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,
177 String title, boolean embedded)
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet,
184 String title, boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
238 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
239 followMouseOverFlag.setState(viewport.isFollowHighlight());
240 showGroupConsensus.setState(viewport.isShowGroupConsensus());
241 showGroupConservation.setState(viewport.isShowGroupConservation());
242 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
243 showSequenceLogo.setState(viewport.isShowSequenceLogo());
244 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
245 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
246 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
247 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
248 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showAlignmentAnnotations.setState(true);
250 showSequenceAnnotations.setState(false);
252 seqLimits.setState(viewport.getShowJVSuffix());
256 String param = applet.getParameter("sortBy");
259 if (param.equalsIgnoreCase("Id"))
261 sortIDMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Pairwise Identity"))
265 sortPairwiseMenuItem_actionPerformed();
267 else if (param.equalsIgnoreCase("Length"))
269 sortLengthMenuItem_actionPerformed();
273 param = applet.getParameter("wrap");
276 if (param.equalsIgnoreCase("true"))
278 wrapMenuItem.setState(true);
279 wrapMenuItem_actionPerformed();
282 param = applet.getParameter("centrecolumnlabels");
285 centreColumnLabelFlag.setState(true);
286 centreColumnLabelFlag_stateChanged();
290 if (viewport.getAlignment().isNucleotide())
292 conservationMenuItem.setEnabled(false);
293 clustalColour.setEnabled(false);
294 BLOSUM62Colour.setEnabled(false);
295 zappoColour.setEnabled(false);
296 taylorColour.setEnabled(false);
297 hydrophobicityColour.setEnabled(false);
298 helixColour.setEnabled(false);
299 strandColour.setEnabled(false);
300 turnColour.setEnabled(false);
301 buriedColour.setEnabled(false);
302 viewport.updateStrucConsensus(alignPanel);
303 if (viewport.getAlignment().hasRNAStructure())
305 RNAHelixColour.setEnabled(true);
309 RNAHelixColour.setEnabled(false);
314 RNAHelixColour.setEnabled(false);
315 purinePyrimidineColour.setEnabled(false);
316 nucleotideColour.setEnabled(false);
318 // Some JVMS send keyevents to Top frame or lowest panel,
319 // Havent worked out why yet. So add to both this frame and seqCanvas for
321 this.addKeyListener(this);
322 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
323 alignPanel.idPanel.idCanvas.addKeyListener(this);
324 alignPanel.scalePanel.addKeyListener(this);
325 alignPanel.annotationPanel.addKeyListener(this);
326 alignPanel.annotationPanelHolder.addKeyListener(this);
327 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
328 alignPanel.alabels.addKeyListener(this);
330 setAnnotationsVisibility();
334 addToDisplay(embedded);
341 public void addToDisplay(boolean embedded)
343 createAlignFrameWindow(embedded);
345 alignPanel.adjustAnnotationHeight();
346 alignPanel.paintAlignment(true);
349 public AlignViewport getAlignViewport()
354 public SeqCanvas getSeqcanvas()
356 return alignPanel.seqPanel.seqCanvas;
360 * Load a features file onto the alignment
363 * file URL, content, or other resolvable path
365 * is protocol for accessing data referred to by file
368 public boolean parseFeaturesFile(String file, DataSourceType type)
370 return parseFeaturesFile(file, type, true);
374 * Load a features file onto the alignment
377 * file URL, content, or other resolvable path
379 * is protocol for accessing data referred to by file
380 * @param autoenabledisplay
381 * when true, display features flag will be automatically enabled if
382 * features are loaded
383 * @return true if data parsed as a features file
385 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
386 boolean autoenabledisplay)
388 boolean featuresFile = false;
391 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
392 .getFeatureRenderer().getFeatureColours();
393 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
394 "relaxedidmatch", false);
395 featuresFile = new FeaturesFile(file, sourceType).parse(
396 viewport.getAlignment(), colours, true, relaxedIdMatching);
397 } catch (Exception ex)
399 ex.printStackTrace();
404 if (autoenabledisplay)
406 viewport.setShowSequenceFeatures(true);
407 sequenceFeatures.setState(true);
409 if (alignPanel.seqPanel.seqCanvas.fr != null)
411 // update the min/max ranges where necessary
412 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
414 if (viewport.featureSettings != null)
416 viewport.featureSettings.refreshTable();
418 alignPanel.paintAlignment(true);
419 statusBar.setText(MessageManager
420 .getString("label.successfully_added_features_alignment"));
426 public void keyPressed(KeyEvent evt)
428 ViewportRanges ranges = viewport.getRanges();
430 if (viewport.cursorMode
431 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
432 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
433 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
434 && Character.isDigit(evt.getKeyChar()))
436 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
439 switch (evt.getKeyCode())
441 case 27: // escape key
442 deselectAllSequenceMenuItem_actionPerformed();
444 alignPanel.alabels.cancelDrag();
447 if (evt.isControlDown() || evt.isMetaDown())
449 cut_actionPerformed();
453 if (viewport.cursorMode && !evt.isControlDown())
455 alignPanel.seqPanel.setCursorColumn();
457 if (evt.isControlDown() || evt.isMetaDown())
459 copy_actionPerformed();
463 if (evt.isControlDown())
465 paste(evt.isShiftDown());
469 if (evt.isControlDown() || evt.isMetaDown())
471 selectAllSequenceMenuItem_actionPerformed();
474 case KeyEvent.VK_DOWN:
475 if (viewport.cursorMode)
477 alignPanel.seqPanel.moveCursor(0, 1);
481 moveSelectedSequences(false);
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.moveCursor(0, -1);
492 moveSelectedSequences(true);
496 case KeyEvent.VK_LEFT:
497 if (evt.isAltDown() || !viewport.cursorMode)
499 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
503 alignPanel.seqPanel.moveCursor(-1, 0);
507 case KeyEvent.VK_RIGHT:
508 if (evt.isAltDown() || !viewport.cursorMode)
510 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
514 alignPanel.seqPanel.moveCursor(1, 0);
518 case KeyEvent.VK_SPACE:
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
522 || evt.isShiftDown() || evt.isAltDown());
526 case KeyEvent.VK_DELETE:
527 case KeyEvent.VK_BACK_SPACE:
528 if (viewport.cursorMode)
530 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
531 || evt.isShiftDown() || evt.isAltDown());
535 cut_actionPerformed();
536 alignPanel.seqPanel.seqCanvas.repaint();
541 if (viewport.cursorMode)
543 alignPanel.seqPanel.setCursorRow();
547 if (viewport.cursorMode)
549 alignPanel.seqPanel.setCursorPosition();
553 case KeyEvent.VK_ENTER:
554 case KeyEvent.VK_COMMA:
555 if (viewport.cursorMode)
557 alignPanel.seqPanel.setCursorRowAndColumn();
562 if (viewport.cursorMode)
564 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
568 if (viewport.cursorMode)
570 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
575 viewport.cursorMode = !viewport.cursorMode;
576 statusBar.setText(MessageManager.formatMessage(
577 "label.keyboard_editing_mode",
578 new String[] { (viewport.cursorMode ? "on" : "off") }));
579 if (viewport.cursorMode)
581 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
582 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
587 if (evt.isControlDown())
589 findMenuItem_actionPerformed();
595 boolean toggleSeqs = !evt.isControlDown();
596 boolean toggleCols = !evt.isShiftDown();
597 toggleHiddenRegions(toggleSeqs, toggleCols);
601 case KeyEvent.VK_PAGE_UP:
605 case KeyEvent.VK_PAGE_DOWN:
610 if (evt.isControlDown())
612 undoMenuItem_actionPerformed();
617 if (evt.isControlDown())
619 redoMenuItem_actionPerformed();
624 if (evt.isControlDown())
631 if (evt.isControlDown())
633 trimAlignment(false);
638 if (evt.isControlDown())
640 if (evt.isShiftDown())
642 this.removeAllGapsMenuItem_actionPerformed();
646 removeGappedColumnMenuItem_actionPerformed();
651 if (evt.isControlDown())
655 invertColSel_actionPerformed();
659 invertSequenceMenuItem_actionPerformed();
665 if (evt.isControlDown())
667 if (evt.isShiftDown())
669 this.unGroup_actionPerformed();
673 this.createGroup_actionPerformed();
679 if (evt.isControlDown())
681 this.deleteGroups_actionPerformed();
686 if (evt.isControlDown())
693 alignPanel.paintAlignment(true);
697 * called by key handler and the hide all/show all menu items
702 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
704 boolean hide = false;
705 SequenceGroup sg = viewport.getSelectionGroup();
706 if (!toggleSeqs && !toggleCols)
708 // Hide everything by the current selection - this is a hack - we do the
709 // invert and then hide
710 // first check that there will be visible columns after the invert.
711 if (viewport.hasSelectedColumns()
712 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
715 // now invert the sequence set, if required - empty selection implies
716 // that no hiding is required.
719 invertSequenceMenuItem_actionPerformed();
720 sg = viewport.getSelectionGroup();
724 viewport.expandColSelection(sg, true);
725 // finally invert the column selection and get the new sequence
726 // selection and indicate it should be hidden.
727 invertColSel_actionPerformed();
734 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
737 viewport.hideAllSelectedSeqs();
739 else if (!(toggleCols && viewport.hasSelectedColumns()))
741 viewport.showAllHiddenSeqs();
747 if (viewport.hasSelectedColumns())
749 viewport.hideSelectedColumns();
752 viewport.setSelectionGroup(sg);
757 viewport.showAllHiddenColumns();
759 viewport.sendSelection();
764 public void keyReleased(KeyEvent evt)
769 public void keyTyped(KeyEvent evt)
774 public void itemStateChanged(ItemEvent evt)
776 final Object source = evt.getSource();
777 if (source == displayNonconservedMenuItem)
779 displayNonconservedMenuItem_actionPerformed();
781 else if (source == colourTextMenuItem)
783 colourTextMenuItem_actionPerformed();
785 else if (source == wrapMenuItem)
787 wrapMenuItem_actionPerformed();
789 else if (source == scaleAbove)
791 viewport.setScaleAboveWrapped(scaleAbove.getState());
793 else if (source == scaleLeft)
795 viewport.setScaleLeftWrapped(scaleLeft.getState());
797 else if (source == scaleRight)
799 viewport.setScaleRightWrapped(scaleRight.getState());
801 else if (source == seqLimits)
803 seqLimits_itemStateChanged();
805 else if (source == viewBoxesMenuItem)
807 viewport.setShowBoxes(viewBoxesMenuItem.getState());
809 else if (source == viewTextMenuItem)
811 viewport.setShowText(viewTextMenuItem.getState());
813 else if (source == renderGapsMenuItem)
815 viewport.setRenderGaps(renderGapsMenuItem.getState());
817 else if (source == annotationPanelMenuItem)
819 boolean showAnnotations = annotationPanelMenuItem.getState();
820 showAlignmentAnnotations.setEnabled(showAnnotations);
821 showSequenceAnnotations.setEnabled(showAnnotations);
822 viewport.setShowAnnotation(showAnnotations);
823 alignPanel.setAnnotationVisible(showAnnotations);
825 else if (source == sequenceFeatures)
827 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
828 alignPanel.seqPanel.seqCanvas.repaint();
830 else if (source == showAlignmentAnnotations)
832 setAnnotationsVisibility();
834 else if (source == showSequenceAnnotations)
836 setAnnotationsVisibility();
838 else if (source == sortAnnBySequence)
840 boolean newState = sortAnnBySequence.getState();
841 sortAnnByLabel.setState(false);
842 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
843 : SequenceAnnotationOrder.NONE);
844 setViewportAnnotationOrder();
846 else if (source == sortAnnByLabel)
848 boolean newState = sortAnnByLabel.getState();
849 sortAnnBySequence.setState(false);
850 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
851 : SequenceAnnotationOrder.NONE);
852 setViewportAnnotationOrder();
854 else if (source == showAutoFirst)
856 showAutoLast.setState(!showAutoFirst.getState());
857 setShowAutoCalculatedAbove(showAutoFirst.getState());
858 setViewportAnnotationOrder();
860 else if (source == showAutoLast)
862 showAutoFirst.setState(!showAutoLast.getState());
863 setShowAutoCalculatedAbove(showAutoFirst.getState());
864 setViewportAnnotationOrder();
866 else if (source == conservationMenuItem)
868 conservationMenuItem_actionPerformed();
870 else if (source == abovePIDThreshold)
872 abovePIDThreshold_actionPerformed();
874 else if (source == applyToAllGroups)
876 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
878 else if (source == autoCalculate)
880 viewport.autoCalculateConsensus = autoCalculate.getState();
882 else if (source == sortByTree)
884 viewport.sortByTree = sortByTree.getState();
886 else if (source == this.centreColumnLabelFlag)
888 centreColumnLabelFlag_stateChanged();
890 else if (source == this.followMouseOverFlag)
892 mouseOverFlag_stateChanged();
894 else if (source == showGroupConsensus)
896 showGroupConsensus_actionPerformed();
898 else if (source == showGroupConservation)
900 showGroupConservation_actionPerformed();
902 else if (source == showSequenceLogo)
904 showSequenceLogo_actionPerformed();
906 else if (source == normSequenceLogo)
908 normSequenceLogo_actionPerformed();
910 else if (source == showConsensusHistogram)
912 showConsensusHistogram_actionPerformed();
914 else if (source == applyAutoAnnotationSettings)
916 applyAutoAnnotationSettings_actionPerformed();
918 alignPanel.paintAlignment(true);
922 * Set the visibility state of sequence-related and/or alignment-related
923 * annotations depending on checkbox selections, and repaint.
