2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
110 import java.net.URLEncoder;
111 import java.util.Arrays;
112 import java.util.Deque;
113 import java.util.HashMap;
114 import java.util.List;
115 import java.util.Map;
116 import java.util.StringTokenizer;
117 import java.util.Vector;
119 import org.jmol.viewer.Viewer;
121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
122 ItemListener, KeyListener, AlignViewControllerGuiI
124 public AlignViewControllerI avc;
126 public AlignmentPanel alignPanel;
128 public AlignViewport viewport;
130 // width and height may be overridden by applet parameters
131 int frameWidth = 700;
133 int frameHeight = 500;
135 String jalviewServletURL;
138 * Flag for showing autocalculated consensus above or below other consensus
141 private boolean showAutoCalculatedAbove;
143 private SequenceAnnotationOrder annotationSortOrder;
146 * Constructor that creates the frame and adds it to the display.
153 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156 this(al, applet, title, embedded, true);
160 * Constructor that optionally allows the frame to be displayed or only
167 * @param addToDisplay
169 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
170 boolean embedded, boolean addToDisplay)
172 this(al, null, null, applet, title, embedded, addToDisplay);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 HiddenColumns hidden, JalviewLite applet, String title,
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet, String title,
184 boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
237 viewport.updateInformation(alignPanel);
239 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
240 followMouseOverFlag.setState(viewport.isFollowHighlight());
241 showGroupConsensus.setState(viewport.isShowGroupConsensus());
242 showGroupConservation.setState(viewport.isShowGroupConservation());
243 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
244 showSequenceLogo.setState(viewport.isShowSequenceLogo());
245 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
246 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
247 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
248 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
250 showAlignmentAnnotations.setState(true);
251 showSequenceAnnotations.setState(false);
253 seqLimits.setState(viewport.getShowJVSuffix());
257 String param = applet.getParameter("sortBy");
260 if (param.equalsIgnoreCase("Id"))
262 sortIDMenuItem_actionPerformed();
264 else if (param.equalsIgnoreCase("Pairwise Identity"))
266 sortPairwiseMenuItem_actionPerformed();
268 else if (param.equalsIgnoreCase("Length"))
270 sortLengthMenuItem_actionPerformed();
274 param = applet.getParameter("wrap");
277 if (param.equalsIgnoreCase("true"))
279 wrapMenuItem.setState(true);
280 wrapMenuItem_actionPerformed();
283 param = applet.getParameter("centrecolumnlabels");
286 centreColumnLabelFlag.setState(true);
287 centreColumnLabelFlag_stateChanged();
291 if (viewport.getAlignment().isNucleotide())
293 conservationMenuItem.setEnabled(false);
294 clustalColour.setEnabled(false);
295 BLOSUM62Colour.setEnabled(false);
296 zappoColour.setEnabled(false);
297 taylorColour.setEnabled(false);
298 hydrophobicityColour.setEnabled(false);
299 helixColour.setEnabled(false);
300 strandColour.setEnabled(false);
301 turnColour.setEnabled(false);
302 buriedColour.setEnabled(false);
303 viewport.updateStrucConsensus(alignPanel);
304 if (viewport.getAlignment().hasRNAStructure())
306 RNAHelixColour.setEnabled(true);
310 RNAHelixColour.setEnabled(false);
315 RNAHelixColour.setEnabled(false);
316 purinePyrimidineColour.setEnabled(false);
317 nucleotideColour.setEnabled(false);
319 // Some JVMS send keyevents to Top frame or lowest panel,
320 // Havent worked out why yet. So add to both this frame and seqCanvas for
