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, 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, true);
419 setStatus(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 setStatus(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 // TODO: repaint flags set only if the keystroke warrants it
695 alignPanel.paintAlignment(true, true);
699 * called by key handler and the hide all/show all menu items
704 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
706 boolean hide = false;
707 SequenceGroup sg = viewport.getSelectionGroup();
708 if (!toggleSeqs && !toggleCols)
710 // Hide everything by the current selection - this is a hack - we do the
711 // invert and then hide
712 // first check that there will be visible columns after the invert.
713 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
714 && sg.getStartRes() <= sg.getEndRes()))
716 // now invert the sequence set, if required - empty selection implies
717 // that no hiding is required.
720 invertSequenceMenuItem_actionPerformed();
721 sg = viewport.getSelectionGroup();
725 viewport.expandColSelection(sg, true);
726 // finally invert the column selection and get the new sequence
727 // selection and indicate it should be hidden.
728 invertColSel_actionPerformed();
735 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
738 viewport.hideAllSelectedSeqs();
740 else if (!(toggleCols && viewport.hasSelectedColumns()))
742 viewport.showAllHiddenSeqs();
748 if (viewport.hasSelectedColumns())
750 viewport.hideSelectedColumns();
753 viewport.setSelectionGroup(sg);
758 viewport.showAllHiddenColumns();
760 viewport.sendSelection();
765 public void keyReleased(KeyEvent evt)
770 public void keyTyped(KeyEvent evt)
775 public void itemStateChanged(ItemEvent evt)
777 final Object source = evt.getSource();
778 if (source == displayNonconservedMenuItem)
780 displayNonconservedMenuItem_actionPerformed();
782 else if (source == colourTextMenuItem)
784 colourTextMenuItem_actionPerformed();
786 else if (source == wrapMenuItem)
788 wrapMenuItem_actionPerformed();
790 else if (source == scaleAbove)
792 viewport.setScaleAboveWrapped(scaleAbove.getState());
794 else if (source == scaleLeft)
796 viewport.setScaleLeftWrapped(scaleLeft.getState());
798 else if (source == scaleRight)
800 viewport.setScaleRightWrapped(scaleRight.getState());
802 else if (source == seqLimits)
804 seqLimits_itemStateChanged();
806 else if (source == viewBoxesMenuItem)
808 viewport.setShowBoxes(viewBoxesMenuItem.getState());
810 else if (source == viewTextMenuItem)
812 viewport.setShowText(viewTextMenuItem.getState());
814 else if (source == renderGapsMenuItem)
816 viewport.setRenderGaps(renderGapsMenuItem.getState());
818 else if (source == annotationPanelMenuItem)
820 boolean showAnnotations = annotationPanelMenuItem.getState();
821 showAlignmentAnnotations.setEnabled(showAnnotations);
822 showSequenceAnnotations.setEnabled(showAnnotations);
823 viewport.setShowAnnotation(showAnnotations);
824 alignPanel.setAnnotationVisible(showAnnotations);
826 else if (source == sequenceFeatures)
828 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
829 alignPanel.seqPanel.seqCanvas.repaint();
831 else if (source == showAlignmentAnnotations)
833 setAnnotationsVisibility();
835 else if (source == showSequenceAnnotations)
837 setAnnotationsVisibility();
839 else if (source == sortAnnBySequence)
841 boolean newState = sortAnnBySequence.getState();
842 sortAnnByLabel.setState(false);
843 setAnnotationSortOrder(
844 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
845 : SequenceAnnotationOrder.NONE);
846 setViewportAnnotationOrder();
848 else if (source == sortAnnByLabel)
850 boolean newState = sortAnnByLabel.getState();
851 sortAnnBySequence.setState(false);
852 setAnnotationSortOrder(
853 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
854 : SequenceAnnotationOrder.NONE);
855 setViewportAnnotationOrder();
857 else if (source == showAutoFirst)
859 showAutoLast.setState(!showAutoFirst.getState());
860 setShowAutoCalculatedAbove(showAutoFirst.getState());
861 setViewportAnnotationOrder();
863 else if (source == showAutoLast)
865 showAutoFirst.setState(!showAutoLast.getState());
866 setShowAutoCalculatedAbove(showAutoFirst.getState());
867 setViewportAnnotationOrder();
869 else if (source == conservationMenuItem)
871 conservationMenuItem_actionPerformed();
873 else if (source == abovePIDThreshold)
875 abovePIDThreshold_actionPerformed();
877 else if (source == applyToAllGroups)
879 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
881 else if (source == autoCalculate)
883 viewport.autoCalculateConsensus = autoCalculate.getState();
885 else if (source == sortByTree)
887 viewport.sortByTree = sortByTree.getState();
889 else if (source == this.centreColumnLabelFlag)
891 centreColumnLabelFlag_stateChanged();
893 else if (source == this.followMouseOverFlag)
895 mouseOverFlag_stateChanged();
897 else if (source == showGroupConsensus)
899 showGroupConsensus_actionPerformed();
901 else if (source == showGroupConservation)
903 showGroupConservation_actionPerformed();
905 else if (source == showSequenceLogo)
907 showSequenceLogo_actionPerformed();
909 else if (source == normSequenceLogo)
911 normSequenceLogo_actionPerformed();
913 else if (source == showConsensusHistogram)
915 showConsensusHistogram_actionPerformed();
917 else if (source == applyAutoAnnotationSettings)
919 applyAutoAnnotationSettings_actionPerformed();
921 // TODO: repaint flags set only if warranted
922 alignPanel.paintAlignment(true, true);
926 * Set the visibility state of sequence-related and/or alignment-related
927 * annotations depending on checkbox selections, and repaint.
931 private void setAnnotationsVisibility()
933 boolean showForAlignment = showAlignmentAnnotations.getState();
934 boolean showForSequences = showSequenceAnnotations.getState();
935 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
937 for (AlignmentAnnotation aa : alignPanel.getAlignment()
938 .getAlignmentAnnotation())
940 boolean visible = (aa.sequenceRef == null ? showForAlignment
942 aa.visible = visible;
945 alignPanel.validateAnnotationDimensions(true);
950 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
952 this.annotationSortOrder = order;
956 * Set flags on the viewport that control annotation ordering
958 private void setViewportAnnotationOrder()
960 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
962 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
965 private void setShowAutoCalculatedAbove(boolean showAbove)
967 this.showAutoCalculatedAbove = showAbove;
970 private void mouseOverFlag_stateChanged()
972 viewport.setFollowHighlight(followMouseOverFlag.getState());
973 // TODO: could kick the scrollTo mechanism to reset view for current
977 private void centreColumnLabelFlag_stateChanged()
979 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
980 this.alignPanel.annotationPanel.repaint();
984 public void actionPerformed(ActionEvent evt)
986 viewport.applet.currentAlignFrame = this;
988 Object source = evt.getSource();
990 if (source == inputText)
992 inputText_actionPerformed();
994 else if (source == loadTree)
996 loadTree_actionPerformed();
998 else if (source == loadApplication)
1000 launchFullApplication();
1002 else if (source == loadAnnotations)
1006 else if (source == outputAnnotations)
1008 outputAnnotations(true);
1010 else if (source == outputFeatures)
1012 outputFeatures(true, "Jalview");
1014 else if (source == closeMenuItem)
1016 closeMenuItem_actionPerformed();
1018 else if (source == copy)
1020 copy_actionPerformed();
1022 else if (source == undoMenuItem)
1024 undoMenuItem_actionPerformed();
1026 else if (source == redoMenuItem)
1028 redoMenuItem_actionPerformed();
1030 else if (source == inputText)
1032 inputText_actionPerformed();
1034 else if (source == closeMenuItem)
1036 closeMenuItem_actionPerformed();
1038 else if (source == undoMenuItem)
1040 undoMenuItem_actionPerformed();
1042 else if (source == redoMenuItem)
1044 redoMenuItem_actionPerformed();
1046 else if (source == copy)
1048 copy_actionPerformed();
1050 else if (source == pasteNew)
1052 pasteNew_actionPerformed();
1054 else if (source == pasteThis)
1056 pasteThis_actionPerformed();
1058 else if (source == cut)
1060 cut_actionPerformed();
1062 else if (source == delete)
1064 delete_actionPerformed();
1066 else if (source == createGroup)
1068 createGroup_actionPerformed();
1070 else if (source == unGroup)
1072 unGroup_actionPerformed();
1074 else if (source == grpsFromSelection)
1076 makeGrpsFromSelection_actionPerformed();
1078 else if (source == deleteGroups)
1080 deleteGroups_actionPerformed();
1082 else if (source == selectAllSequenceMenuItem)
1084 selectAllSequenceMenuItem_actionPerformed();
1086 else if (source == deselectAllSequenceMenuItem)
1088 deselectAllSequenceMenuItem_actionPerformed();
1090 else if (source == invertSequenceMenuItem)
1092 invertSequenceMenuItem_actionPerformed();
1093 // uncomment to slave sequence selections in split frame
1094 // viewport.sendSelection();
1096 else if (source == invertColSel)
1098 viewport.invertColumnSelection();
1099 alignPanel.paintAlignment(false, false);
1100 viewport.sendSelection();
1102 else if (source == remove2LeftMenuItem)
1104 trimAlignment(true);
1106 else if (source == remove2RightMenuItem)
1108 trimAlignment(false);
1110 else if (source == removeGappedColumnMenuItem)
1112 removeGappedColumnMenuItem_actionPerformed();
1114 else if (source == removeAllGapsMenuItem)
1116 removeAllGapsMenuItem_actionPerformed();
1118 else if (source == findMenuItem)
1120 findMenuItem_actionPerformed();
1122 else if (source == font)
1124 new FontChooser(alignPanel);
1126 else if (source == newView)
1130 else if (source == showColumns)
1132 viewport.showAllHiddenColumns();
1133 alignPanel.paintAlignment(true, true);
1134 viewport.sendSelection();
1136 else if (source == showSeqs)
1138 viewport.showAllHiddenSeqs();
1139 alignPanel.paintAlignment(true, true);
1140 // uncomment if we want to slave sequence selections in split frame
1141 // viewport.sendSelection();
1143 else if (source == hideColumns)
1145 viewport.hideSelectedColumns();
1146 alignPanel.paintAlignment(true, true);
1147 viewport.sendSelection();
1149 else if (source == hideSequences
1150 && viewport.getSelectionGroup() != null)
1152 viewport.hideAllSelectedSeqs();
1153 alignPanel.paintAlignment(true, true);
1154 // uncomment if we want to slave sequence selections in split frame
1155 // viewport.sendSelection();
1157 else if (source == hideAllButSelection)
1159 toggleHiddenRegions(false, false);
1160 alignPanel.paintAlignment(true, true);
1161 viewport.sendSelection();
1163 else if (source == hideAllSelection)
1165 SequenceGroup sg = viewport.getSelectionGroup();
1166 viewport.expandColSelection(sg, false);
1167 viewport.hideAllSelectedSeqs();
1168 viewport.hideSelectedColumns();
1169 alignPanel.paintAlignment(true, true);
1170 viewport.sendSelection();
1172 else if (source == showAllHidden)