927 private void setAnnotationsVisibility()
929 boolean showForAlignment = showAlignmentAnnotations.getState();
930 boolean showForSequences = showSequenceAnnotations.getState();
931 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
933 for (AlignmentAnnotation aa : alignPanel.getAlignment()
934 .getAlignmentAnnotation())
936 boolean visible = (aa.sequenceRef == null ? showForAlignment
938 aa.visible = visible;
941 alignPanel.validateAnnotationDimensions(true);
946 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
948 this.annotationSortOrder = order;
952 * Set flags on the viewport that control annotation ordering
954 private void setViewportAnnotationOrder()
956 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
958 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
961 private void setShowAutoCalculatedAbove(boolean showAbove)
963 this.showAutoCalculatedAbove = showAbove;
966 private void mouseOverFlag_stateChanged()
968 viewport.setFollowHighlight(followMouseOverFlag.getState());
969 // TODO: could kick the scrollTo mechanism to reset view for current
973 private void centreColumnLabelFlag_stateChanged()
975 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
976 this.alignPanel.annotationPanel.repaint();
980 public void actionPerformed(ActionEvent evt)
982 viewport.applet.currentAlignFrame = this;
984 Object source = evt.getSource();
986 if (source == inputText)
988 inputText_actionPerformed();
990 else if (source == loadTree)
992 loadTree_actionPerformed();
994 else if (source == loadApplication)
996 launchFullApplication();
998 else if (source == loadAnnotations)
1002 else if (source == outputAnnotations)
1004 outputAnnotations(true);
1006 else if (source == outputFeatures)
1008 outputFeatures(true, "Jalview");
1010 else if (source == closeMenuItem)
1012 closeMenuItem_actionPerformed();
1014 else if (source == copy)
1016 copy_actionPerformed();
1018 else if (source == undoMenuItem)
1020 undoMenuItem_actionPerformed();
1022 else if (source == redoMenuItem)
1024 redoMenuItem_actionPerformed();
1026 else if (source == inputText)
1028 inputText_actionPerformed();
1030 else if (source == closeMenuItem)
1032 closeMenuItem_actionPerformed();
1034 else if (source == undoMenuItem)
1036 undoMenuItem_actionPerformed();
1038 else if (source == redoMenuItem)
1040 redoMenuItem_actionPerformed();
1042 else if (source == copy)
1044 copy_actionPerformed();
1046 else if (source == pasteNew)
1048 pasteNew_actionPerformed();
1050 else if (source == pasteThis)
1052 pasteThis_actionPerformed();
1054 else if (source == cut)
1056 cut_actionPerformed();
1058 else if (source == delete)
1060 delete_actionPerformed();
1062 else if (source == createGroup)
1064 createGroup_actionPerformed();
1066 else if (source == unGroup)
1068 unGroup_actionPerformed();
1070 else if (source == grpsFromSelection)
1072 makeGrpsFromSelection_actionPerformed();
1074 else if (source == deleteGroups)
1076 deleteGroups_actionPerformed();
1078 else if (source == selectAllSequenceMenuItem)
1080 selectAllSequenceMenuItem_actionPerformed();
1082 else if (source == deselectAllSequenceMenuItem)
1084 deselectAllSequenceMenuItem_actionPerformed();
1086 else if (source == invertSequenceMenuItem)
1088 invertSequenceMenuItem_actionPerformed();
1089 // uncomment to slave sequence selections in split frame
1090 // viewport.sendSelection();
1092 else if (source == invertColSel)
1094 viewport.invertColumnSelection();
1095 alignPanel.paintAlignment(true);
1096 viewport.sendSelection();
1098 else if (source == remove2LeftMenuItem)
1100 trimAlignment(true);
1102 else if (source == remove2RightMenuItem)
1104 trimAlignment(false);
1106 else if (source == removeGappedColumnMenuItem)
1108 removeGappedColumnMenuItem_actionPerformed();
1110 else if (source == removeAllGapsMenuItem)
1112 removeAllGapsMenuItem_actionPerformed();
1114 else if (source == findMenuItem)
1116 findMenuItem_actionPerformed();
1118 else if (source == font)
1120 new FontChooser(alignPanel);
1122 else if (source == newView)
1126 else if (source == showColumns)
1128 viewport.showAllHiddenColumns();
1129 alignPanel.paintAlignment(true);
1130 viewport.sendSelection();
1132 else if (source == showSeqs)
1134 viewport.showAllHiddenSeqs();
1135 alignPanel.paintAlignment(true);
1136 // uncomment if we want to slave sequence selections in split frame
1137 // viewport.sendSelection();
1139 else if (source == hideColumns)
1141 viewport.hideSelectedColumns();
1142 alignPanel.paintAlignment(true);
1143 viewport.sendSelection();
1145 else if (source == hideSequences
1146 && viewport.getSelectionGroup() != null)
1148 viewport.hideAllSelectedSeqs();
1149 alignPanel.paintAlignment(true);
1150 // uncomment if we want to slave sequence selections in split frame
1151 // viewport.sendSelection();
1153 else if (source == hideAllButSelection)
1155 toggleHiddenRegions(false, false);
1156 alignPanel.paintAlignment(true);
1157 viewport.sendSelection();
1159 else if (source == hideAllSelection)
1161 SequenceGroup sg = viewport.getSelectionGroup();
1162 viewport.expandColSelection(sg, false);
1163 viewport.hideAllSelectedSeqs();
1164 viewport.hideSelectedColumns();
1165 alignPanel.paintAlignment(true);
1166 viewport.sendSelection();
1168 else if (source == showAllHidden)
1170 viewport.showAllHiddenColumns();
1171 viewport.showAllHiddenSeqs();
1172 alignPanel.paintAlignment(true);
1173 viewport.sendSelection();
1175 else if (source == showGroupConsensus)
1177 showGroupConsensus_actionPerformed();
1179 else if (source == showGroupConservation)
1181 showGroupConservation_actionPerformed();
1183 else if (source == showSequenceLogo)
1185 showSequenceLogo_actionPerformed();
1187 else if (source == normSequenceLogo)
1189 normSequenceLogo_actionPerformed();
1191 else if (source == showConsensusHistogram)
1193 showConsensusHistogram_actionPerformed();
1195 else if (source == applyAutoAnnotationSettings)
1197 applyAutoAnnotationSettings_actionPerformed();
1199 else if (source == featureSettings)
1201 new FeatureSettings(alignPanel);
1203 else if (source == alProperties)
1205 StringBuffer contents = new jalview.io.AlignmentProperties(
1206 viewport.getAlignment()).formatAsString();
1207 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1208 cap.setText(contents.toString());
1209 Frame frame = new Frame();
1211 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1212 "label.alignment_properties", new String[] { getTitle() }),
1215 else if (source == overviewMenuItem)
1217 overviewMenuItem_actionPerformed();
1219 else if (source == noColourmenuItem)
1223 else if (source == clustalColour)
1225 abovePIDThreshold.setState(false);
1226 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1228 else if (source == zappoColour)
1230 changeColour(new ZappoColourScheme());
1232 else if (source == taylorColour)
1234 changeColour(new TaylorColourScheme());
1236 else if (source == hydrophobicityColour)
1238 changeColour(new HydrophobicColourScheme());
1240 else if (source == helixColour)
1242 changeColour(new HelixColourScheme());
1244 else if (source == strandColour)
1246 changeColour(new StrandColourScheme());
1248 else if (source == turnColour)
1250 changeColour(new TurnColourScheme());
1252 else if (source == buriedColour)
1254 changeColour(new BuriedColourScheme());
1256 else if (source == nucleotideColour)
1258 changeColour(new NucleotideColourScheme());
1260 else if (source == purinePyrimidineColour)
1262 changeColour(new PurinePyrimidineColourScheme());
1264 // else if (source == RNAInteractionColour)
1266 // changeColour(new RNAInteractionColourScheme());
1268 else if (source == RNAHelixColour)
1270 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1271 // new RNAHelicesColourChooser(viewport, alignPanel);
1273 else if (source == modifyPID)
1275 modifyPID_actionPerformed();
1277 else if (source == modifyConservation)
1279 modifyConservation_actionPerformed();
1281 else if (source == userDefinedColour)
1283 new UserDefinedColours(alignPanel, null);
1285 else if (source == PIDColour)
1287 changeColour(new PIDColourScheme());
1289 else if (source == BLOSUM62Colour)
1291 changeColour(new Blosum62ColourScheme());
1293 else if (source == tcoffeeColour)
1295 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1297 else if (source == annotationColour)
1299 new AnnotationColourChooser(viewport, alignPanel);
1301 else if (source == annotationColumnSelection)
1303 new AnnotationColumnChooser(viewport, alignPanel);
1305 else if (source == sortPairwiseMenuItem)
1307 sortPairwiseMenuItem_actionPerformed();
1309 else if (source == sortIDMenuItem)
1311 sortIDMenuItem_actionPerformed();
1313 else if (source == sortLengthMenuItem)
1315 sortLengthMenuItem_actionPerformed();
1317 else if (source == sortGroupMenuItem)
1319 sortGroupMenuItem_actionPerformed();
1321 else if (source == removeRedundancyMenuItem)
1323 removeRedundancyMenuItem_actionPerformed();
1325 else if (source == pairwiseAlignmentMenuItem)
1327 pairwiseAlignmentMenuItem_actionPerformed();
1329 else if (source == PCAMenuItem)
1331 PCAMenuItem_actionPerformed();
1333 else if (source == averageDistanceTreeMenuItem)
1335 averageDistanceTreeMenuItem_actionPerformed();
1337 else if (source == neighbourTreeMenuItem)
1339 neighbourTreeMenuItem_actionPerformed();
1341 else if (source == njTreeBlosumMenuItem)
1343 njTreeBlosumMenuItem_actionPerformed();
1345 else if (source == avDistanceTreeBlosumMenuItem)
1347 avTreeBlosumMenuItem_actionPerformed();
1349 else if (source == documentation)
1351 documentation_actionPerformed();
1353 else if (source == about)
1355 about_actionPerformed();
1360 public void inputText_actionPerformed()
1362 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1363 Frame frame = new Frame();
1365 jalview.bin.JalviewLite.addFrame(frame,
1366 MessageManager.getString("label.input_cut_paste"), 500, 500);
1369 protected void outputText_actionPerformed(ActionEvent e)
1371 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1372 Frame frame = new Frame();
1374 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1375 "label.alignment_output_command",
1376 new Object[] { e.getActionCommand() }), 600, 500);
1378 FileFormatI fileFormat = FileFormats.getInstance().forName(
1379 e.getActionCommand());
1380 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1381 fileFormat, viewport.getAlignment(),
1382 viewport.getShowJVSuffix()));
1385 public void loadAnnotations()
1387 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388 cap.setText(MessageManager
1389 .getString("label.paste_features_annotations_Tcoffee_here"));
1390 cap.setAnnotationImport();
1391 Frame frame = new Frame();
1393 jalview.bin.JalviewLite.addFrame(frame,
1394 MessageManager.getString("action.paste_annotations"), 400, 300);
1398 public String outputAnnotations(boolean displayTextbox)
1400 String annotation = new AnnotationFile()
1401 .printAnnotationsForView(viewport);
1405 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1406 Frame frame = new Frame();
1408 jalview.bin.JalviewLite.addFrame(frame,
1409 MessageManager.getString("label.annotations"), 600, 500);
1410 cap.setText(annotation);
1416 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1418 if (alignPanel.getFeatureRenderer() != null
1419 && viewport.getFeaturesDisplayed() != null)
1421 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1427 private List<String> getDisplayedFeatureGroups()
1429 if (alignPanel.getFeatureRenderer() != null
1430 && viewport.getFeaturesDisplayed() != null)
1432 return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1438 public String outputFeatures(boolean displayTextbox, String format)
1441 FeaturesFile formatter = new FeaturesFile();
1442 if (format.equalsIgnoreCase("Jalview"))
1444 features = formatter.printJalviewFormat(viewport.getAlignment()
1445 .getSequencesArray(), getDisplayedFeatureCols(),
1446 getDisplayedFeatureGroups(), true);
1450 features = formatter.printGffFormat(viewport.getAlignment()
1451 .getSequencesArray(), getDisplayedFeatureCols(),
1452 getDisplayedFeatureGroups(), true);
1457 boolean frimport = false;
1458 if (features == null || features.equals("No Features Visible"))
1460 features = "# No features visible - paste some and import them here.";
1464 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1467 cap.setAnnotationImport();
1469 Frame frame = new Frame();
1471 jalview.bin.JalviewLite.addFrame(frame,
1472 MessageManager.getString("label.features"), 600, 500);
1473 cap.setText(features);
1477 if (features == null)
1486 void launchFullApplication()
1488 StringBuffer url = new StringBuffer(jalviewServletURL);
1490 // allow servlet parameters to be passed in applet parameter
1491 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1493 url.append(firstSep);
1496 + appendProtocol(viewport.applet.getParameter("file")));
1498 if (viewport.applet.getParameter("features") != null)
1500 url.append("&features=");
1501 url.append(appendProtocol(viewport.applet.getParameter("features")));
1504 if (viewport.applet.getParameter("annotations") != null)
1506 url.append("&annotations=");
1507 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1510 if (viewport.applet.getParameter("jnetfile") != null
1511 || viewport.applet.getParameter("jpredfile") != null)
1513 url.append("&annotations=");
1514 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1515 .getParameter("jnetfile") : viewport.applet