322 this.addKeyListener(this);
323 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
324 alignPanel.idPanel.idCanvas.addKeyListener(this);
325 alignPanel.scalePanel.addKeyListener(this);
326 alignPanel.annotationPanel.addKeyListener(this);
327 alignPanel.annotationPanelHolder.addKeyListener(this);
328 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
329 alignPanel.alabels.addKeyListener(this);
331 setAnnotationsVisibility();
335 addToDisplay(embedded);
342 public void addToDisplay(boolean embedded)
344 createAlignFrameWindow(embedded);
346 alignPanel.adjustAnnotationHeight();
347 alignPanel.paintAlignment(true);
350 public AlignViewport getAlignViewport()
355 public SeqCanvas getSeqcanvas()
357 return alignPanel.seqPanel.seqCanvas;
361 * Load a features file onto the alignment
364 * file URL, content, or other resolvable path
366 * is protocol for accessing data referred to by file
369 public boolean parseFeaturesFile(String file, DataSourceType type)
371 return parseFeaturesFile(file, type, true);
375 * Load a features file onto the alignment
378 * file URL, content, or other resolvable path
380 * is protocol for accessing data referred to by file
381 * @param autoenabledisplay
382 * when true, display features flag will be automatically enabled if
383 * features are loaded
384 * @return true if data parsed as a features file
386 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
387 boolean autoenabledisplay)
389 boolean featuresFile = false;
392 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
393 .getFeatureRenderer().getFeatureColours();
394 boolean relaxedIdMatching = viewport.applet
395 .getDefaultParameter("relaxedidmatch", false);
396 featuresFile = new FeaturesFile(file, sourceType).parse(
397 viewport.getAlignment(), colours, true, relaxedIdMatching);
398 } catch (Exception ex)
400 ex.printStackTrace();
405 if (autoenabledisplay)
407 viewport.setShowSequenceFeatures(true);
408 sequenceFeatures.setState(true);
410 if (alignPanel.seqPanel.seqCanvas.fr != null)
412 // update the min/max ranges where necessary
413 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
415 if (viewport.featureSettings != null)
417 viewport.featureSettings.refreshTable();
419 alignPanel.paintAlignment(true);
420 statusBar.setText(MessageManager
421 .getString("label.successfully_added_features_alignment"));
427 public void keyPressed(KeyEvent evt)
429 ViewportRanges ranges = viewport.getRanges();
431 if (viewport.cursorMode
432 && ((evt.getKeyCode() >= KeyEvent.VK_0
433 && evt.getKeyCode() <= KeyEvent.VK_9)
434 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
435 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
436 && Character.isDigit(evt.getKeyChar()))
438 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
441 switch (evt.getKeyCode())
443 case 27: // escape key
444 deselectAllSequenceMenuItem_actionPerformed();
446 alignPanel.alabels.cancelDrag();
449 if (evt.isControlDown() || evt.isMetaDown())
451 cut_actionPerformed();
455 if (viewport.cursorMode && !evt.isControlDown())
457 alignPanel.seqPanel.setCursorColumn();
459 if (evt.isControlDown() || evt.isMetaDown())
461 copy_actionPerformed();
465 if (evt.isControlDown())
467 paste(evt.isShiftDown());
471 if (evt.isControlDown() || evt.isMetaDown())
473 selectAllSequenceMenuItem_actionPerformed();
476 case KeyEvent.VK_DOWN:
477 if (viewport.cursorMode)
479 alignPanel.seqPanel.moveCursor(0, 1);
483 moveSelectedSequences(false);
488 if (viewport.cursorMode)
490 alignPanel.seqPanel.moveCursor(0, -1);
494 moveSelectedSequences(true);
498 case KeyEvent.VK_LEFT:
499 if (evt.isAltDown() || !viewport.cursorMode)
501 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
505 alignPanel.seqPanel.moveCursor(-1, 0);
509 case KeyEvent.VK_RIGHT:
510 if (evt.isAltDown() || !viewport.cursorMode)