1174 viewport.showAllHiddenColumns();
1175 viewport.showAllHiddenSeqs();
1176 alignPanel.paintAlignment(true, true);
1177 viewport.sendSelection();
1179 else if (source == showGroupConsensus)
1181 showGroupConsensus_actionPerformed();
1183 else if (source == showGroupConservation)
1185 showGroupConservation_actionPerformed();
1187 else if (source == showSequenceLogo)
1189 showSequenceLogo_actionPerformed();
1191 else if (source == normSequenceLogo)
1193 normSequenceLogo_actionPerformed();
1195 else if (source == showConsensusHistogram)
1197 showConsensusHistogram_actionPerformed();
1199 else if (source == applyAutoAnnotationSettings)
1201 applyAutoAnnotationSettings_actionPerformed();
1203 else if (source == featureSettings)
1205 new FeatureSettings(alignPanel);
1207 else if (source == alProperties)
1209 StringBuffer contents = new jalview.io.AlignmentProperties(
1210 viewport.getAlignment()).formatAsString();
1211 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212 cap.setText(contents.toString());
1213 Frame frame = new Frame();
1215 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1216 .formatMessage("label.alignment_properties", new String[]
1217 { getTitle() }), 400, 250);
1219 else if (source == overviewMenuItem)
1221 overviewMenuItem_actionPerformed();
1223 else if (source == noColourmenuItem)
1227 else if (source == clustalColour)
1229 abovePIDThreshold.setState(false);
1230 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1232 else if (source == zappoColour)
1234 changeColour(new ZappoColourScheme());
1236 else if (source == taylorColour)
1238 changeColour(new TaylorColourScheme());
1240 else if (source == hydrophobicityColour)
1242 changeColour(new HydrophobicColourScheme());
1244 else if (source == helixColour)
1246 changeColour(new HelixColourScheme());
1248 else if (source == strandColour)
1250 changeColour(new StrandColourScheme());
1252 else if (source == turnColour)
1254 changeColour(new TurnColourScheme());
1256 else if (source == buriedColour)
1258 changeColour(new BuriedColourScheme());
1260 else if (source == nucleotideColour)
1262 changeColour(new NucleotideColourScheme());
1264 else if (source == purinePyrimidineColour)
1266 changeColour(new PurinePyrimidineColourScheme());
1268 // else if (source == RNAInteractionColour)
1270 // changeColour(new RNAInteractionColourScheme());
1272 else if (source == RNAHelixColour)
1274 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1275 // new RNAHelicesColourChooser(viewport, alignPanel);
1277 else if (source == modifyPID)
1279 modifyPID_actionPerformed();
1281 else if (source == modifyConservation)
1283 modifyConservation_actionPerformed();
1285 else if (source == userDefinedColour)
1287 new UserDefinedColours(alignPanel, null);
1289 else if (source == PIDColour)
1291 changeColour(new PIDColourScheme());
1293 else if (source == BLOSUM62Colour)
1295 changeColour(new Blosum62ColourScheme());
1297 else if (source == tcoffeeColour)
1299 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1301 else if (source == annotationColour)
1303 new AnnotationColourChooser(viewport, alignPanel);
1305 else if (source == annotationColumnSelection)
1307 new AnnotationColumnChooser(viewport, alignPanel);
1309 else if (source == sortPairwiseMenuItem)
1311 sortPairwiseMenuItem_actionPerformed();
1313 else if (source == sortIDMenuItem)
1315 sortIDMenuItem_actionPerformed();
1317 else if (source == sortLengthMenuItem)
1319 sortLengthMenuItem_actionPerformed();
1321 else if (source == sortGroupMenuItem)
1323 sortGroupMenuItem_actionPerformed();
1325 else if (source == removeRedundancyMenuItem)
1327 removeRedundancyMenuItem_actionPerformed();
1329 else if (source == pairwiseAlignmentMenuItem)
1331 pairwiseAlignmentMenuItem_actionPerformed();
1333 else if (source == PCAMenuItem)
1335 PCAMenuItem_actionPerformed();
1337 else if (source == averageDistanceTreeMenuItem)
1339 averageDistanceTreeMenuItem_actionPerformed();
1341 else if (source == neighbourTreeMenuItem)
1343 neighbourTreeMenuItem_actionPerformed();
1345 else if (source == njTreeBlosumMenuItem)
1347 njTreeBlosumMenuItem_actionPerformed();
1349 else if (source == avDistanceTreeBlosumMenuItem)
1351 avTreeBlosumMenuItem_actionPerformed();
1353 else if (source == documentation)
1355 documentation_actionPerformed();
1357 else if (source == about)
1359 about_actionPerformed();
1364 public void inputText_actionPerformed()
1366 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1367 Frame frame = new Frame();
1369 jalview.bin.JalviewLite.addFrame(frame,
1370 MessageManager.getString("label.input_cut_paste"), 500, 500);
1373 protected void outputText_actionPerformed(ActionEvent e)
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376 Frame frame = new Frame();
1378 JalviewLite.addFrame(frame, MessageManager
1379 .formatMessage("label.alignment_output_command", new Object[]
1380 { e.getActionCommand() }), 600, 500);
1382 FileFormatI fileFormat = FileFormats.getInstance()
1383 .forName(e.getActionCommand());
1385 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1386 viewport.getAlignment(), viewport.getShowJVSuffix()));
1389 public void loadAnnotations()
1391 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1392 cap.setText(MessageManager
1393 .getString("label.paste_features_annotations_Tcoffee_here"));
1394 cap.setAnnotationImport();
1395 Frame frame = new Frame();
1397 jalview.bin.JalviewLite.addFrame(frame,
1398 MessageManager.getString("action.paste_annotations"), 400, 300);
1402 public String outputAnnotations(boolean displayTextbox)
1404 String annotation = new AnnotationFile()
1405 .printAnnotationsForView(viewport);
1409 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1410 Frame frame = new Frame();
1412 jalview.bin.JalviewLite.addFrame(frame,
1413 MessageManager.getString("label.annotations"), 600, 500);
1414 cap.setText(annotation);
1420 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1422 if (alignPanel.getFeatureRenderer() != null
1423 && viewport.getFeaturesDisplayed() != null)
1425 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1431 private List<String> getDisplayedFeatureGroups()
1433 if (alignPanel.getFeatureRenderer() != null
1434 && viewport.getFeaturesDisplayed() != null)
1436 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1442 public String outputFeatures(boolean displayTextbox, String format)
1445 FeaturesFile formatter = new FeaturesFile();
1446 if (format.equalsIgnoreCase("Jalview"))
1448 features = formatter.printJalviewFormat(
1449 viewport.getAlignment().getSequencesArray(),
1450 alignPanel.getFeatureRenderer(), true);
1454 features = formatter.printGffFormat(viewport.getAlignment()
1455 .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
1460 boolean frimport = false;
1461 if (features == null || features.equals("No Features Visible"))
1463 features = "# No features visible - paste some and import them here.";
1467 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1470 cap.setAnnotationImport();
1472 Frame frame = new Frame();
1474 jalview.bin.JalviewLite.addFrame(frame,
1475 MessageManager.getString("label.features"), 600, 500);
1476 cap.setText(features);
1480 if (features == null)
1489 void launchFullApplication()
1491 StringBuffer url = new StringBuffer(jalviewServletURL);
1493 // allow servlet parameters to be passed in applet parameter
1494 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1496 url.append(firstSep);
1499 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1501 if (viewport.applet.getParameter("features") != null)
1503 url.append("&features=");
1504 url.append(appendProtocol(viewport.applet.getParameter("features")));
1507 if (viewport.applet.getParameter("annotations") != null)
1509 url.append("&annotations=");
1511 appendProtocol(viewport.applet.getParameter("annotations")));
1514 if (viewport.applet.getParameter("jnetfile") != null
1515 || viewport.applet.getParameter("jpredfile") != null)
1517 url.append("&annotations=");
1518 url.append(appendProtocol(
1519 viewport.applet.getParameter("jnetfile") != null
1520 ? viewport.applet.getParameter("jnetfile")
1521 : viewport.applet.getParameter("jpredfile")));
1524 if (viewport.applet.getParameter("defaultColour") != null)
1526 url.append("&colour=" + removeWhiteSpace(
1527 viewport.applet.getParameter("defaultColour")));
1530 if (viewport.applet.getParameter("userDefinedColour") != null)
1532 url.append("&colour=" + removeWhiteSpace(
1533 viewport.applet.getParameter("userDefinedColour")));
1535 if (viewport.applet.getParameter("tree") != null)
1538 + appendProtocol(viewport.applet.getParameter("tree")));
1540 if (viewport.applet.getParameter("treeFile") != null)
1543 + appendProtocol(viewport.applet.getParameter("treeFile")));
1546 showURL(url.toString(), "FULL_APP");
1549 String removeWhiteSpace(String colour)
1551 StringBuffer sb = new StringBuffer();
1552 for (int i = 0; i < colour.length(); i++)
1554 if (Character.isWhitespace(colour.charAt(i)))
1560 sb.append(colour.charAt(i));
1564 return sb.toString();
1567 String appendProtocol(String url)
1572 url = URLEncoder.encode(url);
1575 * When we finally deprecate 1.1 compatibility, we can start to use
1576 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1577 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1578 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1579 * ex.printStackTrace(); }
1581 catch (java.net.MalformedURLException ex)
1583 url = viewport.applet.getCodeBase() + url;
1588 public void closeMenuItem_actionPerformed()
1590 PaintRefresher.RemoveComponent(alignPanel);
1591 if (alignPanel.seqPanel != null
1592 && alignPanel.seqPanel.seqCanvas != null)
1594 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1596 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1598 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1601 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1607 if (alignPanel != null && alignPanel.overviewPanel != null)
1609 alignPanel.overviewPanel.dispose();
1618 void updateEditMenuBar()
1621 if (viewport.getHistoryList().size() > 0)
1623 undoMenuItem.setEnabled(true);
1624 CommandI command = viewport.getHistoryList().peek();
1625 undoMenuItem.setLabel(MessageManager
1626 .formatMessage("label.undo_command", new Object[]
1627 { command.getDescription() }));
1631 undoMenuItem.setEnabled(false);
1632 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1635 if (viewport.getRedoList().size() > 0)
1637 redoMenuItem.setEnabled(true);
1639 CommandI command = viewport.getRedoList().peek();
1640 redoMenuItem.setLabel(MessageManager
1641 .formatMessage("label.redo_command", new Object[]
1642 { command.getDescription() }));
1646 redoMenuItem.setEnabled(false);
1647 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1655 public void addHistoryItem(CommandI command)
1657 if (command.getSize() > 0)
1659 viewport.addToHistoryList(command);
1660 viewport.clearRedoList();
1661 updateEditMenuBar();
1662 viewport.updateHiddenColumns();
1667 * TODO: JAL-1104 DOCUMENT ME!