1516 .getParameter("jpredfile")));
1519 if (viewport.applet.getParameter("defaultColour") != null)
1521 url.append("&colour="
1522 + removeWhiteSpace(viewport.applet
1523 .getParameter("defaultColour")));
1526 if (viewport.applet.getParameter("userDefinedColour") != null)
1528 url.append("&colour="
1529 + removeWhiteSpace(viewport.applet
1530 .getParameter("userDefinedColour")));
1532 if (viewport.applet.getParameter("tree") != null)
1535 + appendProtocol(viewport.applet.getParameter("tree")));
1537 if (viewport.applet.getParameter("treeFile") != null)
1540 + appendProtocol(viewport.applet.getParameter("treeFile")));
1543 showURL(url.toString(), "FULL_APP");
1546 String removeWhiteSpace(String colour)
1548 StringBuffer sb = new StringBuffer();
1549 for (int i = 0; i < colour.length(); i++)
1551 if (Character.isWhitespace(colour.charAt(i)))
1557 sb.append(colour.charAt(i));
1561 return sb.toString();
1564 String appendProtocol(String url)
1569 url = URLEncoder.encode(url);
1572 * When we finally deprecate 1.1 compatibility, we can start to use
1573 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1574 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1575 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1576 * ex.printStackTrace(); }
1578 catch (java.net.MalformedURLException ex)
1580 url = viewport.applet.getCodeBase() + url;
1585 public void closeMenuItem_actionPerformed()
1587 PaintRefresher.RemoveComponent(alignPanel);
1588 if (alignPanel.seqPanel != null
1589 && alignPanel.seqPanel.seqCanvas != null)
1591 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1593 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1595 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1598 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1613 void updateEditMenuBar()
1616 if (viewport.getHistoryList().size() > 0)
1618 undoMenuItem.setEnabled(true);
1619 CommandI command = viewport.getHistoryList().peek();
1620 undoMenuItem.setLabel(MessageManager.formatMessage(
1621 "label.undo_command",
1622 new Object[] { command.getDescription() }));
1626 undoMenuItem.setEnabled(false);
1627 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1630 if (viewport.getRedoList().size() > 0)
1632 redoMenuItem.setEnabled(true);
1634 CommandI command = viewport.getRedoList().peek();
1635 redoMenuItem.setLabel(MessageManager.formatMessage(
1636 "label.redo_command",
1637 new Object[] { command.getDescription() }));
1641 redoMenuItem.setEnabled(false);
1642 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1650 public void addHistoryItem(CommandI command)
1652 if (command.getSize() > 0)
1654 viewport.addToHistoryList(command);
1655 viewport.clearRedoList();
1656 updateEditMenuBar();
1657 viewport.updateHiddenColumns();
1662 * TODO: JAL-1104 DOCUMENT ME!
1667 protected void undoMenuItem_actionPerformed()
1669 if (viewport.getHistoryList().isEmpty())
1674 CommandI command = viewport.getHistoryList().pop();
1675 viewport.addToRedoList(command);
1676 command.undoCommand(null);
1678 AlignmentViewport originalSource = getOriginatingSource(command);
1680 if (originalSource != viewport)
1683 .println("Warning: Viewport object mismatch whilst undoing");
1685 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1686 // viewport.getColumnSelection().getHiddenColumns()
1688 updateEditMenuBar();
1689 originalSource.firePropertyChange("alignment", null, originalSource
1690 .getAlignment().getSequences());
1694 * TODO: JAL-1104 DOCUMENT ME!
1699 protected void redoMenuItem_actionPerformed()
1701 if (viewport.getRedoList().isEmpty())
1706 CommandI command = viewport.getRedoList().pop();
1707 viewport.addToHistoryList(command);
1708 command.doCommand(null);
1710 AlignmentViewport originalSource = getOriginatingSource(command);
1712 if (originalSource != viewport)
1715 .println("Warning: Viewport object mismatch whilst re-doing");
1717 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1718 // viewport.getColumnSelection().getHiddenColumns()
1721 updateEditMenuBar();
1722 originalSource.firePropertyChange("alignment", null, originalSource
1723 .getAlignment().getSequences());
1726 AlignmentViewport getOriginatingSource(CommandI command)
1728 AlignmentViewport originalSource = null;
1729 // For sequence removal and addition, we need to fire
1730 // the property change event FROM the viewport where the
1731 // original alignment was altered
1732 AlignmentI al = null;
1733 if (command instanceof EditCommand)
1735 EditCommand editCommand = (EditCommand) command;
1736 al = editCommand.getAlignment();
1737 Vector comps = (Vector) PaintRefresher.components.get(viewport
1738 .getSequenceSetId());
1739 for (int i = 0; i < comps.size(); i++)
1741 if (comps.elementAt(i) instanceof AlignmentPanel)
1743 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1745 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1752 if (originalSource == null)
1754 // The original view is closed, we must validate
1755 // the current view against the closed view first
1758 PaintRefresher.validateSequences(al, viewport.getAlignment());
1761 originalSource = viewport;
1764 return originalSource;
1768 * Move the currently selected sequences up or down one position in the
1773 public void moveSelectedSequences(boolean up)
1775 SequenceGroup sg = viewport.getSelectionGroup();
1780 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1781 up ? null : viewport.getHiddenRepSequences(), up);
1782 alignPanel.paintAlignment(true);
1785 * Also move cDNA/protein complement sequences
1787 AlignViewportI complement = viewport.getCodingComplement();
1788 if (complement != null)
1790 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1791 viewport, complement);
1792 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1793 up ? null : complement.getHiddenRepSequences(), up);
1794 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1798 synchronized void slideSequences(boolean right, int size)
1800 List<SequenceI> sg = new Vector<>();
1801 if (viewport.cursorMode)
1803 sg.add(viewport.getAlignment().getSequenceAt(
1804 alignPanel.seqPanel.seqCanvas.cursorY));
1806 else if (viewport.getSelectionGroup() != null
1807 && viewport.getSelectionGroup().getSize() != viewport
1808 .getAlignment().getHeight())
1810 sg = viewport.getSelectionGroup().getSequences(
1811 viewport.getHiddenRepSequences());
1819 Vector<SequenceI> invertGroup = new Vector();
1821 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1823 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1825 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1829 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1831 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1833 for (int i = 0; i < invertGroup.size(); i++)
1835 seqs2[i] = invertGroup.elementAt(i);
1838 SlideSequencesCommand ssc;
1841 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1842 size, viewport.getGapCharacter());
1846 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1847 size, viewport.getGapCharacter());
1850 int groupAdjustment = 0;
1851 if (ssc.getGapsInsertedBegin() && right)
1853 if (viewport.cursorMode)
1855 alignPanel.seqPanel.moveCursor(size, 0);
1859 groupAdjustment = size;
1862 else if (!ssc.getGapsInsertedBegin() && !right)
1864 if (viewport.cursorMode)
1866 alignPanel.seqPanel.moveCursor(-size, 0);
1870 groupAdjustment = -size;
1874 if (groupAdjustment != 0)
1876 viewport.getSelectionGroup().setStartRes(
1877 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1878 viewport.getSelectionGroup().setEndRes(
1879 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1882 boolean appendHistoryItem = false;
1883 Deque<CommandI> historyList = viewport.getHistoryList();
1884 if (historyList != null && historyList.size() > 0
1885 && historyList.peek() instanceof SlideSequencesCommand)
1887 appendHistoryItem = ssc
1888 .appendSlideCommand((SlideSequencesCommand) historyList
1892 if (!appendHistoryItem)
1894 addHistoryItem(ssc);
1900 static StringBuffer copiedSequences;
1902 static Vector<int[]> copiedHiddenColumns;
1904 protected void copy_actionPerformed()
1906 if (viewport.getSelectionGroup() == null)
1911 SequenceGroup sg = viewport.getSelectionGroup();
1912 copiedSequences = new StringBuffer();
1913 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1914 for (int i = 0; i < sg.getSize(); i++)
1916 SequenceI seq = sg.getSequenceAt(i);
1917 int index = viewport.getAlignment().findIndex(seq);
1918 orderedSeqs.put(index, seq);
1921 int index = 0, startRes, endRes;
1924 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1926 copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1927 .getHiddenColumns().getHiddenColumnsCopy());
1928 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1929 for (int[] region : copiedHiddenColumns)
1931 region[0] = region[0] - hiddenOffset;
1932 region[1] = region[1] - hiddenOffset;
1937 copiedHiddenColumns = null;
1940 for (int i = 0; i < sg.getSize(); i++)
1942 SequenceI seq = null;
1946 if (orderedSeqs.containsKey(index))
1948 seq = orderedSeqs.get(index);
1959 // Returns residue following index if gap
1960 startRes = seq.findPosition(sg.getStartRes());
1963 // Need to find the residue preceeding index if gap
1966 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1968 ch = seq.getCharAt(j);
1969 if (!jalview.util.Comparison.isGap((ch)))
1977 endRes += seq.getStart() - 1;
1980 copiedSequences.append(seq.getName()
1986 + seq.getSequenceAsString(sg.getStartRes(),
1987 sg.getEndRes() + 1) + "\n");
1992 protected void pasteNew_actionPerformed()
1997 protected void pasteThis_actionPerformed()
2002 void paste(boolean newAlignment)
2007 if (copiedSequences == null)
2012 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2013 Vector seqs = new Vector();
2014 while (st.hasMoreElements())
2016 String name = st.nextToken();
2017 int start = Integer.parseInt(st.nextToken());
2018 int end = Integer.parseInt(st.nextToken());
2019 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2021 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2022 for (int i = 0; i < seqs.size(); i++)
2024 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2029 String newtitle = MessageManager
2030 .getString("label.copied_sequences");
2031 if (getTitle().startsWith(
2032 MessageManager.getString("label.copied_sequences")))
2034 newtitle = getTitle();
2038 newtitle = newtitle.concat(MessageManager.formatMessage(
2039 "label.from_msname", new String[] { getTitle() }));
2041 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2042 viewport.applet, newtitle, false);
2043 if (copiedHiddenColumns != null)
2045 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2047 int[] region = copiedHiddenColumns.elementAt(i);
2048 af.viewport.hideColumns(region[0], region[1]);
2052 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2057 addSequences(newSeqs);
2060 } catch (Exception ex)
2062 } // could be anything being pasted in here
2066 void addSequences(SequenceI[] seqs)
2068 for (int i = 0; i < seqs.length; i++)
2070 viewport.getAlignment().addSequence(seqs[i]);
2074 addHistoryItem(new EditCommand(
2075 MessageManager.getString("label.add_sequences"), Action.PASTE,
2076 seqs, 0, viewport.getAlignment().getWidth(),
2077 viewport.getAlignment()));
2079 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2080 viewport.getAlignment().getWidth();
2081 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2086 protected void cut_actionPerformed()
2088 copy_actionPerformed();
2089 delete_actionPerformed();
2092 protected void delete_actionPerformed()
2095 SequenceGroup sg = viewport.getSelectionGroup();
2101 Vector seqs = new Vector();
2103 for (int i = 0; i < sg.getSize(); i++)
2105 seq = sg.getSequenceAt(i);
2106 seqs.addElement(seq);
2110 * If the cut affects all sequences, warn, remove highlighted columns
2112 if (sg.getSize() == viewport.getAlignment().getHeight())
2114 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2115 .getAlignment().getWidth()) ? true : false;
2116 if (isEntireAlignWidth)
2118 String title = MessageManager.getString("label.delete_all");
2119 Panel infoPanel = new Panel();
2120 infoPanel.setLayout(new FlowLayout());
2122 .add(new Label(MessageManager.getString("warn.delete_all")));
2124 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2125 dialog.setMainPanel(infoPanel);
2126 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2127 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2128 dialog.setVisible(true);
2135 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2136 sg.getEndRes() + 1);
2139 SequenceI[] cut = new SequenceI[seqs.size()];
2140 for (int i = 0; i < seqs.size(); i++)
2142 cut[i] = (SequenceI) seqs.elementAt(i);
2146 * //ADD HISTORY ITEM
2148 addHistoryItem(new EditCommand(
2149 MessageManager.getString("label.cut_sequences"), Action.CUT,
2150 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2151 viewport.getAlignment()));
2153 viewport.setSelectionGroup(null);
2154 viewport.getAlignment().deleteGroup(sg);
2156 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2159 if (viewport.getAlignment().getHeight() < 1)
2161 this.setVisible(false);
2163 viewport.sendSelection();
2167 * group consensus toggled
2170 protected void showGroupConsensus_actionPerformed()
2172 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2173 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2178 * group conservation toggled.