512 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
516 alignPanel.seqPanel.moveCursor(1, 0);
520 case KeyEvent.VK_SPACE:
521 if (viewport.cursorMode)
523 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
524 || evt.isShiftDown() || evt.isAltDown());
528 case KeyEvent.VK_DELETE:
529 case KeyEvent.VK_BACK_SPACE:
530 if (viewport.cursorMode)
532 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
533 || evt.isShiftDown() || evt.isAltDown());
537 cut_actionPerformed();
538 alignPanel.seqPanel.seqCanvas.repaint();
543 if (viewport.cursorMode)
545 alignPanel.seqPanel.setCursorRow();
549 if (viewport.cursorMode)
551 alignPanel.seqPanel.setCursorPosition();
555 case KeyEvent.VK_ENTER:
556 case KeyEvent.VK_COMMA:
557 if (viewport.cursorMode)
559 alignPanel.seqPanel.setCursorRowAndColumn();
564 if (viewport.cursorMode)
566 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
570 if (viewport.cursorMode)
572 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
577 viewport.cursorMode = !viewport.cursorMode;
578 statusBar.setText(MessageManager
579 .formatMessage("label.keyboard_editing_mode", new String[]
580 { (viewport.cursorMode ? "on" : "off") }));
581 if (viewport.cursorMode)
583 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
584 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
589 if (evt.isControlDown())
591 findMenuItem_actionPerformed();
597 boolean toggleSeqs = !evt.isControlDown();
598 boolean toggleCols = !evt.isShiftDown();
599 toggleHiddenRegions(toggleSeqs, toggleCols);
603 case KeyEvent.VK_PAGE_UP:
607 case KeyEvent.VK_PAGE_DOWN:
612 if (evt.isControlDown())
614 undoMenuItem_actionPerformed();
619 if (evt.isControlDown())
621 redoMenuItem_actionPerformed();
626 if (evt.isControlDown())
633 if (evt.isControlDown())
635 trimAlignment(false);
640 if (evt.isControlDown())
642 if (evt.isShiftDown())
644 this.removeAllGapsMenuItem_actionPerformed();
648 removeGappedColumnMenuItem_actionPerformed();
653 if (evt.isControlDown())
657 invertColSel_actionPerformed();
661 invertSequenceMenuItem_actionPerformed();
667 if (evt.isControlDown())
669 if (evt.isShiftDown())
671 this.unGroup_actionPerformed();
675 this.createGroup_actionPerformed();
681 if (evt.isControlDown())
683 this.deleteGroups_actionPerformed();
688 if (evt.isControlDown())
695 alignPanel.paintAlignment(true);
699 * called by key handler and the hide all/show all menu items
704 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
706 boolean hide = false;
707 SequenceGroup sg = viewport.getSelectionGroup();
708 if (!toggleSeqs && !toggleCols)
710 // Hide everything by the current selection - this is a hack - we do the
711 // invert and then hide
712 // first check that there will be visible columns after the invert.
713 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
714 && sg.getStartRes() <= sg.getEndRes()))
716 // now invert the sequence set, if required - empty selection implies
717 // that no hiding is required.
720 invertSequenceMenuItem_actionPerformed();
721 sg = viewport.getSelectionGroup();
725 viewport.expandColSelection(sg, true);
726 // finally invert the column selection and get the new sequence
727 // selection and indicate it should be hidden.
728 invertColSel_actionPerformed();
735 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
738 viewport.hideAllSelectedSeqs();
740 else if (!(toggleCols && viewport.hasSelectedColumns()))
742 viewport.showAllHiddenSeqs();
748 if (viewport.hasSelectedColumns())
750 viewport.hideSelectedColumns();
753 viewport.setSelectionGroup(sg);
758 viewport.showAllHiddenColumns();
760 viewport.sendSelection();
765 public void keyReleased(KeyEvent evt)
770 public void keyTyped(KeyEvent evt)
775 public void itemStateChanged(ItemEvent evt)
777 final Object source = evt.getSource();