1672 protected void undoMenuItem_actionPerformed()
1674 if (viewport.getHistoryList().isEmpty())
1679 CommandI command = viewport.getHistoryList().pop();
1680 viewport.addToRedoList(command);
1681 command.undoCommand(null);
1683 AlignmentViewport originalSource = getOriginatingSource(command);
1685 if (originalSource != viewport)
1688 .println("Warning: Viewport object mismatch whilst undoing");
1690 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1691 // viewport.getColumnSelection().getHiddenColumns()
1693 updateEditMenuBar();
1694 originalSource.firePropertyChange("alignment", null,
1695 originalSource.getAlignment().getSequences());
1699 * TODO: JAL-1104 DOCUMENT ME!
1704 protected void redoMenuItem_actionPerformed()
1706 if (viewport.getRedoList().isEmpty())
1711 CommandI command = viewport.getRedoList().pop();
1712 viewport.addToHistoryList(command);
1713 command.doCommand(null);
1715 AlignmentViewport originalSource = getOriginatingSource(command);
1717 if (originalSource != viewport)
1720 .println("Warning: Viewport object mismatch whilst re-doing");
1722 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1723 // viewport.getColumnSelection().getHiddenColumns()
1726 updateEditMenuBar();
1727 originalSource.firePropertyChange("alignment", null,
1728 originalSource.getAlignment().getSequences());
1731 AlignmentViewport getOriginatingSource(CommandI command)
1733 AlignmentViewport originalSource = null;
1734 // For sequence removal and addition, we need to fire
1735 // the property change event FROM the viewport where the
1736 // original alignment was altered
1737 AlignmentI al = null;
1738 if (command instanceof EditCommand)
1740 EditCommand editCommand = (EditCommand) command;
1741 al = editCommand.getAlignment();
1742 Vector comps = PaintRefresher.components
1743 .get(viewport.getSequenceSetId());
1744 for (int i = 0; i < comps.size(); i++)
1746 if (comps.elementAt(i) instanceof AlignmentPanel)
1748 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1750 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1757 if (originalSource == null)
1759 // The original view is closed, we must validate
1760 // the current view against the closed view first
1763 PaintRefresher.validateSequences(al, viewport.getAlignment());
1766 originalSource = viewport;
1769 return originalSource;
1773 * Move the currently selected sequences up or down one position in the
1778 public void moveSelectedSequences(boolean up)
1780 SequenceGroup sg = viewport.getSelectionGroup();
1785 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1786 up ? null : viewport.getHiddenRepSequences(), up);
1787 alignPanel.paintAlignment(true, false);
1790 * Also move cDNA/protein complement sequences
1792 AlignViewportI complement = viewport.getCodingComplement();
1793 if (complement != null)
1795 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1796 viewport, complement);
1797 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1798 up ? null : complement.getHiddenRepSequences(), up);
1799 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1804 synchronized void slideSequences(boolean right, int size)
1806 List<SequenceI> sg = new Vector<>();
1807 if (viewport.cursorMode)
1809 sg.add(viewport.getAlignment()
1810 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1812 else if (viewport.getSelectionGroup() != null
1813 && viewport.getSelectionGroup().getSize() != viewport
1814 .getAlignment().getHeight())
1816 sg = viewport.getSelectionGroup()
1817 .getSequences(viewport.getHiddenRepSequences());
1825 Vector<SequenceI> invertGroup = new Vector();
1827 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1829 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1831 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1835 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1837 SequenceI[] seqs2 = invertGroup
1838 .toArray(new SequenceI[invertGroup.size()]);
1839 for (int i = 0; i < invertGroup.size(); i++)
1841 seqs2[i] = invertGroup.elementAt(i);
1844 SlideSequencesCommand ssc;
1847 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1848 viewport.getGapCharacter());
1852 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1853 viewport.getGapCharacter());
1856 int groupAdjustment = 0;
1857 if (ssc.getGapsInsertedBegin() && right)
1859 if (viewport.cursorMode)
1861 alignPanel.seqPanel.moveCursor(size, 0);
1865 groupAdjustment = size;
1868 else if (!ssc.getGapsInsertedBegin() && !right)
1870 if (viewport.cursorMode)
1872 alignPanel.seqPanel.moveCursor(-size, 0);
1876 groupAdjustment = -size;
1880 if (groupAdjustment != 0)
1882 viewport.getSelectionGroup().setStartRes(
1883 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1884 viewport.getSelectionGroup().setEndRes(
1885 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1888 boolean appendHistoryItem = false;
1889 Deque<CommandI> historyList = viewport.getHistoryList();
1890 if (historyList != null && historyList.size() > 0
1891 && historyList.peek() instanceof SlideSequencesCommand)
1893 appendHistoryItem = ssc.appendSlideCommand(
1894 (SlideSequencesCommand) historyList.peek());
1897 if (!appendHistoryItem)
1899 addHistoryItem(ssc);
1905 static StringBuffer copiedSequences;
1907 static HiddenColumns copiedHiddenColumns;
1909 protected void copy_actionPerformed()
1911 if (viewport.getSelectionGroup() == null)
1916 SequenceGroup sg = viewport.getSelectionGroup();
1917 copiedSequences = new StringBuffer();
1918 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1919 for (int i = 0; i < sg.getSize(); i++)
1921 SequenceI seq = sg.getSequenceAt(i);
1922 int index = viewport.getAlignment().findIndex(seq);
1923 orderedSeqs.put(index, seq);
1926 int index = 0, startRes, endRes;
1929 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1931 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1932 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1934 // create new HiddenColumns object with copy of hidden regions
1935 // between startRes and endRes, offset by startRes
1936 copiedHiddenColumns = new HiddenColumns(
1937 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1938 hiddenCutoff, hiddenOffset);
1942 copiedHiddenColumns = null;
1945 for (int i = 0; i < sg.getSize(); i++)
1947 SequenceI seq = null;
1951 if (orderedSeqs.containsKey(index))
1953 seq = orderedSeqs.get(index);
1964 // Returns residue following index if gap
1965 startRes = seq.findPosition(sg.getStartRes());
1968 // Need to find the residue preceeding index if gap
1971 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1973 ch = seq.getCharAt(j);
1974 if (!jalview.util.Comparison.isGap((ch)))
1982 endRes += seq.getStart() - 1;
1985 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1986 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1993 protected void pasteNew_actionPerformed()
1998 protected void pasteThis_actionPerformed()
2003 void paste(boolean newAlignment)
2007 if (copiedSequences == null)
2012 StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2014 Vector seqs = new Vector();
2015 while (st.hasMoreElements())
2017 String name = st.nextToken();
2018 int start = Integer.parseInt(st.nextToken());
2019 int end = Integer.parseInt(st.nextToken());
2020 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2022 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2023 for (int i = 0; i < seqs.size(); i++)
2025 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2030 String newtitle = MessageManager
2031 .getString("label.copied_sequences");
2032 if (getTitle().startsWith(
2033 MessageManager.getString("label.copied_sequences")))
2035 newtitle = getTitle();
2039 newtitle = newtitle.concat(MessageManager
2040 .formatMessage("label.from_msname", new String[]
2043 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2044 viewport.applet, newtitle, false);
2045 af.viewport.setHiddenColumns(copiedHiddenColumns);
2047 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2052 addSequences(newSeqs);
2055 } catch (Exception ex)
2057 } // could be anything being pasted in here
2061 void addSequences(SequenceI[] seqs)
2063 for (int i = 0; i < seqs.length; i++)
2065 viewport.getAlignment().addSequence(seqs[i]);
2069 addHistoryItem(new EditCommand(
2070 MessageManager.getString("label.add_sequences"), Action.PASTE,
2071 seqs, 0, viewport.getAlignment().getWidth(),
2072 viewport.getAlignment()));
2074 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2075 viewport.getAlignment().getWidth();
2076 viewport.firePropertyChange("alignment", null,
2077 viewport.getAlignment().getSequences());
2081 protected void cut_actionPerformed()
2083 copy_actionPerformed();
2084 delete_actionPerformed();
2087 protected void delete_actionPerformed()
2090 SequenceGroup sg = viewport.getSelectionGroup();
2096 Vector seqs = new Vector();
2098 for (int i = 0; i < sg.getSize(); i++)
2100 seq = sg.getSequenceAt(i);
2101 seqs.addElement(seq);
2105 * If the cut affects all sequences, warn, remove highlighted columns
2107 if (sg.getSize() == viewport.getAlignment().getHeight())
2109 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2110 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2111 if (isEntireAlignWidth)
2113 String title = MessageManager.getString("label.delete_all");
2114 Panel infoPanel = new Panel();
2115 infoPanel.setLayout(new FlowLayout());
2117 new Label(MessageManager.getString("warn.delete_all")));
2119 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2120 dialog.setMainPanel(infoPanel);
2121 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2122 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2123 dialog.setVisible(true);
2130 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2131 sg.getEndRes() + 1);
2134 SequenceI[] cut = new SequenceI[seqs.size()];
2135 for (int i = 0; i < seqs.size(); i++)
2137 cut[i] = (SequenceI) seqs.elementAt(i);
2141 * //ADD HISTORY ITEM
2143 addHistoryItem(new EditCommand(
2144 MessageManager.getString("label.cut_sequences"), Action.CUT,
2145 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2146 viewport.getAlignment()));
2148 viewport.setSelectionGroup(null);
2149 viewport.getAlignment().deleteGroup(sg);
2151 viewport.firePropertyChange("alignment", null,
2152 viewport.getAlignment().getSequences());
2154 if (viewport.getAlignment().getHeight() < 1)
2156 this.setVisible(false);
2158 viewport.sendSelection();
2162 * group consensus toggled
2165 protected void showGroupConsensus_actionPerformed()
2167 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2168 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2173 * group conservation toggled.