2180 protected void showGroupConservation_actionPerformed()
2182 viewport.setShowGroupConservation(showGroupConservation.getState());
2183 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2191 * .event.ActionEvent)
2193 protected void showConsensusHistogram_actionPerformed()
2195 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2196 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2203 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2204 * .event.ActionEvent)
2206 protected void showSequenceLogo_actionPerformed()
2208 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2212 protected void normSequenceLogo_actionPerformed()
2214 showSequenceLogo.setState(true);
2215 viewport.setShowSequenceLogo(true);
2216 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2217 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2220 protected void applyAutoAnnotationSettings_actionPerformed()
2222 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2225 protected void makeGrpsFromSelection_actionPerformed()
2227 if (avc.makeGroupsFromSelection())
2229 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2230 alignPanel.updateAnnotation();
2231 alignPanel.paintAlignment(true);
2235 protected void createGroup_actionPerformed()
2240 protected void unGroup_actionPerformed()
2244 alignPanel.alignmentChanged();
2248 protected void deleteGroups_actionPerformed()
2250 if (avc.deleteGroups())
2252 alignPanel.alignmentChanged();
2256 public void selectAllSequenceMenuItem_actionPerformed()
2258 SequenceGroup sg = new SequenceGroup();
2259 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2261 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2263 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2264 viewport.setSelectionGroup(sg);
2265 // JAL-2034 - should delegate to
2266 // alignPanel to decide if overview needs
2268 alignPanel.paintAlignment(false);
2269 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2270 viewport.sendSelection();
2273 public void deselectAllSequenceMenuItem_actionPerformed()
2275 if (viewport.cursorMode)
2277 alignPanel.seqPanel.keyboardNo1 = null;
2278 alignPanel.seqPanel.keyboardNo2 = null;
2280 viewport.setSelectionGroup(null);
2281 viewport.getColumnSelection().clear();
2282 viewport.setSelectionGroup(null);
2283 alignPanel.idPanel.idCanvas.searchResults = null;
2284 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2285 // JAL-2034 - should delegate to
2286 // alignPanel to decide if overview needs
2288 alignPanel.paintAlignment(false);
2289 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2290 viewport.sendSelection();
2293 public void invertSequenceMenuItem_actionPerformed()
2295 SequenceGroup sg = viewport.getSelectionGroup();
2296 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2298 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2301 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2302 viewport.sendSelection();
2305 public void invertColSel_actionPerformed()
2307 viewport.invertColumnSelection();
2308 alignPanel.paintAlignment(true);
2309 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2310 viewport.sendSelection();
2313 void trimAlignment(boolean trimLeft)
2315 AlignmentI al = viewport.getAlignment();
2316 ViewportRanges ranges = viewport.getRanges();
2317 ColumnSelection colSel = viewport.getColumnSelection();
2320 if (!colSel.isEmpty())
2324 column = colSel.getMin();
2328 column = colSel.getMax();
2332 if (viewport.getSelectionGroup() != null)
2334 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2335 viewport.getHiddenRepSequences());
2339 seqs = al.getSequencesArray();
2342 TrimRegionCommand trimRegion;
2345 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2347 ranges.setStartRes(0);
2351 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2355 statusBar.setText(MessageManager.formatMessage(
2356 "label.removed_columns",
2357 new String[] { Integer.valueOf(trimRegion.getSize())
2359 addHistoryItem(trimRegion);
2361 for (SequenceGroup sg : al.getGroups())
2363 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2364 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2370 viewport.firePropertyChange("alignment", null, al.getSequences());
2374 public void removeGappedColumnMenuItem_actionPerformed()
2376 AlignmentI al = viewport.getAlignment();
2377 ViewportRanges ranges = viewport.getRanges();
2379 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2382 if (viewport.getSelectionGroup() != null)
2384 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385 viewport.getHiddenRepSequences());
2386 start = viewport.getSelectionGroup().getStartRes();
2387 end = viewport.getSelectionGroup().getEndRes();
2391 seqs = viewport.getAlignment().getSequencesArray();
2394 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2395 "Remove Gapped Columns", seqs, start, end,
2396 viewport.getAlignment());
2398 addHistoryItem(removeGapCols);
2400 statusBar.setText(MessageManager.formatMessage(
2401 "label.removed_empty_columns",
2402 new String[] { Integer.valueOf(removeGapCols.getSize())
2405 // This is to maintain viewport position on first residue
2406 // of first sequence
2407 SequenceI seq = al.getSequenceAt(0);
2408 int startRes = seq.findPosition(ranges.getStartRes());
2409 // ShiftList shifts;
2410 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2411 // edit.alColumnChanges=shifts.getInverse();
2412 // if (viewport.hasHiddenColumns)
2413 // viewport.getColumnSelection().compensateForEdits(shifts);
2414 ranges.setStartRes(seq.findIndex(startRes) - 1);
2415 viewport.firePropertyChange("alignment", null, al.getSequences());
2419 public void removeAllGapsMenuItem_actionPerformed()
2421 AlignmentI al = viewport.getAlignment();
2422 ViewportRanges ranges = viewport.getRanges();
2424 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2427 if (viewport.getSelectionGroup() != null)
2429 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2430 viewport.getHiddenRepSequences());
2431 start = viewport.getSelectionGroup().getStartRes();
2432 end = viewport.getSelectionGroup().getEndRes();
2436 seqs = viewport.getAlignment().getSequencesArray();
2439 // This is to maintain viewport position on first residue
2440 // of first sequence
2441 SequenceI seq = al.getSequenceAt(0);
2442 int startRes = seq.findPosition(ranges.getStartRes());
2444 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2447 ranges.setStartRes(seq.findIndex(startRes) - 1);
2449 viewport.firePropertyChange("alignment", null, al.getSequences());
2453 public void findMenuItem_actionPerformed()
2455 new Finder(alignPanel);
2459 * create a new view derived from the current view
2462 * @return frame for the new view
2464 public AlignFrame newView(String viewtitle)
2467 if (viewport.hasHiddenRows())
2469 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2470 .getFullAlignment().getSequencesArray());
2474 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2477 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2479 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2481 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2483 newal.addAnnotation(viewport.getAlignment()
2484 .getAlignmentAnnotation()[i]);
2489 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2491 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2492 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2493 PaintRefresher.Register(newaf.alignPanel,
2494 newaf.alignPanel.av.getSequenceSetId());
2496 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2497 newaf.alignPanel.av.getSequenceSetId());
2498 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2499 newaf.alignPanel.av.getSequenceSetId());
2501 Vector comps = (Vector) PaintRefresher.components.get(viewport
2502 .getSequenceSetId());
2504 for (int i = 0; i < comps.size(); i++)
2506 if (comps.elementAt(i) instanceof AlignmentPanel)
2512 String title = new String(this.getTitle());
2513 if (viewtitle != null)
2515 title = viewtitle + " ( " + title + ")";
2519 if (title.indexOf("(View") > -1)
2521 title = title.substring(0, title.indexOf("(View"));
2523 title += "(View " + viewSize + ")";
2526 newaf.setTitle(title.toString());
2528 newaf.viewport.setHistoryList(viewport.getHistoryList());
2529 newaf.viewport.setRedoList(viewport.getRedoList());
2535 * @return list of feature groups on the view
2537 public String[] getFeatureGroups()
2539 FeatureRenderer fr = null;
2540 if (alignPanel != null
2541 && (fr = alignPanel.getFeatureRenderer()) != null)
2543 List<String> gps = fr.getFeatureGroups();
2544 String[] _gps = gps.toArray(new String[gps.size()]);
2551 * get sequence feature groups that are hidden or shown
2557 public String[] getFeatureGroupsOfState(boolean visible)
2559 FeatureRenderer fr = null;
2560 if (alignPanel != null
2561 && (fr = alignPanel.getFeatureRenderer()) != null)
2563 List<String> gps = fr.getGroups(visible);
2564 String[] _gps = gps.toArray(new String[gps.size()]);
2571 * Change the display state for the given feature groups
2574 * list of group strings
2576 * visible or invisible
2578 public void setFeatureGroupState(String[] groups, boolean state)
2580 FeatureRenderer fr = null;
2581 this.sequenceFeatures.setState(true);
2582 viewport.setShowSequenceFeatures(true);
2583 if (alignPanel != null
2584 && (fr = alignPanel.getFeatureRenderer()) != null)
2587 fr.setGroupVisibility(Arrays.asList(groups), state);
2588 alignPanel.seqPanel.seqCanvas.repaint();
2589 if (alignPanel.overviewPanel != null)
2591 alignPanel.overviewPanel.updateOverviewImage();
2596 public void seqLimits_itemStateChanged()
2598 viewport.setShowJVSuffix(seqLimits.getState());
2599 alignPanel.fontChanged();
2600 alignPanel.paintAlignment(true);
2603 protected void colourTextMenuItem_actionPerformed()
2605 viewport.setColourText(colourTextMenuItem.getState());
2606 alignPanel.paintAlignment(true);
2609 protected void displayNonconservedMenuItem_actionPerformed()
2611 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2612 alignPanel.paintAlignment(true);
2615 protected void wrapMenuItem_actionPerformed()
2617 viewport.setWrapAlignment(wrapMenuItem.getState());
2618 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2619 scaleAbove.setEnabled(wrapMenuItem.getState());
2620 scaleLeft.setEnabled(wrapMenuItem.getState());
2621 scaleRight.setEnabled(wrapMenuItem.getState());
2622 alignPanel.paintAlignment(true);
2625 public void overviewMenuItem_actionPerformed()
2627 if (alignPanel.overviewPanel != null)
2632 Frame frame = new Frame();
2633 final OverviewPanel overview = new OverviewPanel(alignPanel);
2634 frame.add(overview);
2635 // +50 must allow for applet frame window
2636 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2637 "label.overview_params", new String[] { this.getTitle() }),
2638 overview.getPreferredSize().width,
2639 overview.getPreferredSize().height + 50);
2642 final AlignmentPanel ap = alignPanel;
2643 frame.addWindowListener(new WindowAdapter()
2646 public void windowClosing(WindowEvent e)
2651 ap.setOverviewPanel(null);
2656 alignPanel.setOverviewPanel(overview);
2661 public void changeColour(ColourSchemeI cs)
2663 viewport.setGlobalColourScheme(cs);
2665 alignPanel.paintAlignment(true);
2668 protected void modifyPID_actionPerformed()
2670 if (viewport.getAbovePIDThreshold()
2671 && viewport.getGlobalColourScheme() != null)
2673 SliderPanel.setPIDSliderSource(alignPanel,
2674 viewport.getResidueShading(), alignPanel.getViewName());
2675 SliderPanel.showPIDSlider();
2679 protected void modifyConservation_actionPerformed()
2681 if (viewport.getConservationSelected()
2682 && viewport.getGlobalColourScheme() != null)
2684 SliderPanel.setConservationSlider(alignPanel,
2685 viewport.getResidueShading(), alignPanel.getViewName());
2686 SliderPanel.showConservationSlider();
2690 protected void conservationMenuItem_actionPerformed()
2692 boolean selected = conservationMenuItem.getState();
2693 modifyConservation.setEnabled(selected);
2694 viewport.setConservationSelected(selected);
2695 viewport.getResidueShading().setConservationApplied(selected);
2697 changeColour(viewport.getGlobalColourScheme());
2701 modifyConservation_actionPerformed();
2705 SliderPanel.hideConservationSlider();