778 if (source == displayNonconservedMenuItem)
780 displayNonconservedMenuItem_actionPerformed();
782 else if (source == colourTextMenuItem)
784 colourTextMenuItem_actionPerformed();
786 else if (source == wrapMenuItem)
788 wrapMenuItem_actionPerformed();
790 else if (source == scaleAbove)
792 viewport.setScaleAboveWrapped(scaleAbove.getState());
794 else if (source == scaleLeft)
796 viewport.setScaleLeftWrapped(scaleLeft.getState());
798 else if (source == scaleRight)
800 viewport.setScaleRightWrapped(scaleRight.getState());
802 else if (source == seqLimits)
804 seqLimits_itemStateChanged();
806 else if (source == viewBoxesMenuItem)
808 viewport.setShowBoxes(viewBoxesMenuItem.getState());
810 else if (source == viewTextMenuItem)
812 viewport.setShowText(viewTextMenuItem.getState());
814 else if (source == renderGapsMenuItem)
816 viewport.setRenderGaps(renderGapsMenuItem.getState());
818 else if (source == annotationPanelMenuItem)
820 boolean showAnnotations = annotationPanelMenuItem.getState();
821 showAlignmentAnnotations.setEnabled(showAnnotations);
822 showSequenceAnnotations.setEnabled(showAnnotations);
823 viewport.setShowAnnotation(showAnnotations);
824 alignPanel.setAnnotationVisible(showAnnotations);
826 else if (source == sequenceFeatures)
828 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
829 alignPanel.seqPanel.seqCanvas.repaint();
831 else if (source == showAlignmentAnnotations)
833 setAnnotationsVisibility();
835 else if (source == showSequenceAnnotations)
837 setAnnotationsVisibility();
839 else if (source == sortAnnBySequence)
841 boolean newState = sortAnnBySequence.getState();
842 sortAnnByLabel.setState(false);
843 setAnnotationSortOrder(
844 newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
845 : SequenceAnnotationOrder.NONE);
846 setViewportAnnotationOrder();
848 else if (source == sortAnnByLabel)
850 boolean newState = sortAnnByLabel.getState();
851 sortAnnBySequence.setState(false);
852 setAnnotationSortOrder(
853 newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
854 : SequenceAnnotationOrder.NONE);
855 setViewportAnnotationOrder();
857 else if (source == showAutoFirst)
859 showAutoLast.setState(!showAutoFirst.getState());
860 setShowAutoCalculatedAbove(showAutoFirst.getState());
861 setViewportAnnotationOrder();
863 else if (source == showAutoLast)
865 showAutoFirst.setState(!showAutoLast.getState());
866 setShowAutoCalculatedAbove(showAutoFirst.getState());
867 setViewportAnnotationOrder();
869 else if (source == conservationMenuItem)
871 conservationMenuItem_actionPerformed();
873 else if (source == abovePIDThreshold)
875 abovePIDThreshold_actionPerformed();
877 else if (source == applyToAllGroups)
879 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
881 else if (source == autoCalculate)
883 viewport.autoCalculateConsensus = autoCalculate.getState();
885 else if (source == sortByTree)
887 viewport.sortByTree = sortByTree.getState();
889 else if (source == this.centreColumnLabelFlag)
891 centreColumnLabelFlag_stateChanged();
893 else if (source == this.followMouseOverFlag)
895 mouseOverFlag_stateChanged();
897 else if (source == showGroupConsensus)
899 showGroupConsensus_actionPerformed();
901 else if (source == showGroupConservation)
903 showGroupConservation_actionPerformed();
905 else if (source == showSequenceLogo)
907 showSequenceLogo_actionPerformed();
909 else if (source == normSequenceLogo)
911 normSequenceLogo_actionPerformed();
913 else if (source == showConsensusHistogram)
915 showConsensusHistogram_actionPerformed();
917 else if (source == applyAutoAnnotationSettings)
919 applyAutoAnnotationSettings_actionPerformed();
921 alignPanel.paintAlignment(true);
925 * Set the visibility state of sequence-related and/or alignment-related
926 * annotations depending on checkbox selections, and repaint.