2175 protected void showGroupConservation_actionPerformed()
2177 viewport.setShowGroupConservation(showGroupConservation.getState());
2178 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2185 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2186 * .event.ActionEvent)
2188 protected void showConsensusHistogram_actionPerformed()
2190 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2191 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2198 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2199 * .event.ActionEvent)
2201 protected void showSequenceLogo_actionPerformed()
2203 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2204 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2207 protected void normSequenceLogo_actionPerformed()
2209 showSequenceLogo.setState(true);
2210 viewport.setShowSequenceLogo(true);
2211 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2212 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2215 protected void applyAutoAnnotationSettings_actionPerformed()
2217 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2220 protected void makeGrpsFromSelection_actionPerformed()
2222 if (avc.makeGroupsFromSelection())
2224 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2225 alignPanel.updateAnnotation();
2226 alignPanel.paintAlignment(true, true);
2230 protected void createGroup_actionPerformed()
2235 protected void unGroup_actionPerformed()
2239 alignPanel.alignmentChanged();
2243 protected void deleteGroups_actionPerformed()
2245 if (avc.deleteGroups())
2247 alignPanel.alignmentChanged();
2251 public void selectAllSequenceMenuItem_actionPerformed()
2253 SequenceGroup sg = new SequenceGroup();
2254 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2256 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2258 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2259 viewport.setSelectionGroup(sg);
2260 // JAL-2034 - should delegate to
2261 // alignPanel to decide if overview needs
2263 alignPanel.paintAlignment(false, false);
2264 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2265 viewport.sendSelection();
2268 public void deselectAllSequenceMenuItem_actionPerformed()
2270 if (viewport.cursorMode)
2272 alignPanel.seqPanel.keyboardNo1 = null;
2273 alignPanel.seqPanel.keyboardNo2 = null;
2275 viewport.setSelectionGroup(null);
2276 viewport.getColumnSelection().clear();
2277 viewport.setSelectionGroup(null);
2278 alignPanel.idPanel.idCanvas.searchResults = null;
2279 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2280 // JAL-2034 - should delegate to
2281 // alignPanel to decide if overview needs
2283 alignPanel.paintAlignment(false, false);
2284 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2285 viewport.sendSelection();
2288 public void invertSequenceMenuItem_actionPerformed()
2290 SequenceGroup sg = viewport.getSelectionGroup();
2291 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2293 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2296 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297 viewport.sendSelection();
2300 public void invertColSel_actionPerformed()
2302 viewport.invertColumnSelection();
2303 alignPanel.paintAlignment(true, false);
2304 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2305 viewport.sendSelection();
2308 void trimAlignment(boolean trimLeft)
2310 AlignmentI al = viewport.getAlignment();
2311 ViewportRanges ranges = viewport.getRanges();
2312 ColumnSelection colSel = viewport.getColumnSelection();
2315 if (!colSel.isEmpty())
2319 column = colSel.getMin();
2323 column = colSel.getMax();
2327 if (viewport.getSelectionGroup() != null)
2329 seqs = viewport.getSelectionGroup()
2330 .getSequencesAsArray(viewport.getHiddenRepSequences());
2334 seqs = al.getSequencesArray();
2337 TrimRegionCommand trimRegion;
2340 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2342 ranges.setStartRes(0);
2346 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2350 setStatus(MessageManager
2351 .formatMessage("label.removed_columns", new String[]
2352 { Integer.valueOf(trimRegion.getSize()).toString() }));
2353 addHistoryItem(trimRegion);
2355 for (SequenceGroup sg : al.getGroups())
2357 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2358 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2364 viewport.firePropertyChange("alignment", null, al.getSequences());
2368 public void removeGappedColumnMenuItem_actionPerformed()
2370 AlignmentI al = viewport.getAlignment();
2371 ViewportRanges ranges = viewport.getRanges();
2373 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2376 if (viewport.getSelectionGroup() != null)
2378 seqs = viewport.getSelectionGroup()
2379 .getSequencesAsArray(viewport.getHiddenRepSequences());
2380 start = viewport.getSelectionGroup().getStartRes();
2381 end = viewport.getSelectionGroup().getEndRes();
2385 seqs = viewport.getAlignment().getSequencesArray();
2388 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2389 "Remove Gapped Columns", seqs, start, end,
2390 viewport.getAlignment());
2392 addHistoryItem(removeGapCols);
2394 setStatus(MessageManager
2395 .formatMessage("label.removed_empty_columns", new String[]
2396 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2398 // This is to maintain viewport position on first residue
2399 // of first sequence
2400 SequenceI seq = al.getSequenceAt(0);
2401 int startRes = seq.findPosition(ranges.getStartRes());
2402 // ShiftList shifts;
2403 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2404 // edit.alColumnChanges=shifts.getInverse();
2405 // if (viewport.hasHiddenColumns)
2406 // viewport.getColumnSelection().compensateForEdits(shifts);
2407 ranges.setStartRes(seq.findIndex(startRes) - 1);
2408 viewport.firePropertyChange("alignment", null, al.getSequences());
2412 public void removeAllGapsMenuItem_actionPerformed()
2414 AlignmentI al = viewport.getAlignment();
2415 ViewportRanges ranges = viewport.getRanges();
2417 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2420 if (viewport.getSelectionGroup() != null)
2422 seqs = viewport.getSelectionGroup()
2423 .getSequencesAsArray(viewport.getHiddenRepSequences());
2424 start = viewport.getSelectionGroup().getStartRes();
2425 end = viewport.getSelectionGroup().getEndRes();
2429 seqs = viewport.getAlignment().getSequencesArray();
2432 // This is to maintain viewport position on first residue
2433 // of first sequence
2434 SequenceI seq = al.getSequenceAt(0);
2435 int startRes = seq.findPosition(ranges.getStartRes());
2438 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2440 ranges.setStartRes(seq.findIndex(startRes) - 1);
2442 viewport.firePropertyChange("alignment", null, al.getSequences());
2446 public void findMenuItem_actionPerformed()
2448 new Finder(alignPanel);
2452 * create a new view derived from the current view
2455 * @return frame for the new view
2457 public AlignFrame newView(String viewtitle)
2460 if (viewport.hasHiddenRows())
2462 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2463 .getFullAlignment().getSequencesArray());
2467 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2470 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2472 for (int i = 0; i < viewport.getAlignment()
2473 .getAlignmentAnnotation().length; i++)
2475 if (!viewport.getAlignment()
2476 .getAlignmentAnnotation()[i].autoCalculated)
2478 newal.addAnnotation(
2479 viewport.getAlignment().getAlignmentAnnotation()[i]);
2484 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2486 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2487 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2488 PaintRefresher.Register(newaf.alignPanel,
2489 newaf.alignPanel.av.getSequenceSetId());
2491 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2492 newaf.alignPanel.av.getSequenceSetId());
2493 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2494 newaf.alignPanel.av.getSequenceSetId());
2496 Vector comps = PaintRefresher.components
2497 .get(viewport.getSequenceSetId());
2499 for (int i = 0; i < comps.size(); i++)
2501 if (comps.elementAt(i) instanceof AlignmentPanel)
2507 String title = new String(this.getTitle());
2508 if (viewtitle != null)
2510 title = viewtitle + " ( " + title + ")";
2514 if (title.indexOf("(View") > -1)
2516 title = title.substring(0, title.indexOf("(View"));
2518 title += "(View " + viewSize + ")";
2521 newaf.setTitle(title.toString());
2523 newaf.viewport.setHistoryList(viewport.getHistoryList());
2524 newaf.viewport.setRedoList(viewport.getRedoList());
2530 * @return list of feature groups on the view
2532 public String[] getFeatureGroups()
2534 FeatureRenderer fr = null;
2535 if (alignPanel != null
2536 && (fr = alignPanel.getFeatureRenderer()) != null)
2538 List<String> gps = fr.getFeatureGroups();
2539 String[] _gps = gps.toArray(new String[gps.size()]);
2546 * get sequence feature groups that are hidden or shown
2552 public String[] getFeatureGroupsOfState(boolean visible)
2554 FeatureRenderer fr = null;
2555 if (alignPanel != null
2556 && (fr = alignPanel.getFeatureRenderer()) != null)
2558 List<String> gps = fr.getGroups(visible);
2559 String[] _gps = gps.toArray(new String[gps.size()]);
2566 * Change the display state for the given feature groups
2569 * list of group strings
2571 * visible or invisible
2573 public void setFeatureGroupState(String[] groups, boolean state)
2575 FeatureRenderer fr = null;
2576 this.sequenceFeatures.setState(true);
2577 viewport.setShowSequenceFeatures(true);
2578 if (alignPanel != null
2579 && (fr = alignPanel.getFeatureRenderer()) != null)
2582 fr.setGroupVisibility(Arrays.asList(groups), state);
2583 alignPanel.seqPanel.seqCanvas.repaint();
2584 if (alignPanel.overviewPanel != null)
2586 alignPanel.overviewPanel.updateOverviewImage();
2591 public void seqLimits_itemStateChanged()
2593 viewport.setShowJVSuffix(seqLimits.getState());
2594 alignPanel.fontChanged();
2595 alignPanel.paintAlignment(true, false);
2598 protected void colourTextMenuItem_actionPerformed()
2600 viewport.setColourText(colourTextMenuItem.getState());
2601 alignPanel.paintAlignment(false, false);
2604 protected void displayNonconservedMenuItem_actionPerformed()
2606 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2607 alignPanel.paintAlignment(false, false);
2610 protected void wrapMenuItem_actionPerformed()
2612 viewport.setWrapAlignment(wrapMenuItem.getState());
2613 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2614 scaleAbove.setEnabled(wrapMenuItem.getState());
2615 scaleLeft.setEnabled(wrapMenuItem.getState());
2616 scaleRight.setEnabled(wrapMenuItem.getState());
2617 alignPanel.paintAlignment(true, false);
2620 public void overviewMenuItem_actionPerformed()
2622 if (alignPanel.overviewPanel != null)
2627 Frame frame = new Frame();
2628 final OverviewPanel overview = new OverviewPanel(alignPanel);
2629 frame.add(overview);
2630 // +50 must allow for applet frame window
2631 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2632 .formatMessage("label.overview_params", new String[]
2633 { this.getTitle() }), overview.getPreferredSize().width,
2634 overview.getPreferredSize().height + 50);
2637 final AlignmentPanel ap = alignPanel;
2638 frame.addWindowListener(new WindowAdapter()
2641 public void windowClosing(WindowEvent e)
2646 ap.setOverviewPanel(null);
2651 alignPanel.setOverviewPanel(overview);
2656 public void changeColour(ColourSchemeI cs)
2658 viewport.setGlobalColourScheme(cs);
2660 alignPanel.paintAlignment(true, true);
2663 protected void modifyPID_actionPerformed()
2665 if (viewport.getAbovePIDThreshold()
2666 && viewport.getGlobalColourScheme() != null)
2668 SliderPanel.setPIDSliderSource(alignPanel,
2669 viewport.getResidueShading(), alignPanel.getViewName());
2670 SliderPanel.showPIDSlider();
2674 protected void modifyConservation_actionPerformed()
2676 if (viewport.getConservationSelected()
2677 && viewport.getGlobalColourScheme() != null)
2679 SliderPanel.setConservationSlider(alignPanel,
2680 viewport.getResidueShading(), alignPanel.getViewName());
2681 SliderPanel.showConservationSlider();
2685 protected void conservationMenuItem_actionPerformed()
2687 boolean selected = conservationMenuItem.getState();
2688 modifyConservation.setEnabled(selected);
2689 viewport.setConservationSelected(selected);
2690 viewport.getResidueShading().setConservationApplied(selected);
2692 changeColour(viewport.getGlobalColourScheme());
2696 modifyConservation_actionPerformed();
2700 SliderPanel.hideConservationSlider();
2704 public void abovePIDThreshold_actionPerformed()
2706 boolean selected = abovePIDThreshold.getState();
2707 modifyPID.setEnabled(selected);
2708 viewport.setAbovePIDThreshold(selected);
2711 viewport.getResidueShading().setThreshold(0,
2712 viewport.isIgnoreGapsConsensus());
2715 changeColour(viewport.getGlobalColourScheme());
2719 modifyPID_actionPerformed();
2723 SliderPanel.hidePIDSlider();
2727 public void sortPairwiseMenuItem_actionPerformed()
2729 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730 AlignmentSorter.sortByPID(viewport.getAlignment(),
2731 viewport.getAlignment().getSequenceAt(0));
2733 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2734 viewport.getAlignment()));
2735 alignPanel.paintAlignment(true, false);
2738 public void sortIDMenuItem_actionPerformed()
2740 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741 AlignmentSorter.sortByID(viewport.getAlignment());
2743 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2744 alignPanel.paintAlignment(true, false);
2747 public void sortLengthMenuItem_actionPerformed()
2749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750 AlignmentSorter.sortByLength(viewport.getAlignment());
2751 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2752 viewport.getAlignment()));
2753 alignPanel.paintAlignment(true, false);
2756 public void sortGroupMenuItem_actionPerformed()
2758 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2759 AlignmentSorter.sortByGroup(viewport.getAlignment());
2760 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2761 viewport.getAlignment()));
2762 alignPanel.paintAlignment(true, false);
2766 public void removeRedundancyMenuItem_actionPerformed()
2768 new RedundancyPanel(alignPanel);
2771 public void pairwiseAlignmentMenuItem_actionPerformed()
2773 if (viewport.getSelectionGroup() != null
2774 && viewport.getSelectionGroup().getSize() > 1)
2776 Frame frame = new Frame();
2777 frame.add(new PairwiseAlignPanel(alignPanel));
2778 jalview.bin.JalviewLite.addFrame(frame,
2779 MessageManager.getString("action.pairwise_alignment"), 600,
2784 public void PCAMenuItem_actionPerformed()
2786 // are the sequences aligned?