2709 public void abovePIDThreshold_actionPerformed()
2711 boolean selected = abovePIDThreshold.getState();
2712 modifyPID.setEnabled(selected);
2713 viewport.setAbovePIDThreshold(selected);
2716 viewport.getResidueShading().setThreshold(0,
2717 viewport.isIgnoreGapsConsensus());
2720 changeColour(viewport.getGlobalColourScheme());
2724 modifyPID_actionPerformed();
2728 SliderPanel.hidePIDSlider();
2732 public void sortPairwiseMenuItem_actionPerformed()
2734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2736 .getAlignment().getSequenceAt(0));
2738 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2739 viewport.getAlignment()));
2740 alignPanel.paintAlignment(true);
2743 public void sortIDMenuItem_actionPerformed()
2745 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2746 AlignmentSorter.sortByID(viewport.getAlignment());
2747 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2748 viewport.getAlignment()));
2749 alignPanel.paintAlignment(true);
2752 public void sortLengthMenuItem_actionPerformed()
2754 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2755 AlignmentSorter.sortByLength(viewport.getAlignment());
2756 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2757 viewport.getAlignment()));
2758 alignPanel.paintAlignment(true);
2761 public void sortGroupMenuItem_actionPerformed()
2763 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2764 AlignmentSorter.sortByGroup(viewport.getAlignment());
2765 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2766 viewport.getAlignment()));
2767 alignPanel.paintAlignment(true);
2771 public void removeRedundancyMenuItem_actionPerformed()
2773 new RedundancyPanel(alignPanel);
2776 public void pairwiseAlignmentMenuItem_actionPerformed()
2778 if (viewport.getSelectionGroup() != null
2779 && viewport.getSelectionGroup().getSize() > 1)
2781 Frame frame = new Frame();
2782 frame.add(new PairwiseAlignPanel(alignPanel));
2783 jalview.bin.JalviewLite.addFrame(frame,
2784 MessageManager.getString("action.pairwise_alignment"), 600,
2789 public void PCAMenuItem_actionPerformed()
2791 // are the sequences aligned?
2792 if (!viewport.getAlignment().isAligned(false))
2795 int Width = viewport.getAlignment().getWidth();
2797 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2799 current = viewport.getAlignment().getSequenceAt(i);
2801 if (current.getLength() < Width)
2803 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2806 alignPanel.paintAlignment(true);
2809 if ((viewport.getSelectionGroup() != null
2810 && viewport.getSelectionGroup().getSize() < 4 && viewport
2811 .getSelectionGroup().getSize() > 0)
2812 || viewport.getAlignment().getHeight() < 4)
2819 new PCAPanel(viewport);
2820 } catch (java.lang.OutOfMemoryError ex)
2826 public void averageDistanceTreeMenuItem_actionPerformed()
2828 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2829 "Average distance tree using PID");
2832 public void neighbourTreeMenuItem_actionPerformed()
2834 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2835 "Neighbour joining tree using PID");
2838 protected void njTreeBlosumMenuItem_actionPerformed()
2840 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2841 .getBlosum62().getName(),
2842 "Neighbour joining tree using BLOSUM62");
2845 protected void avTreeBlosumMenuItem_actionPerformed()
2847 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2848 .getBlosum62().getName(),
2849 "Average distance tree using BLOSUM62");
2852 void newTreePanel(String type, String pwType, String title)
2854 // are the sequences aligned?
2855 if (!viewport.getAlignment().isAligned(false))
2858 int Width = viewport.getAlignment().getWidth();
2860 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2862 current = viewport.getAlignment().getSequenceAt(i);
2864 if (current.getLength() < Width)
2866 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2869 alignPanel.paintAlignment(true);
2873 if ((viewport.getSelectionGroup() != null && viewport
2874 .getSelectionGroup().getSize() > 1)
2875 || (viewport.getAlignment().getHeight() > 1))
2877 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2879 addTreeMenuItem(tp, title);
2881 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2885 void loadTree_actionPerformed()
2887 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2888 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2889 cap.setTreeImport();
2890 Frame frame = new Frame();
2892 jalview.bin.JalviewLite.addFrame(frame,
2893 MessageManager.getString("label.paste_newick_file"), 400, 300);
2896 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2898 TreePanel tp = new TreePanel(alignPanel, treeFile,
2899 MessageManager.getString("label.load_tree_from_file"), tree);
2900 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2901 addTreeMenuItem(tp, treeFile);
2905 * sort the alignment using the given treePanel
2908 * tree used to sort view
2910 * string used for undo event name
2912 public void sortByTree(TreePanel treePanel, String title)
2914 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2916 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2917 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2918 // HistoryItem.SORT));
2919 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2920 "label.order_by_params", new String[] { title }), oldOrder,
2921 viewport.getAlignment()));
2922 alignPanel.paintAlignment(true);
2926 * Do any automatic reordering of the alignment and add the necessary bits to
2927 * the menu structure for the new tree
2932 protected void addTreeMenuItem(final TreePanel treePanel,
2935 final MenuItem item = new MenuItem(title);
2936 sortByTreeMenu.add(item);
2937 item.addActionListener(new java.awt.event.ActionListener()
2940 public void actionPerformed(ActionEvent evt)
2942 sortByTree(treePanel, title); // treePanel.getTitle());
2946 treePanel.addWindowListener(new WindowAdapter()
2949 public void windowOpened(WindowEvent e)
2951 if (viewport.sortByTree)
2953 sortByTree(treePanel, title);
2955 super.windowOpened(e);
2959 public void windowClosing(WindowEvent e)
2961 sortByTreeMenu.remove(item);
2966 public boolean sortBy(AlignmentOrder alorder, String undoname)
2968 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2969 if (viewport.applet.debug)
2971 System.err.println("Sorting " + alorder.getOrder().size()
2972 + " in alignment '" + getTitle() + "'");
2974 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2975 if (undoname != null)
2977 addHistoryItem(new OrderCommand(undoname, oldOrder,
2978 viewport.getAlignment()));
2980 alignPanel.paintAlignment(true);
2984 protected void documentation_actionPerformed()
2986 alignPanel.av.applet.openJalviewHelpUrl();
2989 protected void about_actionPerformed()
2992 class AboutPanel extends Canvas
2998 public AboutPanel(String version, String builddate)
3000 this.version = version;
3001 this.builddate = builddate;
3005 public void paint(Graphics g)
3007 g.setColor(Color.white);
3008 g.fillRect(0, 0, getSize().width, getSize().height);
3009 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3010 FontMetrics fm = g.getFontMetrics();
3011 int fh = fm.getHeight();
3013 g.setColor(Color.black);
3014 // TODO: update this text for each release or centrally store it for
3015 // lite and application
3016 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3017 g.drawString(MessageManager.formatMessage(
3018 "label.jalviewLite_release", new String[] { version }), x,
3020 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3021 g.drawString(MessageManager.formatMessage(
3022 "label.jaview_build_date", new String[] { builddate }), x,
3024 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3025 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3027 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3028 x + 50, y += fh + 8);
3030 MessageManager.getString("label.jalview_dev_managers"), x,
3032 g.drawString(MessageManager
3033 .getString("label.jalview_distribution_lists"), x, y += fh);
3034 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3037 MessageManager.getString("label.jalview_cite_1_authors"),
3040 MessageManager.getString("label.jalview_cite_1_title"), x,
3042 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3047 Frame frame = new Frame();
3048 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3050 jalview.bin.JalviewLite.addFrame(frame,
3051 MessageManager.getString("label.jalview"), 580, 220);
3055 public void showURL(String url, String target)
3057 if (viewport.applet == null)
3059 System.out.println("Not running as applet - no browser available.");
3063 viewport.applet.showURL(url, target);
3067 // ////////////////////////////////////////////////////////////////////////////////
3068 // JBuilder Graphics here
3070 MenuBar alignFrameMenuBar = new MenuBar();
3072 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3074 MenuItem loadApplication = new MenuItem(
3075 MessageManager.getString("label.view_full_application"));
3077 MenuItem loadTree = new MenuItem(
3078 MessageManager.getString("label.load_associated_tree"));
3080 MenuItem loadAnnotations = new MenuItem(
3081 MessageManager.getString("label.load_features_annotations"));
3083 MenuItem outputFeatures = new MenuItem(
3084 MessageManager.getString("label.export_features"));
3086 MenuItem outputAnnotations = new MenuItem(
3087 MessageManager.getString("label.export_annotations"));
3089 MenuItem closeMenuItem = new MenuItem(
3090 MessageManager.getString("action.close"));
3092 MenuItem selectAllSequenceMenuItem = new MenuItem(
3093 MessageManager.getString("action.select_all"));
3095 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3096 MessageManager.getString("action.deselect_all"));
3098 MenuItem invertSequenceMenuItem = new MenuItem(
3099 MessageManager.getString("action.invert_selection"));
3101 MenuItem remove2LeftMenuItem = new MenuItem();
3103 MenuItem remove2RightMenuItem = new MenuItem();
3105 MenuItem removeGappedColumnMenuItem = new MenuItem();
3107 MenuItem removeAllGapsMenuItem = new MenuItem();
3109 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3111 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3113 MenuItem sortPairwiseMenuItem = new MenuItem();
3115 MenuItem sortIDMenuItem = new MenuItem();
3117 MenuItem sortLengthMenuItem = new MenuItem();
3119 MenuItem sortGroupMenuItem = new MenuItem();
3121 MenuItem removeRedundancyMenuItem = new MenuItem();
3123 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3125 MenuItem PCAMenuItem = new MenuItem();
3127 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3129 MenuItem neighbourTreeMenuItem = new MenuItem();
3131 BorderLayout borderLayout1 = new BorderLayout();
3133 public Label statusBar = new Label();
3135 MenuItem clustalColour = new MenuItem();
3137 MenuItem zappoColour = new MenuItem();
3139 MenuItem taylorColour = new MenuItem();
3141 MenuItem hydrophobicityColour = new MenuItem();
3143 MenuItem helixColour = new MenuItem();
3145 MenuItem strandColour = new MenuItem();
3147 MenuItem turnColour = new MenuItem();
3149 MenuItem buriedColour = new MenuItem();
3151 MenuItem purinePyrimidineColour = new MenuItem();
3153 // MenuItem RNAInteractionColour = new MenuItem();
3155 MenuItem RNAHelixColour = new MenuItem();
3157 MenuItem userDefinedColour = new MenuItem();
3159 MenuItem PIDColour = new MenuItem();
3161 MenuItem BLOSUM62Colour = new MenuItem();
3163 MenuItem tcoffeeColour = new MenuItem();
3165 MenuItem njTreeBlosumMenuItem = new MenuItem();
3167 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3169 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3171 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3173 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3175 MenuItem alProperties = new MenuItem(
3176 MessageManager.getString("label.alignment_props"));
3178 MenuItem overviewMenuItem = new MenuItem();
3180 MenuItem undoMenuItem = new MenuItem();
3182 MenuItem redoMenuItem = new MenuItem();
3184 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3186 MenuItem noColourmenuItem = new MenuItem();
3188 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3190 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3192 MenuItem findMenuItem = new MenuItem();
