source
4057 // TODO: this code should be a refactored to an io package
4058 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4060 if (protocol == null)
4066 pdbentry.setProperty("protocol", protocol);
4067 toaddpdb.addPDBId(pdbentry);
4068 alignPanel.getStructureSelectionManager()
4069 .registerPDBEntry(pdbentry);
4075 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4079 Vector sequences = new Vector();
4080 for (int i = 0; i < seqs.length; i++)
4082 if (seqs[i] != null)
4085 .addElement(new Object[]
4086 { seqs[i], (chains != null) ? chains[i] : null });
4089 seqs = new SequenceI[sequences.size()];
4090 chains = new String[sequences.size()];
4091 for (int i = 0, isize = sequences.size(); i < isize; i++)
4093 Object[] oj = (Object[]) sequences.elementAt(i);
4095 seqs[i] = (SequenceI) oj[0];
4096 chains[i] = (String) oj[1];
4099 return new Object[] { seqs, chains };
4103 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4104 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4106 // Scrub any null sequences from the array
4107 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4108 seqs = (SequenceI[]) sqch[0];
4109 chains = (String[]) sqch[1];
4110 if (seqs == null || seqs.length == 0)
4113 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4115 if (protocol == null)
4117 String sourceType = (String) pdb.getProperty("protocol");
4120 protocol = DataSourceType.valueOf(sourceType);
4121 } catch (IllegalArgumentException e)
4125 if (protocol == null)
4127 System.err.println("Couldn't work out protocol to open structure: "
4132 if (applet.useXtrnalSviewer)
4134 // register the association(s) and quit, don't create any windows.
4135 if (StructureSelectionManager.getStructureSelectionManager(applet)
4136 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4138 System.err.println("Failed to map " + pdb.getFile() + " ("
4139 + protocol + ") to any sequences");
4143 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4145 // can only do alignments with Jmol
4146 // find the last jmol window assigned to this alignment
4147 AppletJmol ajm = null, tajm;
4148 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4149 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4151 tajm = (AppletJmol) jmols.elementAt(i);
4152 if (tajm.ap.alignFrame == this)
4161 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4162 // try and add the pdb structure
4167 // otherwise, create a new window
4168 if (applet.jmolAvailable)
4170 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4171 applet.lastFrameX += 40;
4172 applet.lastFrameY += 40;
4176 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4181 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4182 SequenceI[][] seqs, String[][] chains, String[] protocols)
4184 // TODO Auto-generated method stub
4185 System.err.println("Aligned Structure View: Not yet implemented.");
4189 * modify the current selection, providing the user has not made a selection
4193 * - sequences from this alignment
4195 * - columns to be selected on the alignment
4197 public void select(SequenceGroup sel, ColumnSelection csel,
4198 HiddenColumns hidden)
4200 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4203 public void scrollTo(int row, int column)
4205 alignPanel.seqPanel.scrollTo(row, column);
4208 public void scrollToRow(int row)
4210 alignPanel.seqPanel.scrollToRow(row);
4213 public void scrollToColumn(int column)
4215 alignPanel.seqPanel.scrollToColumn(column);
4219 * @return the alignments unique ID.
4221 public String getSequenceSetId()
4223 return viewport.getSequenceSetId();
4227 * Load the (T-Coffee) score file from the specified url
4230 * File/URL/T-COFFEE score file contents
4231 * @throws IOException
4232 * @return true if alignment was annotated with data from source
4234 public boolean loadScoreFile(String source) throws IOException
4237 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4238 AppletFormatAdapter.checkProtocol(source));
4239 if (!file.isValid())
4241 // TODO: raise dialog for gui
4242 System.err.println("Problems parsing T-Coffee scores: "
4243 + file.getWarningMessage());
4244 System.err.println("Origin was:\n" + source);
4249 * check that the score matrix matches the alignment dimensions
4252 if ((aln = viewport.getAlignment()) != null
4253 && (aln.getHeight() != file.getHeight()
4254 || aln.getWidth() != file.getWidth()))
4256 // TODO: raise a dialog box here rather than bomb out.
4258 "The scores matrix does not match the alignment dimensions");
4262 // TODO add parameter to indicate if matching should be done
4263 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4265 alignPanel.fontChanged();
4266 tcoffeeColour.setEnabled(true);
4267 // switch to this color
4268 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4273 System.err.println("Problems resolving T-Coffee scores:");
4274 if (file.getWarningMessage() != null)
4276 System.err.println(file.getWarningMessage());
4282 public SplitFrame getSplitFrame()
4284 return this.splitFrame;
4287 public void setSplitFrame(SplitFrame sf)
4289 this.splitFrame = sf;
4292 // may not need this
4294 public void setShowSeqFeatures(boolean b)
4296 // showSeqFeatures.setSelected(b);
4297 viewport.setShowSequenceFeatures(b);
4302 public void setMenusForViewport()
4304 // setMenusFromViewport(viewport);
4309 public void refreshFeatureUI(boolean enableIfNecessary)
4311 if (enableIfNecessary)
4313 sequenceFeatures.setState(true);
4314 alignPanel.av.setShowSequenceFeatures(true);
4319 public FeatureSettingsControllerI getFeatureSettingsUI()
4321 return alignPanel.av.featureSettings;