2787 if (!viewport.getAlignment().isAligned(false))
2790 int Width = viewport.getAlignment().getWidth();
2792 for (int i = 0; i < viewport.getAlignment().getSequences()
2795 current = viewport.getAlignment().getSequenceAt(i);
2797 if (current.getLength() < Width)
2799 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2802 alignPanel.paintAlignment(false, false);
2805 if ((viewport.getSelectionGroup() != null
2806 && viewport.getSelectionGroup().getSize() < 4
2807 && viewport.getSelectionGroup().getSize() > 0)
2808 || viewport.getAlignment().getHeight() < 4)
2815 new PCAPanel(viewport);
2816 } catch (java.lang.OutOfMemoryError ex)
2822 public void averageDistanceTreeMenuItem_actionPerformed()
2824 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2825 "Average distance tree using PID");
2828 public void neighbourTreeMenuItem_actionPerformed()
2830 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2831 "Neighbour joining tree using PID");
2834 protected void njTreeBlosumMenuItem_actionPerformed()
2836 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2837 ScoreModels.getInstance().getBlosum62().getName(),
2838 "Neighbour joining tree using BLOSUM62");
2841 protected void avTreeBlosumMenuItem_actionPerformed()
2843 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2844 ScoreModels.getInstance().getBlosum62().getName(),
2845 "Average distance tree using BLOSUM62");
2848 void newTreePanel(String type, String pwType, String title)
2850 // are the sequences aligned?
2851 if (!viewport.getAlignment().isAligned(false))
2854 int Width = viewport.getAlignment().getWidth();
2856 for (int i = 0; i < viewport.getAlignment().getSequences()
2859 current = viewport.getAlignment().getSequenceAt(i);
2861 if (current.getLength() < Width)
2863 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2866 alignPanel.paintAlignment(false, false);
2870 if ((viewport.getSelectionGroup() != null
2871 && viewport.getSelectionGroup().getSize() > 1)
2872 || (viewport.getAlignment().getHeight() > 1))
2874 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2876 addTreeMenuItem(tp, title);
2878 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2882 void loadTree_actionPerformed()
2884 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2885 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2886 cap.setTreeImport();
2887 Frame frame = new Frame();
2889 jalview.bin.JalviewLite.addFrame(frame,
2890 MessageManager.getString("label.paste_newick_file"), 400, 300);
2893 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2895 TreePanel tp = new TreePanel(alignPanel, treeFile,
2896 MessageManager.getString("label.load_tree_from_file"), tree);
2897 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2898 addTreeMenuItem(tp, treeFile);
2902 * sort the alignment using the given treePanel
2905 * tree used to sort view
2907 * string used for undo event name
2909 public void sortByTree(TreePanel treePanel, String title)
2911 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2912 AlignmentSorter.sortByTree(viewport.getAlignment(),
2913 treePanel.getTree());
2914 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2915 // HistoryItem.SORT));
2916 addHistoryItem(new OrderCommand(MessageManager
2917 .formatMessage("label.order_by_params", new String[]
2918 { title }), oldOrder, viewport.getAlignment()));
2919 alignPanel.paintAlignment(true, false);
2923 * Do any automatic reordering of the alignment and add the necessary bits to
2924 * the menu structure for the new tree
2929 protected void addTreeMenuItem(final TreePanel treePanel,
2932 final MenuItem item = new MenuItem(title);
2933 sortByTreeMenu.add(item);
2934 item.addActionListener(new java.awt.event.ActionListener()
2937 public void actionPerformed(ActionEvent evt)
2939 sortByTree(treePanel, title); // treePanel.getTitle());
2943 treePanel.addWindowListener(new WindowAdapter()
2946 public void windowOpened(WindowEvent e)
2948 if (viewport.sortByTree)
2950 sortByTree(treePanel, title);
2952 super.windowOpened(e);
2956 public void windowClosing(WindowEvent e)
2958 sortByTreeMenu.remove(item);
2963 public boolean sortBy(AlignmentOrder alorder, String undoname)
2965 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2966 if (viewport.applet.debug)
2968 System.err.println("Sorting " + alorder.getOrder().size()
2969 + " in alignment '" + getTitle() + "'");
2971 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2972 if (undoname != null)
2974 addHistoryItem(new OrderCommand(undoname, oldOrder,
2975 viewport.getAlignment()));
2977 alignPanel.paintAlignment(true, false);
2981 protected void documentation_actionPerformed()
2983 alignPanel.av.applet.openJalviewHelpUrl();
2986 protected void about_actionPerformed()
2989 class AboutPanel extends Canvas
2995 public AboutPanel(String version, String builddate)
2997 this.version = version;
2998 this.builddate = builddate;
3002 public void paint(Graphics g)
3004 g.setColor(Color.white);
3005 g.fillRect(0, 0, getSize().width, getSize().height);
3006 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3007 FontMetrics fm = g.getFontMetrics();
3008 int fh = fm.getHeight();
3010 g.setColor(Color.black);
3011 // TODO: update this text for each release or centrally store it for
3012 // lite and application
3013 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3014 g.drawString(MessageManager
3015 .formatMessage("label.jalviewLite_release", new String[]
3016 { version }), x, y += fh);
3017 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3018 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3020 { builddate }), x, y += fh);
3021 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3022 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3024 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3025 x + 50, y += fh + 8);
3026 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3028 g.drawString(MessageManager
3029 .getString("label.jalview_distribution_lists"), x, y += fh);
3030 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3033 MessageManager.getString("label.jalview_cite_1_authors"), x,
3035 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3037 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3042 Frame frame = new Frame();
3043 frame.add(new AboutPanel(JalviewLite.getVersion(),
3044 JalviewLite.getBuildDate()));
3045 jalview.bin.JalviewLite.addFrame(frame,
3046 MessageManager.getString("label.jalview"), 580, 220);
3050 public void showURL(String url, String target)
3052 if (viewport.applet == null)
3054 System.out.println("Not running as applet - no browser available.");
3058 viewport.applet.showURL(url, target);
3062 // ////////////////////////////////////////////////////////////////////////////////
3063 // JBuilder Graphics here
3065 MenuBar alignFrameMenuBar = new MenuBar();
3067 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3069 MenuItem loadApplication = new MenuItem(
3070 MessageManager.getString("label.view_full_application"));
3072 MenuItem loadTree = new MenuItem(
3073 MessageManager.getString("label.load_associated_tree"));
3075 MenuItem loadAnnotations = new MenuItem(
3076 MessageManager.getString("label.load_features_annotations"));
3078 MenuItem outputFeatures = new MenuItem(
3079 MessageManager.getString("label.export_features"));
3081 MenuItem outputAnnotations = new MenuItem(
3082 MessageManager.getString("label.export_annotations"));
3084 MenuItem closeMenuItem = new MenuItem(
3085 MessageManager.getString("action.close"));
3087 MenuItem selectAllSequenceMenuItem = new MenuItem(
3088 MessageManager.getString("action.select_all"));
3090 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3091 MessageManager.getString("action.deselect_all"));
3093 MenuItem invertSequenceMenuItem = new MenuItem(
3094 MessageManager.getString("action.invert_selection"));
3096 MenuItem remove2LeftMenuItem = new MenuItem();
3098 MenuItem remove2RightMenuItem = new MenuItem();
3100 MenuItem removeGappedColumnMenuItem = new MenuItem();
3102 MenuItem removeAllGapsMenuItem = new MenuItem();
3104 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3106 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3108 MenuItem sortPairwiseMenuItem = new MenuItem();
3110 MenuItem sortIDMenuItem = new MenuItem();
3112 MenuItem sortLengthMenuItem = new MenuItem();
3114 MenuItem sortGroupMenuItem = new MenuItem();
3116 MenuItem removeRedundancyMenuItem = new MenuItem();
3118 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3120 MenuItem PCAMenuItem = new MenuItem();
3122 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3124 MenuItem neighbourTreeMenuItem = new MenuItem();
3126 BorderLayout borderLayout1 = new BorderLayout();
3128 public Label statusBar = new Label();
3130 MenuItem clustalColour = new MenuItem();
3132 MenuItem zappoColour = new MenuItem();
3134 MenuItem taylorColour = new MenuItem();
3136 MenuItem hydrophobicityColour = new MenuItem();
3138 MenuItem helixColour = new MenuItem();
3140 MenuItem strandColour = new MenuItem();
3142 MenuItem turnColour = new MenuItem();
3144 MenuItem buriedColour = new MenuItem();
3146 MenuItem purinePyrimidineColour = new MenuItem();
3148 // MenuItem RNAInteractionColour = new MenuItem();
3150 MenuItem RNAHelixColour = new MenuItem();
3152 MenuItem userDefinedColour = new MenuItem();
3154 MenuItem PIDColour = new MenuItem();
3156 MenuItem BLOSUM62Colour = new MenuItem();
3158 MenuItem tcoffeeColour = new MenuItem();
3160 MenuItem njTreeBlosumMenuItem = new MenuItem();
3162 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3164 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3166 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3168 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3170 MenuItem alProperties = new MenuItem(
3171 MessageManager.getString("label.alignment_props"));
3173 MenuItem overviewMenuItem = new MenuItem();
3175 MenuItem undoMenuItem = new MenuItem();
3177 MenuItem redoMenuItem = new MenuItem();
3179 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3181 MenuItem noColourmenuItem = new MenuItem();
3183 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3185 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3187 MenuItem findMenuItem = new MenuItem();
3189 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3191 MenuItem nucleotideColour = new MenuItem();
3193 MenuItem deleteGroups = new MenuItem();
3195 MenuItem grpsFromSelection = new MenuItem();
3197 MenuItem createGroup = new MenuItem();
3199 MenuItem unGroup = new MenuItem();
3201 MenuItem delete = new MenuItem();
3203 MenuItem copy = new MenuItem();
3205 MenuItem cut = new MenuItem();
3207 Menu pasteMenu = new Menu();
3209 MenuItem pasteNew = new MenuItem();
3211 MenuItem pasteThis = new MenuItem();
3213 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3215 MenuItem font = new MenuItem();
3217 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3219 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3221 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3223 MenuItem modifyPID = new MenuItem();
3225 MenuItem modifyConservation = new MenuItem();
3227 CheckboxMenuItem autoCalculate = null;
3229 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3230 "Sort Alignment With New Tree", true);
3232 Menu sortByTreeMenu = new Menu();
3234 MenuItem inputText = new MenuItem();
3236 MenuItem documentation = new MenuItem();
3238 MenuItem about = new MenuItem();