3194 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3196 MenuItem nucleotideColour = new MenuItem();
3198 MenuItem deleteGroups = new MenuItem();
3200 MenuItem grpsFromSelection = new MenuItem();
3202 MenuItem createGroup = new MenuItem();
3204 MenuItem unGroup = new MenuItem();
3206 MenuItem delete = new MenuItem();
3208 MenuItem copy = new MenuItem();
3210 MenuItem cut = new MenuItem();
3212 Menu pasteMenu = new Menu();
3214 MenuItem pasteNew = new MenuItem();
3216 MenuItem pasteThis = new MenuItem();
3218 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3220 MenuItem font = new MenuItem();
3222 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3224 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3226 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3228 MenuItem modifyPID = new MenuItem();
3230 MenuItem modifyConservation = new MenuItem();
3232 CheckboxMenuItem autoCalculate = null;
3234 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3235 "Sort Alignment With New Tree", true);
3237 Menu sortByTreeMenu = new Menu();
3239 MenuItem inputText = new MenuItem();
3241 MenuItem documentation = new MenuItem();
3243 MenuItem about = new MenuItem();
3245 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3247 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3249 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3251 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3253 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3255 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3257 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3259 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3261 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3264 * Initialise menus and other items
3268 private void jbInit() throws Exception
3270 setMenuBar(alignFrameMenuBar);
3273 * Configure File menu items and actions
3276 .setLabel(MessageManager.getString("label.input_from_textbox"));
3277 inputText.addActionListener(this);
3278 Menu outputTextboxMenu = new Menu(
3279 MessageManager.getString("label.out_to_textbox"));
3280 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3282 MenuItem item = new MenuItem(ff);
3284 item.addActionListener(new java.awt.event.ActionListener()
3287 public void actionPerformed(ActionEvent e)
3289 outputText_actionPerformed(e);
3293 outputTextboxMenu.add(item);
3295 closeMenuItem.addActionListener(this);
3296 loadApplication.addActionListener(this);
3297 loadTree.addActionListener(this);
3298 loadAnnotations.addActionListener(this);
3299 outputFeatures.addActionListener(this);
3300 outputAnnotations.addActionListener(this);
3303 * Configure Edit menu items and actions
3305 undoMenuItem.setEnabled(false);
3306 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3307 undoMenuItem.addActionListener(this);
3308 redoMenuItem.setEnabled(false);
3309 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3310 redoMenuItem.addActionListener(this);
3311 copy.setLabel(MessageManager.getString("action.copy"));
3312 copy.addActionListener(this);
3313 cut.setLabel(MessageManager.getString("action.cut"));
3314 cut.addActionListener(this);
3315 delete.setLabel(MessageManager.getString("action.delete"));
3316 delete.addActionListener(this);
3317 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3318 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3319 pasteNew.addActionListener(this);
3320 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3321 pasteThis.addActionListener(this);
3322 remove2LeftMenuItem.setLabel(MessageManager
3323 .getString("action.remove_left"));
3324 remove2LeftMenuItem.addActionListener(this);
3325 remove2RightMenuItem.setLabel(MessageManager
3326 .getString("action.remove_right"));
3327 remove2RightMenuItem.addActionListener(this);
3328 removeGappedColumnMenuItem.setLabel(MessageManager
3329 .getString("action.remove_empty_columns"));
3330 removeGappedColumnMenuItem.addActionListener(this);
3331 removeAllGapsMenuItem.setLabel(MessageManager
3332 .getString("action.remove_all_gaps"));
3333 removeAllGapsMenuItem.addActionListener(this);
3334 removeRedundancyMenuItem.setLabel(MessageManager
3335 .getString("action.remove_redundancy"));
3336 removeRedundancyMenuItem.addActionListener(this);
3339 * Configure Select menu items and actions
3341 findMenuItem.setLabel(MessageManager.getString("action.find"));
3342 findMenuItem.addActionListener(this);
3343 selectAllSequenceMenuItem.addActionListener(this);
3344 deselectAllSequenceMenuItem.addActionListener(this);
3345 invertSequenceMenuItem.setLabel(MessageManager
3346 .getString("action.invert_sequence_selection"));
3347 invertSequenceMenuItem.addActionListener(this);
3348 invertColSel.setLabel(MessageManager
3349 .getString("action.invert_column_selection"));
3350 invertColSel.addActionListener(this);
3351 deleteGroups.setLabel(MessageManager
3352 .getString("action.undefine_groups"));
3353 deleteGroups.addActionListener(this);
3354 grpsFromSelection.setLabel(MessageManager
3355 .getString("action.make_groups_selection"));
3356 grpsFromSelection.addActionListener(this);
3357 createGroup.setLabel(MessageManager.getString("action.create_group"));
3358 createGroup.addActionListener(this);
3359 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3360 unGroup.addActionListener(this);
3362 annotationColumnSelection.setLabel(MessageManager
3363 .getString("action.select_by_annotation"));
3364 annotationColumnSelection.addActionListener(this);
3367 * Configure View menu items and actions
3369 newView.setLabel(MessageManager.getString("action.new_view"));
3370 newView.addActionListener(this);
3371 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3372 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3373 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3374 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3376 .setLabel(MessageManager.getString("label.selected_columns"));
3377 hideSequences.setLabel(MessageManager
3378 .getString("label.selected_sequences"));
3379 hideAllButSelection.setLabel(MessageManager
3380 .getString("label.all_but_selected_region"));
3381 hideAllSelection.setLabel(MessageManager
3382 .getString("label.selected_region"));
3383 showAllHidden.setLabel(MessageManager
3384 .getString("label.all_sequences_columns"));
3385 showColumns.addActionListener(this);
3386 showSeqs.addActionListener(this);
3387 hideColumns.addActionListener(this);
3388 hideSequences.addActionListener(this);
3389 hideAllButSelection.addActionListener(this);
3390 hideAllSelection.addActionListener(this);
3391 showAllHidden.addActionListener(this);
3392 featureSettings.setLabel(MessageManager
3393 .getString("action.feature_settings"));
3394 featureSettings.addActionListener(this);
3395 sequenceFeatures.setLabel(MessageManager
3396 .getString("label.show_sequence_features"));
3397 sequenceFeatures.addItemListener(this);
3398 sequenceFeatures.setState(false);
3399 followMouseOverFlag.setLabel(MessageManager
3400 .getString("label.automatic_scrolling"));
3401 followMouseOverFlag.addItemListener(this);
3402 alProperties.addActionListener(this);
3403 overviewMenuItem.setLabel(MessageManager
3404 .getString("label.overview_window"));
3405 overviewMenuItem.addActionListener(this);
3408 * Configure Annotations menu items and actions
3410 annotationPanelMenuItem.setLabel(MessageManager
3411 .getString("label.show_annotations"));
3412 annotationPanelMenuItem.addItemListener(this);
3413 showGroupConsensus.setLabel(MessageManager
3414 .getString("label.group_consensus"));
3415 showGroupConservation.setLabel(MessageManager
3416 .getString("label.group_conservation"));
3417 showConsensusHistogram.setLabel(MessageManager
3418 .getString("label.show_consensus_histogram"));
3419 showSequenceLogo.setLabel(MessageManager
3420 .getString("label.show_consensus_logo"));
3421 normSequenceLogo.setLabel(MessageManager
3422 .getString("label.norm_consensus_logo"));
3423 applyAutoAnnotationSettings.setLabel(MessageManager
3424 .getString("label.apply_all_groups"));
3425 applyAutoAnnotationSettings.setState(true);
3426 Menu autoAnnMenu = new Menu(
3427 MessageManager.getString("label.autocalculated_annotation"));
3428 showGroupConsensus.addItemListener(this);
3429 showGroupConservation.addItemListener(this);
3430 showConsensusHistogram.addItemListener(this);
3431 showSequenceLogo.addItemListener(this);
3432 normSequenceLogo.addItemListener(this);
3433 applyAutoAnnotationSettings.addItemListener(this);
3434 showAlignmentAnnotations = new CheckboxMenuItem(
3435 MessageManager.getString("label.show_all_al_annotations"));
3436 showSequenceAnnotations = new CheckboxMenuItem(
3437 MessageManager.getString("label.show_all_seq_annotations"));
3438 sortAnnBySequence = new CheckboxMenuItem(
3439 MessageManager.getString("label.sort_annotations_by_sequence"));
3440 sortAnnByLabel = new CheckboxMenuItem(
3441 MessageManager.getString("label.sort_annotations_by_label"));
3442 showAutoFirst = new CheckboxMenuItem(
3443 MessageManager.getString("label.show_first"));
3444 showAutoFirst.setState(false); // pending applet parameter
3445 setShowAutoCalculatedAbove(showAutoFirst.getState());
3446 showAutoLast = new CheckboxMenuItem(
3447 MessageManager.getString("label.show_last"));
3448 showAutoLast.setState(!showAutoFirst.getState());
3449 showAlignmentAnnotations.addItemListener(this);
3450 showSequenceAnnotations.addItemListener(this);
3451 sortAnnBySequence.addItemListener(this);
3452 sortAnnByLabel.addItemListener(this);
3453 showAutoFirst.addItemListener(this);
3454 showAutoLast.addItemListener(this);
3457 * Configure Format menu items and actions
3459 font.setLabel(MessageManager.getString("action.font"));
3460 font.addActionListener(this);
3461 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3462 scaleAbove.setState(true);
3463 scaleAbove.setEnabled(false);
3464 scaleAbove.addItemListener(this);
3465 scaleLeft.setEnabled(false);
3466 scaleLeft.setState(true);
3467 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3468 scaleLeft.addItemListener(this);
3469 scaleRight.setEnabled(false);
3470 scaleRight.setState(true);
3471 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3472 scaleRight.addItemListener(this);
3473 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3474 viewBoxesMenuItem.setState(true);
3475 viewBoxesMenuItem.addItemListener(this);
3476 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3477 viewTextMenuItem.setState(true);
3478 viewTextMenuItem.addItemListener(this);
3479 colourTextMenuItem.setLabel(MessageManager
3480 .getString("label.colour_text"));
3481 colourTextMenuItem.addItemListener(this);
3482 displayNonconservedMenuItem.setLabel(MessageManager
3483 .getString("label.show_non_conserved"));
3484 displayNonconservedMenuItem.addItemListener(this);
3485 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3486 wrapMenuItem.addItemListener(this);
3487 renderGapsMenuItem.setLabel(MessageManager
3488 .getString("action.show_gaps"));
3489 renderGapsMenuItem.setState(true);
3490 renderGapsMenuItem.addItemListener(this);
3491 centreColumnLabelFlag.setLabel(MessageManager
3492 .getString("label.centre_column_labels"));
3493 centreColumnLabelFlag.addItemListener(this);
3494 seqLimits.setState(true);
3495 seqLimits.setLabel(MessageManager
3496 .getString("label.show_sequence_limits"));
3497 seqLimits.addItemListener(this);
3500 * Configure Colour menu items and actions
3502 applyToAllGroups.setLabel(MessageManager
3503 .getString("label.apply_colour_to_all_groups"));
3504 applyToAllGroups.setState(true);
3505 applyToAllGroups.addItemListener(this);
3506 clustalColour.setLabel(MessageManager
3507 .getString("label.colourScheme_clustal"));
3508 clustalColour.addActionListener(this);
3509 zappoColour.setLabel(MessageManager
3510 .getString("label.colourScheme_zappo"));
3511 zappoColour.addActionListener(this);
3512 taylorColour.setLabel(MessageManager
3513 .getString("label.colourScheme_taylor"));
3514 taylorColour.addActionListener(this);
3515 hydrophobicityColour.setLabel(MessageManager
3516 .getString("label.colourScheme_hydrophobic"));
3517 hydrophobicityColour.addActionListener(this);
3518 helixColour.setLabel(MessageManager
3519 .getString("label.colourScheme_helix_propensity"));
3520 helixColour.addActionListener(this);
3521 strandColour.setLabel(MessageManager
3522 .getString("label.colourScheme_strand_propensity"));
3523 strandColour.addActionListener(this);
3524 turnColour.setLabel(MessageManager
3525 .getString("label.colourScheme_turn_propensity"));
3526 turnColour.addActionListener(this);
3527 buriedColour.setLabel(MessageManager
3528 .getString("label.colourScheme_buried_index"));
3529 buriedColour.addActionListener(this);
3530 purinePyrimidineColour.setLabel(MessageManager
3531 .getString("label.colourScheme_purine/pyrimidine"));
3532 purinePyrimidineColour.addActionListener(this);
3533 // RNAInteractionColour.setLabel(MessageManager
3534 // .getString("label.rna_interaction"));
3535 // RNAInteractionColour.addActionListener(this);
3536 RNAHelixColour.setLabel(MessageManager
3537 .getString("label.colourScheme_rna_helices"));
3538 RNAHelixColour.addActionListener(this);
3539 userDefinedColour.setLabel(MessageManager
3540 .getString("action.user_defined"));
3541 userDefinedColour.addActionListener(this);
3542 PIDColour.setLabel(MessageManager
3543 .getString("label.colourScheme_%_identity"));
3544 PIDColour.addActionListener(this);
3545 BLOSUM62Colour.setLabel(MessageManager
3546 .getString("label.colourScheme_blosum62"));
3547 BLOSUM62Colour.addActionListener(this);
3548 tcoffeeColour.setLabel(MessageManager
3549 .getString("label.colourScheme_t-coffee_scores"));
3550 // it will be enabled only if a score file is provided
3551 tcoffeeColour.setEnabled(false);
3552 tcoffeeColour.addActionListener(this);
3553 conservationMenuItem.setLabel(MessageManager
3554 .getString("action.by_conservation"));
3555 conservationMenuItem.addItemListener(this);
3556 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3557 noColourmenuItem.addActionListener(this);
3558 abovePIDThreshold.setLabel(MessageManager
3559 .getString("label.above_identity_threshold"));
3560 abovePIDThreshold.addItemListener(this);
3561 nucleotideColour.setLabel(MessageManager
3562 .getString("label.colourScheme_nucleotide"));
3563 nucleotideColour.addActionListener(this);
3564 modifyPID.setLabel(MessageManager
3565 .getString("label.modify_identity_threshold"));
3566 modifyPID.setEnabled(abovePIDThreshold.getState());
3567 modifyPID.addActionListener(this);
3568 modifyConservation.setLabel(MessageManager
3569 .getString("label.modify_conservation_threshold"));
3570 modifyConservation.setEnabled(conservationMenuItem.getState());
3571 modifyConservation.addActionListener(this);
3572 annotationColour.setLabel(MessageManager
3573 .getString("action.by_annotation"));
3574 annotationColour.addActionListener(this);
3577 * Configure Calculate menu items and actions
3579 sortPairwiseMenuItem.setLabel(MessageManager
3580 .getString("action.by_pairwise_id"));
3581 sortPairwiseMenuItem.addActionListener(this);
3582 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3583 sortIDMenuItem.addActionListener(this);
3584 sortLengthMenuItem.setLabel(MessageManager
3585 .getString("action.by_length"));
3586 sortLengthMenuItem.addActionListener(this);
3587 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3588 sortGroupMenuItem.addActionListener(this);
3589 pairwiseAlignmentMenuItem.setLabel(MessageManager
3590 .getString("action.pairwise_alignment"));
3591 pairwiseAlignmentMenuItem.addActionListener(this);
3592 PCAMenuItem.setLabel(MessageManager
3593 .getString("label.principal_component_analysis"));
3594 PCAMenuItem.addActionListener(this);
3595 autoCalculate = new CheckboxMenuItem(
3596 MessageManager.getString("label.autocalculate_consensus"), true);
3597 averageDistanceTreeMenuItem.setLabel(MessageManager
3598 .getString("label.average_distance_identity"));
3599 averageDistanceTreeMenuItem.addActionListener(this);
3600 neighbourTreeMenuItem.setLabel(MessageManager
3601 .getString("label.neighbour_joining_identity"));
3602 neighbourTreeMenuItem.addActionListener(this);
3603 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3604 .getString("label.average_distance_blosum62"));
3605 avDistanceTreeBlosumMenuItem.addActionListener(this);
3606 njTreeBlosumMenuItem.setLabel(MessageManager
3607 .getString("label.neighbour_blosum62"));
3608 njTreeBlosumMenuItem.addActionListener(this);
3609 sortByTreeMenu.setLabel(MessageManager
3610 .getString("action.by_tree_order"));
3611 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3612 Menu calculateTreeMenu = new Menu(
3613 MessageManager.getString("action.calculate_tree"));
3614 autoCalculate.addItemListener(this);
3615 sortByTree.addItemListener(this);
3618 * Configure Help menu items and actions
3620 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3621 documentation.setLabel(MessageManager.getString("label.documentation"));
3622 documentation.addActionListener(this);
3623 about.setLabel(MessageManager.getString("label.about"));
3624 about.addActionListener(this);
3627 * Add top level menus to frame
3629 alignFrameMenuBar.add(fileMenu);
3630 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3631 alignFrameMenuBar.add(editMenu);
3632 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3633 alignFrameMenuBar.add(selectMenu);
3634 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3635 alignFrameMenuBar.add(viewMenu);
3636 Menu annotationsMenu = new Menu(
3637 MessageManager.getString("action.annotations"));
3638 alignFrameMenuBar.add(annotationsMenu);
3639 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3640 alignFrameMenuBar.add(formatMenu);
3641 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3642 alignFrameMenuBar.add(colourMenu);
3643 Menu calculateMenu = new Menu(
3644 MessageManager.getString("action.calculate"));
3645 alignFrameMenuBar.add(calculateMenu);
3646 alignFrameMenuBar.add(helpMenu);
3651 fileMenu.add(inputText);
3652 fileMenu.add(loadTree);
3653 fileMenu.add(loadAnnotations);
3654 fileMenu.addSeparator();
3655 fileMenu.add(outputTextboxMenu);
3656 fileMenu.add(outputFeatures);
3657 fileMenu.add(outputAnnotations);
3658 if (jalviewServletURL != null)
3660 fileMenu.add(loadApplication);
3662 fileMenu.addSeparator();
3663 fileMenu.add(closeMenuItem);
3668 editMenu.add(undoMenuItem);
3669 editMenu.add(redoMenuItem);
3672 pasteMenu.add(pasteNew);
3673 pasteMenu.add(pasteThis);
3674 editMenu.add(pasteMenu);
3675 editMenu.add(delete);
3676 editMenu.addSeparator();
3677 editMenu.add(remove2LeftMenuItem);
3678 editMenu.add(remove2RightMenuItem);
3679 editMenu.add(removeGappedColumnMenuItem);
3680 editMenu.add(removeAllGapsMenuItem);
3681 editMenu.add(removeRedundancyMenuItem);
3686 selectMenu.add(findMenuItem);
3687 selectMenu.addSeparator();
3688 selectMenu.add(selectAllSequenceMenuItem);
3689 selectMenu.add(deselectAllSequenceMenuItem);
3690 selectMenu.add(invertSequenceMenuItem);
3691 selectMenu.add(invertColSel);
3692 selectMenu.add(createGroup);
3693 selectMenu.add(unGroup);
3694 selectMenu.add(grpsFromSelection);
3695 selectMenu.add(deleteGroups);
3696 selectMenu.add(annotationColumnSelection);
3701 viewMenu.add(newView);
3702 viewMenu.addSeparator();
3703 showMenu.add(showColumns);
3704 showMenu.add(showSeqs);
3705 showMenu.add(showAllHidden);
3706 viewMenu.add(showMenu);
3707 hideMenu.add(hideColumns);
3708 hideMenu.add(hideSequences);
3709 hideMenu.add(hideAllSelection);
3710 hideMenu.add(hideAllButSelection);
3711 viewMenu.add(hideMenu);
3712 viewMenu.addSeparator();
3713 viewMenu.add(followMouseOverFlag);
3714 viewMenu.addSeparator();
3715 viewMenu.add(sequenceFeatures);
3716 viewMenu.add(featureSettings);
3717 viewMenu.addSeparator();
3718 viewMenu.add(alProperties);
3719 viewMenu.addSeparator();
3720 viewMenu.add(overviewMenuItem);
3725 annotationsMenu.add(annotationPanelMenuItem);
3726 annotationsMenu.addSeparator();
3727 annotationsMenu.add(showAlignmentAnnotations);
3728 annotationsMenu.add(showSequenceAnnotations);
3729 annotationsMenu.add(sortAnnBySequence);
3730 annotationsMenu.add(sortAnnByLabel);
3731 annotationsMenu.addSeparator();
3732 autoAnnMenu.add(showAutoFirst);
3733 autoAnnMenu.add(showAutoLast);
3734 autoAnnMenu.addSeparator();
3735 autoAnnMenu.add(applyAutoAnnotationSettings);
3736 autoAnnMenu.add(showConsensusHistogram);
3737 autoAnnMenu.add(showSequenceLogo);
3738 autoAnnMenu.add(normSequenceLogo);
3739 autoAnnMenu.addSeparator();
3740 autoAnnMenu.add(showGroupConservation);
3741 autoAnnMenu.add(showGroupConsensus);
3742 annotationsMenu.add(autoAnnMenu);
3747 formatMenu.add(font);
3748 formatMenu.add(seqLimits);
3749 formatMenu.add(wrapMenuItem);
3750 formatMenu.add(scaleAbove);
3751 formatMenu.add(scaleLeft);
3752 formatMenu.add(scaleRight);
3753 formatMenu.add(viewBoxesMenuItem);
3754 formatMenu.add(viewTextMenuItem);
3755 formatMenu.add(colourTextMenuItem);
3756 formatMenu.add(displayNonconservedMenuItem);
3757 formatMenu.add(renderGapsMenuItem);
3758 formatMenu.add(centreColumnLabelFlag);
3763 colourMenu.add(applyToAllGroups);
3764 colourMenu.addSeparator();
3765 colourMenu.add(noColourmenuItem);
3766 colourMenu.add(clustalColour);
3767 colourMenu.add(BLOSUM62Colour);
3768 colourMenu.add(PIDColour);
3769 colourMenu.add(zappoColour);
3770 colourMenu.add(taylorColour);
3771 colourMenu.add(hydrophobicityColour);
3772 colourMenu.add(helixColour);
3773 colourMenu.add(strandColour);
3774 colourMenu.add(turnColour);
3775 colourMenu.add(buriedColour);
3776 colourMenu.add(nucleotideColour);
3777 colourMenu.add(purinePyrimidineColour);
3778 // colourMenu.add(RNAInteractionColour);
3779 colourMenu.add(tcoffeeColour);
3780 colourMenu.add(userDefinedColour);
3781 colourMenu.addSeparator();
3782 colourMenu.add(conservationMenuItem);
3783 colourMenu.add(modifyConservation);
3784 colourMenu.add(abovePIDThreshold);
3785 colourMenu.add(modifyPID);
3786 colourMenu.add(annotationColour);
3787 colourMenu.add(RNAHelixColour);
3792 sortMenu.add(sortIDMenuItem);
3793 sortMenu.add(sortLengthMenuItem);
3794 sortMenu.add(sortByTreeMenu);
3795 sortMenu.add(sortGroupMenuItem);
3796 sortMenu.add(sortPairwiseMenuItem);
3797 calculateMenu.add(sortMenu);
3798 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3799 calculateTreeMenu.add(neighbourTreeMenuItem);
3800 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3801 calculateTreeMenu.add(njTreeBlosumMenuItem);
3802 calculateMenu.add(calculateTreeMenu);
3803 calculateMenu.addSeparator();
3804 calculateMenu.add(pairwiseAlignmentMenuItem);
3805 calculateMenu.add(PCAMenuItem);
3806 calculateMenu.add(autoCalculate);
3807 calculateMenu.add(sortByTree);
3812 helpMenu.add(documentation);
3813 helpMenu.add(about);
3818 statusBar.setBackground(Color.white);
3819 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3820 statusBar.setText(MessageManager.getString("label.status_bar"));
3821 this.add(statusBar, BorderLayout.SOUTH);
3825 public void setStatus(String string)
3827 statusBar.setText(string);
3830 MenuItem featureSettings = new MenuItem();
3832 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3834 MenuItem annotationColour = new MenuItem();
3836 MenuItem annotationColumnSelection = new MenuItem();
3838 MenuItem invertColSel = new MenuItem();
3840 MenuItem showColumns = new MenuItem();
3842 MenuItem showSeqs = new MenuItem();
3844 MenuItem hideColumns = new MenuItem();
3846 MenuItem hideSequences = new MenuItem();
3848 MenuItem hideAllButSelection = new MenuItem();
3850 MenuItem hideAllSelection = new MenuItem();
3852 MenuItem showAllHidden = new MenuItem();
3854 MenuItem newView = new MenuItem();
3856 private CheckboxMenuItem showAlignmentAnnotations;
3858 private CheckboxMenuItem showSequenceAnnotations;
3860 private CheckboxMenuItem sortAnnBySequence;
3862 private CheckboxMenuItem sortAnnByLabel;
3864 private CheckboxMenuItem showAutoFirst;
3866 private CheckboxMenuItem showAutoLast;
3868 private SplitFrame splitFrame;
3871 * Attach the alignFrame panels after embedding menus, if necessary. This used
3872 * to be called setEmbedded, but is now creates the dropdown menus in a
3873 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3875 * @param reallyEmbedded
3876 * true to attach the view to the applet area on the page rather than
3879 public void createAlignFrameWindow(boolean reallyEmbedded)
3883 embedAlignFrameInApplet(viewport.applet);
3888 // test and embed menu bar if necessary.