3240 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3242 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3244 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3246 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3248 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3250 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3252 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3254 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3256 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3259 * Initialise menus and other items
3263 private void jbInit() throws Exception
3265 setMenuBar(alignFrameMenuBar);
3268 * Configure File menu items and actions
3271 .setLabel(MessageManager.getString("label.input_from_textbox"));
3272 inputText.addActionListener(this);
3273 Menu outputTextboxMenu = new Menu(
3274 MessageManager.getString("label.out_to_textbox"));
3275 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3277 MenuItem item = new MenuItem(ff);
3279 item.addActionListener(new java.awt.event.ActionListener()
3282 public void actionPerformed(ActionEvent e)
3284 outputText_actionPerformed(e);
3288 outputTextboxMenu.add(item);
3290 closeMenuItem.addActionListener(this);
3291 loadApplication.addActionListener(this);
3292 loadTree.addActionListener(this);
3293 loadAnnotations.addActionListener(this);
3294 outputFeatures.addActionListener(this);
3295 outputAnnotations.addActionListener(this);
3298 * Configure Edit menu items and actions
3300 undoMenuItem.setEnabled(false);
3301 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3302 undoMenuItem.addActionListener(this);
3303 redoMenuItem.setEnabled(false);
3304 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3305 redoMenuItem.addActionListener(this);
3306 copy.setLabel(MessageManager.getString("action.copy"));
3307 copy.addActionListener(this);
3308 cut.setLabel(MessageManager.getString("action.cut"));
3309 cut.addActionListener(this);
3310 delete.setLabel(MessageManager.getString("action.delete"));
3311 delete.addActionListener(this);
3312 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3313 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3314 pasteNew.addActionListener(this);
3315 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3316 pasteThis.addActionListener(this);
3318 .setLabel(MessageManager.getString("action.remove_left"));
3319 remove2LeftMenuItem.addActionListener(this);
3320 remove2RightMenuItem
3321 .setLabel(MessageManager.getString("action.remove_right"));
3322 remove2RightMenuItem.addActionListener(this);
3323 removeGappedColumnMenuItem.setLabel(
3324 MessageManager.getString("action.remove_empty_columns"));
3325 removeGappedColumnMenuItem.addActionListener(this);
3326 removeAllGapsMenuItem
3327 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3328 removeAllGapsMenuItem.addActionListener(this);
3329 removeRedundancyMenuItem
3330 .setLabel(MessageManager.getString("action.remove_redundancy"));
3331 removeRedundancyMenuItem.addActionListener(this);
3334 * Configure Select menu items and actions
3336 findMenuItem.setLabel(MessageManager.getString("action.find"));
3337 findMenuItem.addActionListener(this);
3338 selectAllSequenceMenuItem.addActionListener(this);
3339 deselectAllSequenceMenuItem.addActionListener(this);
3340 invertSequenceMenuItem.setLabel(
3341 MessageManager.getString("action.invert_sequence_selection"));
3342 invertSequenceMenuItem.addActionListener(this);
3343 invertColSel.setLabel(
3344 MessageManager.getString("action.invert_column_selection"));
3345 invertColSel.addActionListener(this);
3347 .setLabel(MessageManager.getString("action.undefine_groups"));
3348 deleteGroups.addActionListener(this);
3349 grpsFromSelection.setLabel(
3350 MessageManager.getString("action.make_groups_selection"));
3351 grpsFromSelection.addActionListener(this);
3352 createGroup.setLabel(MessageManager.getString("action.create_group"));
3353 createGroup.addActionListener(this);
3354 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3355 unGroup.addActionListener(this);
3357 annotationColumnSelection.setLabel(
3358 MessageManager.getString("action.select_by_annotation"));
3359 annotationColumnSelection.addActionListener(this);
3362 * Configure View menu items and actions
3364 newView.setLabel(MessageManager.getString("action.new_view"));
3365 newView.addActionListener(this);
3366 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3367 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3368 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3369 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3371 .setLabel(MessageManager.getString("label.selected_columns"));
3373 .setLabel(MessageManager.getString("label.selected_sequences"));
3374 hideAllButSelection.setLabel(
3375 MessageManager.getString("label.all_but_selected_region"));
3377 .setLabel(MessageManager.getString("label.selected_region"));
3378 showAllHidden.setLabel(
3379 MessageManager.getString("label.all_sequences_columns"));
3380 showColumns.addActionListener(this);
3381 showSeqs.addActionListener(this);
3382 hideColumns.addActionListener(this);
3383 hideSequences.addActionListener(this);
3384 hideAllButSelection.addActionListener(this);
3385 hideAllSelection.addActionListener(this);
3386 showAllHidden.addActionListener(this);
3388 .setLabel(MessageManager.getString("action.feature_settings"));
3389 featureSettings.addActionListener(this);
3390 sequenceFeatures.setLabel(
3391 MessageManager.getString("label.show_sequence_features"));
3392 sequenceFeatures.addItemListener(this);
3393 sequenceFeatures.setState(false);
3394 followMouseOverFlag.setLabel(
3395 MessageManager.getString("label.automatic_scrolling"));
3396 followMouseOverFlag.addItemListener(this);
3397 alProperties.addActionListener(this);
3399 .setLabel(MessageManager.getString("label.overview_window"));
3400 overviewMenuItem.addActionListener(this);
3403 * Configure Annotations menu items and actions
3405 annotationPanelMenuItem
3406 .setLabel(MessageManager.getString("label.show_annotations"));
3407 annotationPanelMenuItem.addItemListener(this);
3409 .setLabel(MessageManager.getString("label.group_consensus"));
3410 showGroupConservation
3411 .setLabel(MessageManager.getString("label.group_conservation"));
3412 showConsensusHistogram.setLabel(
3413 MessageManager.getString("label.show_consensus_histogram"));
3414 showSequenceLogo.setLabel(
3415 MessageManager.getString("label.show_consensus_logo"));
3416 normSequenceLogo.setLabel(
3417 MessageManager.getString("label.norm_consensus_logo"));
3418 applyAutoAnnotationSettings
3419 .setLabel(MessageManager.getString("label.apply_all_groups"));
3420 applyAutoAnnotationSettings.setState(true);
3421 Menu autoAnnMenu = new Menu(
3422 MessageManager.getString("label.autocalculated_annotation"));
3423 showGroupConsensus.addItemListener(this);
3424 showGroupConservation.addItemListener(this);
3425 showConsensusHistogram.addItemListener(this);
3426 showSequenceLogo.addItemListener(this);
3427 normSequenceLogo.addItemListener(this);
3428 applyAutoAnnotationSettings.addItemListener(this);
3429 showAlignmentAnnotations = new CheckboxMenuItem(
3430 MessageManager.getString("label.show_all_al_annotations"));
3431 showSequenceAnnotations = new CheckboxMenuItem(
3432 MessageManager.getString("label.show_all_seq_annotations"));
3433 sortAnnBySequence = new CheckboxMenuItem(
3434 MessageManager.getString("label.sort_annotations_by_sequence"));
3435 sortAnnByLabel = new CheckboxMenuItem(
3436 MessageManager.getString("label.sort_annotations_by_label"));
3437 showAutoFirst = new CheckboxMenuItem(
3438 MessageManager.getString("label.show_first"));
3439 showAutoFirst.setState(false); // pending applet parameter
3440 setShowAutoCalculatedAbove(showAutoFirst.getState());
3441 showAutoLast = new CheckboxMenuItem(
3442 MessageManager.getString("label.show_last"));
3443 showAutoLast.setState(!showAutoFirst.getState());
3444 showAlignmentAnnotations.addItemListener(this);
3445 showSequenceAnnotations.addItemListener(this);
3446 sortAnnBySequence.addItemListener(this);
3447 sortAnnByLabel.addItemListener(this);
3448 showAutoFirst.addItemListener(this);
3449 showAutoLast.addItemListener(this);
3452 * Configure Format menu items and actions
3454 font.setLabel(MessageManager.getString("action.font"));
3455 font.addActionListener(this);
3456 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3457 scaleAbove.setState(true);
3458 scaleAbove.setEnabled(false);
3459 scaleAbove.addItemListener(this);
3460 scaleLeft.setEnabled(false);
3461 scaleLeft.setState(true);
3462 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3463 scaleLeft.addItemListener(this);
3464 scaleRight.setEnabled(false);
3465 scaleRight.setState(true);
3466 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3467 scaleRight.addItemListener(this);
3468 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3469 viewBoxesMenuItem.setState(true);
3470 viewBoxesMenuItem.addItemListener(this);
3471 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3472 viewTextMenuItem.setState(true);
3473 viewTextMenuItem.addItemListener(this);
3475 .setLabel(MessageManager.getString("label.colour_text"));
3476 colourTextMenuItem.addItemListener(this);
3477 displayNonconservedMenuItem
3478 .setLabel(MessageManager.getString("label.show_non_conserved"));
3479 displayNonconservedMenuItem.addItemListener(this);
3480 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3481 wrapMenuItem.addItemListener(this);
3483 .setLabel(MessageManager.getString("action.show_gaps"));
3484 renderGapsMenuItem.setState(true);
3485 renderGapsMenuItem.addItemListener(this);
3486 centreColumnLabelFlag.setLabel(
3487 MessageManager.getString("label.centre_column_labels"));
3488 centreColumnLabelFlag.addItemListener(this);
3489 seqLimits.setState(true);
3491 MessageManager.getString("label.show_sequence_limits"));
3492 seqLimits.addItemListener(this);
3495 * Configure Colour menu items and actions
3497 applyToAllGroups.setLabel(
3498 MessageManager.getString("label.apply_colour_to_all_groups"));
3499 applyToAllGroups.setState(true);
3500 applyToAllGroups.addItemListener(this);
3501 clustalColour.setLabel(
3502 MessageManager.getString("label.colourScheme_clustal"));
3503 clustalColour.addActionListener(this);
3505 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3506 zappoColour.addActionListener(this);
3507 taylorColour.setLabel(
3508 MessageManager.getString("label.colourScheme_taylor"));
3509 taylorColour.addActionListener(this);
3510 hydrophobicityColour.setLabel(
3511 MessageManager.getString("label.colourScheme_hydrophobic"));
3512 hydrophobicityColour.addActionListener(this);
3513 helixColour.setLabel(MessageManager
3514 .getString("label.colourScheme_helix_propensity"));
3515 helixColour.addActionListener(this);
3516 strandColour.setLabel(MessageManager
3517 .getString("label.colourScheme_strand_propensity"));
3518 strandColour.addActionListener(this);
3519 turnColour.setLabel(
3520 MessageManager.getString("label.colourScheme_turn_propensity"));
3521 turnColour.addActionListener(this);
3522 buriedColour.setLabel(
3523 MessageManager.getString("label.colourScheme_buried_index"));
3524 buriedColour.addActionListener(this);
3525 purinePyrimidineColour.setLabel(MessageManager
3526 .getString("label.colourScheme_purine/pyrimidine"));
3527 purinePyrimidineColour.addActionListener(this);