3890 if (embedMenuIfNeeded(alignPanel))
3893 * adjust for status bar height too. ? pointless as overridden by layout
3896 alignPanel.setSize(getSize().width,
3897 getSize().height - statusBar.getHeight());
3899 add(statusBar, BorderLayout.SOUTH);
3900 add(alignPanel, BorderLayout.CENTER);
3901 // and register with the applet so it can pass external API calls to us
3902 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3908 * Add the components of this AlignFrame to the applet container.
3912 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3915 // Explicitly build the embedded menu panel for the on-page applet
3917 // view cannot be closed if its actually on the page
3918 fileMenu.remove(closeMenuItem);
3919 fileMenu.remove(3); // Remove Separator
3920 // construct embedded menu, using default font
3921 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3922 // and actually add the components to the applet area
3923 theApplet.setLayout(new BorderLayout());
3924 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3925 theApplet.add(statusBar, BorderLayout.SOUTH);
3926 // TODO should size be left to the layout manager?
3927 alignPanel.setSize(theApplet.getSize().width,
3928 theApplet.getSize().height - embeddedMenu.getHeight()
3929 - statusBar.getHeight());
3930 theApplet.add(alignPanel, BorderLayout.CENTER);
3931 final AlignFrame me = this;
3932 theApplet.addFocusListener(new FocusListener()
3936 public void focusLost(FocusEvent e)
3938 if (theApplet.currentAlignFrame == me)
3940 theApplet.currentAlignFrame = null;
3945 public void focusGained(FocusEvent e)
3947 theApplet.currentAlignFrame = me;
3950 theApplet.validate();
3954 * create a new binding between structures in an existing jmol viewer instance
3955 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3956 * this does not open a new Jmol window, or modify the display of the
3957 * structures in the original jmol window. Note This method doesn't work
3958 * without an additional javascript library to exchange messages between the
3959 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3962 * JmolViewer instance
3963 * @param sequenceIds
3964 * - sequence Ids to search for associations
3966 public SequenceStructureBinding addStructureViewInstance(
3967 Object jmolviewer, String[] sequenceIds)
3969 Viewer viewer = null;
3972 viewer = (Viewer) jmolviewer;
3973 } catch (ClassCastException ex)
3975 System.err.println("Unsupported viewer object :"
3976 + jmolviewer.getClass());
3980 System.err.println("Can't use this object as a structure viewer:"
3981 + jmolviewer.getClass());
3984 SequenceI[] seqs = null;
3985 if (sequenceIds == null || sequenceIds.length == 0)
3987 seqs = viewport.getAlignment().getSequencesArray();
3991 Vector sqi = new Vector();
3992 AlignmentI al = viewport.getAlignment();
3993 for (int sid = 0; sid < sequenceIds.length; sid++)
3995 SequenceI sq = al.findName(sequenceIds[sid]);
4003 seqs = new SequenceI[sqi.size()];
4004 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4006 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4014 AAStructureBindingModel jmv = null;
4015 // TODO: search for a jmv that involves viewer
4017 { // create a new viewer/jalview binding.
4018 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4025 * bind a pdb file to a sequence in the current view
4028 * - sequenceId within the dataset.
4029 * @param pdbEntryString
4030 * - the short name for the PDB file
4032 * - pdb file - either a URL or a valid PDB file.
4033 * @return true if binding was as success TODO: consider making an exception
4034 * structure for indicating when PDB parsing or sequenceId location
4037 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4040 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4041 boolean needtoadd = false;
4042 if (toaddpdb != null)
4044 Vector pdbe = toaddpdb.getAllPDBEntries();
4045 PDBEntry pdbentry = null;
4046 if (pdbe != null && pdbe.size() > 0)
4048 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4050 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4051 if (!pdbentry.getId().equals(pdbEntryString)
4052 && !pdbentry.getFile().equals(pdbFile))
4062 if (pdbentry == null)
4064 pdbentry = new PDBEntry();
4065 pdbentry.setId(pdbEntryString);
4066 pdbentry.setFile(pdbFile);
4067 needtoadd = true; // add this new entry to sequence.
4069 // resolve data source
4070 // TODO: this code should be a refactored to an io package
4071 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4072 pdbFile, FileFormat.PDB);
4073 if (protocol == null)
4079 pdbentry.setProperty("protocol", protocol);
4080 toaddpdb.addPDBId(pdbentry);
4081 alignPanel.getStructureSelectionManager()
4082 .registerPDBEntry(pdbentry);
4088 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4092 Vector sequences = new Vector();
4093 for (int i = 0; i < seqs.length; i++)
4095 if (seqs[i] != null)
4097 sequences.addElement(new Object[] { seqs[i],
4098 (chains != null) ? chains[i] : null });
4101 seqs = new SequenceI[sequences.size()];
4102 chains = new String[sequences.size()];
4103 for (int i = 0, isize = sequences.size(); i < isize; i++)
4105 Object[] oj = (Object[]) sequences.elementAt(i);
4107 seqs[i] = (SequenceI) oj[0];
4108 chains[i] = (String) oj[1];
4111 return new Object[] { seqs, chains };
4115 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4116 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4118 // Scrub any null sequences from the array
4119 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4120 seqs = (SequenceI[]) sqch[0];
4121 chains = (String[]) sqch[1];
4122 if (seqs == null || seqs.length == 0)
4125 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4127 if (protocol == null)
4129 String sourceType = (String) pdb.getProperty("protocol");
4132 protocol = DataSourceType.valueOf(sourceType);
4133 } catch (IllegalArgumentException e)
4137 if (protocol == null)
4139 System.err.println("Couldn't work out protocol to open structure: "
4144 if (applet.useXtrnalSviewer)
4146 // register the association(s) and quit, don't create any windows.
4147 if (StructureSelectionManager.getStructureSelectionManager(applet)
4148 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4150 System.err.println("Failed to map " + pdb.getFile() + " ("
4151 + protocol + ") to any sequences");
4155 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4157 // can only do alignments with Jmol
4158 // find the last jmol window assigned to this alignment
4159 AppletJmol ajm = null, tajm;
4160 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4161 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4163 tajm = (AppletJmol) jmols.elementAt(i);
4164 if (tajm.ap.alignFrame == this)
4173 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4174 // try and add the pdb structure
4179 // otherwise, create a new window
4180 if (applet.jmolAvailable)
4182 new AppletJmol(pdb, seqs, chains, alignPanel,
4184 applet.lastFrameX += 40;
4185 applet.lastFrameY += 40;
4189 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4194 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4195 SequenceI[][] seqs, String[][] chains, String[] protocols)
4197 // TODO Auto-generated method stub
4198 System.err.println("Aligned Structure View: Not yet implemented.");
4202 * modify the current selection, providing the user has not made a selection
4206 * - sequences from this alignment
4208 * - columns to be selected on the alignment
4210 public void select(SequenceGroup sel, ColumnSelection csel,
4211 HiddenColumns hidden)
4213 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4216 public void scrollTo(int row, int column)
4218 alignPanel.seqPanel.scrollTo(row, column);
4221 public void scrollToRow(int row)
4223 alignPanel.seqPanel.scrollToRow(row);
4226 public void scrollToColumn(int column)
4228 alignPanel.seqPanel.scrollToColumn(column);
4232 * @return the alignments unique ID.
4234 public String getSequenceSetId()
4236 return viewport.getSequenceSetId();
4240 * Load the (T-Coffee) score file from the specified url
4243 * File/URL/T-COFFEE score file contents
4244 * @throws IOException
4245 * @return true if alignment was annotated with data from source
4247 public boolean loadScoreFile(String source) throws IOException
4250 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4251 AppletFormatAdapter.checkProtocol(source));
4252 if (!file.isValid())
4254 // TODO: raise dialog for gui
4255 System.err.println("Problems parsing T-Coffee scores: "
4256 + file.getWarningMessage());
4257 System.err.println("Origin was:\n" + source);
4262 * check that the score matrix matches the alignment dimensions
4265 if ((aln = viewport.getAlignment()) != null
4266 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4269 // TODO: raise a dialog box here rather than bomb out.
4271 .println("The scores matrix does not match the alignment dimensions");
4275 // TODO add parameter to indicate if matching should be done
4276 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4278 alignPanel.fontChanged();
4279 tcoffeeColour.setEnabled(true);
4280 // switch to this color
4281 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4286 System.err.println("Problems resolving T-Coffee scores:");
4287 if (file.getWarningMessage() != null)
4289 System.err.println(file.getWarningMessage());
4295 public SplitFrame getSplitFrame()
4297 return this.splitFrame;
4300 public void setSplitFrame(SplitFrame sf)
4302 this.splitFrame = sf;
4305 // may not need this
4307 public void setShowSeqFeatures(boolean b)
4309 // showSeqFeatures.setSelected(b);
4310 viewport.setShowSequenceFeatures(b);
4315 public void setMenusForViewport()
4317 // setMenusFromViewport(viewport);
4322 public void refreshFeatureUI(boolean enableIfNecessary)
4324 if (enableIfNecessary)
4326 sequenceFeatures.setState(true);
4327 alignPanel.av.setShowSequenceFeatures(true);
4332 public FeatureSettingsControllerI getFeatureSettingsUI()
4334 return alignPanel.av.featureSettings;