3528 // RNAInteractionColour.setLabel(MessageManager
3529 // .getString("label.rna_interaction"));
3530 // RNAInteractionColour.addActionListener(this);
3531 RNAHelixColour.setLabel(
3532 MessageManager.getString("label.colourScheme_rna_helices"));
3533 RNAHelixColour.addActionListener(this);
3535 .setLabel(MessageManager.getString("action.user_defined"));
3536 userDefinedColour.addActionListener(this);
3538 MessageManager.getString("label.colourScheme_%_identity"));
3539 PIDColour.addActionListener(this);
3540 BLOSUM62Colour.setLabel(
3541 MessageManager.getString("label.colourScheme_blosum62"));
3542 BLOSUM62Colour.addActionListener(this);
3543 tcoffeeColour.setLabel(
3544 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3545 // it will be enabled only if a score file is provided
3546 tcoffeeColour.setEnabled(false);
3547 tcoffeeColour.addActionListener(this);
3548 conservationMenuItem
3549 .setLabel(MessageManager.getString("action.by_conservation"));
3550 conservationMenuItem.addItemListener(this);
3551 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3552 noColourmenuItem.addActionListener(this);
3553 abovePIDThreshold.setLabel(
3554 MessageManager.getString("label.above_identity_threshold"));
3555 abovePIDThreshold.addItemListener(this);
3556 nucleotideColour.setLabel(
3557 MessageManager.getString("label.colourScheme_nucleotide"));
3558 nucleotideColour.addActionListener(this);
3560 MessageManager.getString("label.modify_identity_threshold"));
3561 modifyPID.setEnabled(abovePIDThreshold.getState());
3562 modifyPID.addActionListener(this);
3563 modifyConservation.setLabel(MessageManager
3564 .getString("label.modify_conservation_threshold"));
3565 modifyConservation.setEnabled(conservationMenuItem.getState());
3566 modifyConservation.addActionListener(this);
3568 .setLabel(MessageManager.getString("action.by_annotation"));
3569 annotationColour.addActionListener(this);
3572 * Configure Calculate menu items and actions
3574 sortPairwiseMenuItem
3575 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3576 sortPairwiseMenuItem.addActionListener(this);
3577 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3578 sortIDMenuItem.addActionListener(this);
3580 .setLabel(MessageManager.getString("action.by_length"));
3581 sortLengthMenuItem.addActionListener(this);
3582 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3583 sortGroupMenuItem.addActionListener(this);
3584 pairwiseAlignmentMenuItem.setLabel(
3585 MessageManager.getString("action.pairwise_alignment"));
3586 pairwiseAlignmentMenuItem.addActionListener(this);
3587 PCAMenuItem.setLabel(
3588 MessageManager.getString("label.principal_component_analysis"));
3589 PCAMenuItem.addActionListener(this);
3590 autoCalculate = new CheckboxMenuItem(
3591 MessageManager.getString("label.autocalculate_consensus"),
3593 averageDistanceTreeMenuItem.setLabel(
3594 MessageManager.getString("label.average_distance_identity"));
3595 averageDistanceTreeMenuItem.addActionListener(this);
3596 neighbourTreeMenuItem.setLabel(
3597 MessageManager.getString("label.neighbour_joining_identity"));
3598 neighbourTreeMenuItem.addActionListener(this);
3599 avDistanceTreeBlosumMenuItem.setLabel(
3600 MessageManager.getString("label.average_distance_blosum62"));
3601 avDistanceTreeBlosumMenuItem.addActionListener(this);
3602 njTreeBlosumMenuItem
3603 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3604 njTreeBlosumMenuItem.addActionListener(this);
3606 .setLabel(MessageManager.getString("action.by_tree_order"));
3607 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3608 Menu calculateTreeMenu = new Menu(
3609 MessageManager.getString("action.calculate_tree"));
3610 autoCalculate.addItemListener(this);
3611 sortByTree.addItemListener(this);
3614 * Configure Help menu items and actions
3616 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3617 documentation.setLabel(MessageManager.getString("label.documentation"));
3618 documentation.addActionListener(this);
3619 about.setLabel(MessageManager.getString("label.about"));
3620 about.addActionListener(this);
3623 * Add top level menus to frame
3625 alignFrameMenuBar.add(fileMenu);
3626 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3627 alignFrameMenuBar.add(editMenu);
3628 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3629 alignFrameMenuBar.add(selectMenu);
3630 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3631 alignFrameMenuBar.add(viewMenu);
3632 Menu annotationsMenu = new Menu(
3633 MessageManager.getString("action.annotations"));
3634 alignFrameMenuBar.add(annotationsMenu);
3635 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3636 alignFrameMenuBar.add(formatMenu);
3637 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3638 alignFrameMenuBar.add(colourMenu);
3639 Menu calculateMenu = new Menu(
3640 MessageManager.getString("action.calculate"));
3641 alignFrameMenuBar.add(calculateMenu);
3642 alignFrameMenuBar.add(helpMenu);
3647 fileMenu.add(inputText);
3648 fileMenu.add(loadTree);
3649 fileMenu.add(loadAnnotations);
3650 fileMenu.addSeparator();
3651 fileMenu.add(outputTextboxMenu);
3652 fileMenu.add(outputFeatures);
3653 fileMenu.add(outputAnnotations);
3654 if (jalviewServletURL != null)
3656 fileMenu.add(loadApplication);
3658 fileMenu.addSeparator();
3659 fileMenu.add(closeMenuItem);
3664 editMenu.add(undoMenuItem);
3665 editMenu.add(redoMenuItem);
3668 pasteMenu.add(pasteNew);
3669 pasteMenu.add(pasteThis);
3670 editMenu.add(pasteMenu);
3671 editMenu.add(delete);
3672 editMenu.addSeparator();
3673 editMenu.add(remove2LeftMenuItem);
3674 editMenu.add(remove2RightMenuItem);
3675 editMenu.add(removeGappedColumnMenuItem);
3676 editMenu.add(removeAllGapsMenuItem);
3677 editMenu.add(removeRedundancyMenuItem);
3682 selectMenu.add(findMenuItem);
3683 selectMenu.addSeparator();
3684 selectMenu.add(selectAllSequenceMenuItem);
3685 selectMenu.add(deselectAllSequenceMenuItem);
3686 selectMenu.add(invertSequenceMenuItem);
3687 selectMenu.add(invertColSel);
3688 selectMenu.add(createGroup);
3689 selectMenu.add(unGroup);
3690 selectMenu.add(grpsFromSelection);
3691 selectMenu.add(deleteGroups);
3692 selectMenu.add(annotationColumnSelection);
3697 viewMenu.add(newView);
3698 viewMenu.addSeparator();
3699 showMenu.add(showColumns);
3700 showMenu.add(showSeqs);
3701 showMenu.add(showAllHidden);
3702 viewMenu.add(showMenu);
3703 hideMenu.add(hideColumns);
3704 hideMenu.add(hideSequences);
3705 hideMenu.add(hideAllSelection);
3706 hideMenu.add(hideAllButSelection);
3707 viewMenu.add(hideMenu);
3708 viewMenu.addSeparator();
3709 viewMenu.add(followMouseOverFlag);
3710 viewMenu.addSeparator();
3711 viewMenu.add(sequenceFeatures);
3712 viewMenu.add(featureSettings);
3713 viewMenu.addSeparator();
3714 viewMenu.add(alProperties);
3715 viewMenu.addSeparator();
3716 viewMenu.add(overviewMenuItem);
3721 annotationsMenu.add(annotationPanelMenuItem);
3722 annotationsMenu.addSeparator();
3723 annotationsMenu.add(showAlignmentAnnotations);
3724 annotationsMenu.add(showSequenceAnnotations);
3725 annotationsMenu.add(sortAnnBySequence);
3726 annotationsMenu.add(sortAnnByLabel);
3727 annotationsMenu.addSeparator();
3728 autoAnnMenu.add(showAutoFirst);
3729 autoAnnMenu.add(showAutoLast);
3730 autoAnnMenu.addSeparator();
3731 autoAnnMenu.add(applyAutoAnnotationSettings);
3732 autoAnnMenu.add(showConsensusHistogram);
3733 autoAnnMenu.add(showSequenceLogo);
3734 autoAnnMenu.add(normSequenceLogo);
3735 autoAnnMenu.addSeparator();
3736 autoAnnMenu.add(showGroupConservation);
3737 autoAnnMenu.add(showGroupConsensus);
3738 annotationsMenu.add(autoAnnMenu);
3743 formatMenu.add(font);
3744 formatMenu.add(seqLimits);
3745 formatMenu.add(wrapMenuItem);
3746 formatMenu.add(scaleAbove);
3747 formatMenu.add(scaleLeft);
3748 formatMenu.add(scaleRight);
3749 formatMenu.add(viewBoxesMenuItem);
3750 formatMenu.add(viewTextMenuItem);
3751 formatMenu.add(colourTextMenuItem);
3752 formatMenu.add(displayNonconservedMenuItem);
3753 formatMenu.add(renderGapsMenuItem);
3754 formatMenu.add(centreColumnLabelFlag);
3759 colourMenu.add(applyToAllGroups);
3760 colourMenu.addSeparator();
3761 colourMenu.add(noColourmenuItem);
3762 colourMenu.add(clustalColour);
3763 colourMenu.add(BLOSUM62Colour);
3764 colourMenu.add(PIDColour);
3765 colourMenu.add(zappoColour);
3766 colourMenu.add(taylorColour);
3767 colourMenu.add(hydrophobicityColour);
3768 colourMenu.add(helixColour);
3769 colourMenu.add(strandColour);
3770 colourMenu.add(turnColour);
3771 colourMenu.add(buriedColour);
3772 colourMenu.add(nucleotideColour);
3773 colourMenu.add(purinePyrimidineColour);
3774 // colourMenu.add(RNAInteractionColour);
3775 colourMenu.add(tcoffeeColour);
3776 colourMenu.add(userDefinedColour);
3777 colourMenu.addSeparator();
3778 colourMenu.add(conservationMenuItem);
3779 colourMenu.add(modifyConservation);
3780 colourMenu.add(abovePIDThreshold);
3781 colourMenu.add(modifyPID);
3782 colourMenu.add(annotationColour);
3783 colourMenu.add(RNAHelixColour);
3788 sortMenu.add(sortIDMenuItem);
3789 sortMenu.add(sortLengthMenuItem);
3790 sortMenu.add(sortByTreeMenu);
3791 sortMenu.add(sortGroupMenuItem);
3792 sortMenu.add(sortPairwiseMenuItem);
3793 calculateMenu.add(sortMenu);
3794 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3795 calculateTreeMenu.add(neighbourTreeMenuItem);
3796 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3797 calculateTreeMenu.add(njTreeBlosumMenuItem);
3798 calculateMenu.add(calculateTreeMenu);
3799 calculateMenu.addSeparator();
3800 calculateMenu.add(pairwiseAlignmentMenuItem);
3801 calculateMenu.add(PCAMenuItem);
3802 calculateMenu.add(autoCalculate);
3803 calculateMenu.add(sortByTree);
3808 helpMenu.add(documentation);
3809 helpMenu.add(about);
3814 statusBar.setBackground(Color.white);
3815 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3816 setStatus(MessageManager.getString("label.status_bar"));
3817 this.add(statusBar, BorderLayout.SOUTH);
3821 public void setStatus(String string)
3823 statusBar.setText(string);
3826 MenuItem featureSettings = new MenuItem();
3828 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3830 MenuItem annotationColour = new MenuItem();
3832 MenuItem annotationColumnSelection = new MenuItem();
3834 MenuItem invertColSel = new MenuItem();
3836 MenuItem showColumns = new MenuItem();
3838 MenuItem showSeqs = new MenuItem();
3840 MenuItem hideColumns = new MenuItem();
3842 MenuItem hideSequences = new MenuItem();
3844 MenuItem hideAllButSelection = new MenuItem();
3846 MenuItem hideAllSelection = new MenuItem();
3848 MenuItem showAllHidden = new MenuItem();
3850 MenuItem newView = new MenuItem();
3852 private CheckboxMenuItem showAlignmentAnnotations;
3854 private CheckboxMenuItem showSequenceAnnotations;
3856 private CheckboxMenuItem sortAnnBySequence;
3858 private CheckboxMenuItem sortAnnByLabel;
3860 private CheckboxMenuItem showAutoFirst;
3862 private CheckboxMenuItem showAutoLast;
3864 private SplitFrame splitFrame;
3867 * Attach the alignFrame panels after embedding menus, if necessary. This used
3868 * to be called setEmbedded, but is now creates the dropdown menus in a
3869 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3871 * @param reallyEmbedded
3872 * true to attach the view to the applet area on the page rather than
3875 public void createAlignFrameWindow(boolean reallyEmbedded)
3879 embedAlignFrameInApplet(viewport.applet);
3884 // test and embed menu bar if necessary.
3886 if (embedMenuIfNeeded(alignPanel))
3889 * adjust for status bar height too. ? pointless as overridden by layout
3892 alignPanel.setSize(getSize().width,
3893 getSize().height - statusBar.getHeight());
3895 add(statusBar, BorderLayout.SOUTH);
3896 add(alignPanel, BorderLayout.CENTER);
3897 // and register with the applet so it can pass external API calls to us
3898 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3904 * Add the components of this AlignFrame to the applet container.
3908 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3911 // Explicitly build the embedded menu panel for the on-page applet
3913 // view cannot be closed if its actually on the page
3914 fileMenu.remove(closeMenuItem);
3915 fileMenu.remove(3); // Remove Separator
3916 // construct embedded menu, using default font
3917 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3918 // and actually add the components to the applet area
3919 theApplet.setLayout(new BorderLayout());
3920 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3921 theApplet.add(statusBar, BorderLayout.SOUTH);
3922 // TODO should size be left to the layout manager?
3923 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3924 - embeddedMenu.getHeight() - statusBar.getHeight());
3925 theApplet.add(alignPanel, BorderLayout.CENTER);
3926 final AlignFrame me = this;
3927 theApplet.addFocusListener(new FocusListener()
3931 public void focusLost(FocusEvent e)
3933 if (theApplet.currentAlignFrame == me)
3935 theApplet.currentAlignFrame = null;
3940 public void focusGained(FocusEvent e)
3942 theApplet.currentAlignFrame = me;
3945 theApplet.validate();
3949 * create a new binding between structures in an existing jmol viewer instance
3950 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3951 * this does not open a new Jmol window, or modify the display of the
3952 * structures in the original jmol window. Note This method doesn't work
3953 * without an additional javascript library to exchange messages between the
3954 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3957 * JmolViewer instance
3958 * @param sequenceIds
3959 * - sequence Ids to search for associations
3961 public SequenceStructureBinding addStructureViewInstance(
3962 Object jmolviewer, String[] sequenceIds)
3964 Viewer viewer = null;
3967 viewer = (Viewer) jmolviewer;
3968 } catch (ClassCastException ex)
3971 "Unsupported viewer object :" + jmolviewer.getClass());
3975 System.err.println("Can't use this object as a structure viewer:"
3976 + jmolviewer.getClass());
3979 SequenceI[] seqs = null;
3980 if (sequenceIds == null || sequenceIds.length == 0)
3982 seqs = viewport.getAlignment().getSequencesArray();
3986 Vector sqi = new Vector();
3987 AlignmentI al = viewport.getAlignment();
3988 for (int sid = 0; sid < sequenceIds.length; sid++)
3990 SequenceI sq = al.findName(sequenceIds[sid]);
3998 seqs = new SequenceI[sqi.size()];
3999 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4001 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4009 AAStructureBindingModel jmv = null;
4010 // TODO: search for a jmv that involves viewer
4012 { // create a new viewer/jalview binding.
4013 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4020 * bind a pdb file to a sequence in the current view
4023 * - sequenceId within the dataset.
4024 * @param pdbEntryString
4025 * - the short name for the PDB file
4027 * - pdb file - either a URL or a valid PDB file.
4028 * @return true if binding was as success TODO: consider making an exception
4029 * structure for indicating when PDB parsing or sequenceId location
4032 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4035 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4036 boolean needtoadd = false;
4037 if (toaddpdb != null)
4039 Vector pdbe = toaddpdb.getAllPDBEntries();
4040 PDBEntry pdbentry = null;
4041 if (pdbe != null && pdbe.size() > 0)
4043 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4045 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4046 if (!pdbentry.getId().equals(pdbEntryString)
4047 && !pdbentry.getFile().equals(pdbFile))
4057 if (pdbentry == null)
4059 pdbentry = new PDBEntry();
4060 pdbentry.setId(pdbEntryString);
4061 pdbentry.setFile(pdbFile);
4062 needtoadd = true; // add this new entry to sequence.
4064 // resolve data source
4065 // TODO: this code should be a refactored to an io package
4066 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4068 if (protocol == null)
4074 pdbentry.setProperty("protocol", protocol);
4075 toaddpdb.addPDBId(pdbentry);
4076 alignPanel.getStructureSelectionManager()
4077 .registerPDBEntry(pdbentry);
4083 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4087 Vector sequences = new Vector();
4088 for (int i = 0; i < seqs.length; i++)
4090 if (seqs[i] != null)
4093 .addElement(new Object[]
4094 { seqs[i], (chains != null) ? chains[i] : null });
4097 seqs = new SequenceI[sequences.size()];
4098 chains = new String[sequences.size()];
4099 for (int i = 0, isize = sequences.size(); i < isize; i++)
4101 Object[] oj = (Object[]) sequences.elementAt(i);
4103 seqs[i] = (SequenceI) oj[0];
4104 chains[i] = (String) oj[1];
4107 return new Object[] { seqs, chains };
4111 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4112 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4114 // Scrub any null sequences from the array
4115 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4116 seqs = (SequenceI[]) sqch[0];
4117 chains = (String[]) sqch[1];
4118 if (seqs == null || seqs.length == 0)
4121 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4123 if (protocol == null)
4125 String sourceType = (String) pdb.getProperty("protocol");
4128 protocol = DataSourceType.valueOf(sourceType);
4129 } catch (IllegalArgumentException e)
4133 if (protocol == null)
4135 System.err.println("Couldn't work out protocol to open structure: "
4140 if (applet.useXtrnalSviewer)
4142 // register the association(s) and quit, don't create any windows.
4143 if (StructureSelectionManager.getStructureSelectionManager(applet)
4144 .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4146 System.err.println("Failed to map " + pdb.getFile() + " ("
4147 + protocol + ") to any sequences");
4151 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4153 // can only do alignments with Jmol
4154 // find the last jmol window assigned to this alignment
4155 AppletJmol ajm = null, tajm;
4156 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4157 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4159 tajm = (AppletJmol) jmols.elementAt(i);
4160 if (tajm.ap.alignFrame == this)
4169 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4170 // try and add the pdb structure
4175 // otherwise, create a new window
4176 if (applet.jmolAvailable)
4178 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4179 applet.lastFrameX += 40;
4180 applet.lastFrameY += 40;
4184 new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4189 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4190 SequenceI[][] seqs, String[][] chains, String[] protocols)
4192 // TODO Auto-generated method stub
4193 System.err.println("Aligned Structure View: Not yet implemented.");
4197 * modify the current selection, providing the user has not made a selection
4201 * - sequences from this alignment
4203 * - columns to be selected on the alignment
4205 public void select(SequenceGroup sel, ColumnSelection csel,
4206 HiddenColumns hidden)
4208 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4211 public void scrollTo(int row, int column)
4213 alignPanel.seqPanel.scrollTo(row, column);
4216 public void scrollToRow(int row)
4218 alignPanel.seqPanel.scrollToRow(row);
4221 public void scrollToColumn(int column)
4223 alignPanel.seqPanel.scrollToColumn(column);
4227 * @return the alignments unique ID.
4229 public String getSequenceSetId()
4231 return viewport.getSequenceSetId();
4235 * Load the (T-Coffee) score file from the specified url
4238 * File/URL/T-COFFEE score file contents
4239 * @throws IOException
4240 * @return true if alignment was annotated with data from source
4242 public boolean loadScoreFile(String source) throws IOException
4245 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4246 AppletFormatAdapter.checkProtocol(source));
4247 if (!file.isValid())
4249 // TODO: raise dialog for gui
4250 System.err.println("Problems parsing T-Coffee scores: "
4251 + file.getWarningMessage());
4252 System.err.println("Origin was:\n" + source);
4257 * check that the score matrix matches the alignment dimensions
4260 if ((aln = viewport.getAlignment()) != null
4261 && (aln.getHeight() != file.getHeight()
4262 || aln.getWidth() != file.getWidth()))
4264 // TODO: raise a dialog box here rather than bomb out.
4266 "The scores matrix does not match the alignment dimensions");
4270 // TODO add parameter to indicate if matching should be done
4271 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4273 alignPanel.fontChanged();
4274 tcoffeeColour.setEnabled(true);
4275 // switch to this color
4276 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4281 System.err.println("Problems resolving T-Coffee scores:");
4282 if (file.getWarningMessage() != null)
4284 System.err.println(file.getWarningMessage());
4290 public SplitFrame getSplitFrame()
4292 return this.splitFrame;
4295 public void setSplitFrame(SplitFrame sf)
4297 this.splitFrame = sf;
4300 // may not need this
4302 public void setShowSeqFeatures(boolean b)
4304 // showSeqFeatures.setSelected(b);
4305 viewport.setShowSequenceFeatures(b);
4310 public void setMenusForViewport()
4312 // setMenusFromViewport(viewport);
4317 public void refreshFeatureUI(boolean enableIfNecessary)
4319 if (enableIfNecessary)
4321 sequenceFeatures.setState(true);
4322 alignPanel.av.setShowSequenceFeatures(true);
4327 public FeatureSettingsControllerI getFeatureSettingsUI()
4329 return alignPanel.av.featureSettings;