930 private void setAnnotationsVisibility()
932 boolean showForAlignment = showAlignmentAnnotations.getState();
933 boolean showForSequences = showSequenceAnnotations.getState();
934 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
936 for (AlignmentAnnotation aa : alignPanel.getAlignment()
937 .getAlignmentAnnotation())
939 boolean visible = (aa.sequenceRef == null ? showForAlignment
941 aa.visible = visible;
944 alignPanel.validateAnnotationDimensions(true);
949 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
951 this.annotationSortOrder = order;
955 * Set flags on the viewport that control annotation ordering
957 private void setViewportAnnotationOrder()
959 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
961 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
964 private void setShowAutoCalculatedAbove(boolean showAbove)
966 this.showAutoCalculatedAbove = showAbove;
969 private void mouseOverFlag_stateChanged()
971 viewport.setFollowHighlight(followMouseOverFlag.getState());
972 // TODO: could kick the scrollTo mechanism to reset view for current
976 private void centreColumnLabelFlag_stateChanged()
978 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
979 this.alignPanel.annotationPanel.repaint();
983 public void actionPerformed(ActionEvent evt)
985 viewport.applet.currentAlignFrame = this;
987 Object source = evt.getSource();
989 if (source == inputText)
991 inputText_actionPerformed();
993 else if (source == loadTree)
995 loadTree_actionPerformed();
997 else if (source == loadApplication)
999 launchFullApplication();
1001 else if (source == loadAnnotations)
1005 else if (source == outputAnnotations)
1007 outputAnnotations(true);
1009 else if (source == outputFeatures)
1011 outputFeatures(true, "Jalview");
1013 else if (source == closeMenuItem)
1015 closeMenuItem_actionPerformed();
1017 else if (source == copy)
1019 copy_actionPerformed();
1021 else if (source == undoMenuItem)
1023 undoMenuItem_actionPerformed();
1025 else if (source == redoMenuItem)
1027 redoMenuItem_actionPerformed();
1029 else if (source == inputText)
1031 inputText_actionPerformed();
1033 else if (source == closeMenuItem)
1035 closeMenuItem_actionPerformed();
1037 else if (source == undoMenuItem)
1039 undoMenuItem_actionPerformed();
1041 else if (source == redoMenuItem)
1043 redoMenuItem_actionPerformed();
1045 else if (source == copy)
1047 copy_actionPerformed();
1049 else if (source == pasteNew)
1051 pasteNew_actionPerformed();
1053 else if (source == pasteThis)
1055 pasteThis_actionPerformed();
1057 else if (source == cut)
1059 cut_actionPerformed();
1061 else if (source == delete)
1063 delete_actionPerformed();
1065 else if (source == createGroup)
1067 createGroup_actionPerformed();
1069 else if (source == unGroup)
1071 unGroup_actionPerformed();
1073 else if (source == grpsFromSelection)
1075 makeGrpsFromSelection_actionPerformed();
1077 else if (source == deleteGroups)
1079 deleteGroups_actionPerformed();
1081 else if (source == selectAllSequenceMenuItem)
1083 selectAllSequenceMenuItem_actionPerformed();
1085 else if (source == deselectAllSequenceMenuItem)
1087 deselectAllSequenceMenuItem_actionPerformed();
1089 else if (source == invertSequenceMenuItem)
1091 invertSequenceMenuItem_actionPerformed();
1092 // uncomment to slave sequence selections in split frame
1093 // viewport.sendSelection();
1095 else if (source == invertColSel)
1097 viewport.invertColumnSelection();
1098 alignPanel.paintAlignment(true);
1099 viewport.sendSelection();
1101 else if (source == remove2LeftMenuItem)
1103 trimAlignment(true);
1105 else if (source == remove2RightMenuItem)
1107 trimAlignment(false);
1109 else if (source == removeGappedColumnMenuItem)
1111 removeGappedColumnMenuItem_actionPerformed();
1113 else if (source == removeAllGapsMenuItem)
1115 removeAllGapsMenuItem_actionPerformed();
1117 else if (source == findMenuItem)
1119 findMenuItem_actionPerformed();
1121 else if (source == font)
1123 new FontChooser(alignPanel);
1125 else if (source == newView)
1129 else if (source == showColumns)
1131 viewport.showAllHiddenColumns();
1132 alignPanel.paintAlignment(true);
1133 viewport.sendSelection();
1135 else if (source == showSeqs)
1137 viewport.showAllHiddenSeqs();
1138 alignPanel.paintAlignment(true);
1139 // uncomment if we want to slave sequence selections in split frame
1140 // viewport.sendSelection();
1142 else if (source == hideColumns)
1144 viewport.hideSelectedColumns();
1145 alignPanel.paintAlignment(true);
1146 viewport.sendSelection();
1148 else if (source == hideSequences
1149 && viewport.getSelectionGroup() != null)
1151 viewport.hideAllSelectedSeqs();
1152 alignPanel.paintAlignment(true);
1153 // uncomment if we want to slave sequence selections in split frame
1154 // viewport.sendSelection();
1156 else if (source == hideAllButSelection)
1158 toggleHiddenRegions(false, false);
1159 alignPanel.paintAlignment(true);
1160 viewport.sendSelection();
1162 else if (source == hideAllSelection)
1164 SequenceGroup sg = viewport.getSelectionGroup();
1165 viewport.expandColSelection(sg, false);
1166 viewport.hideAllSelectedSeqs();
1167 viewport.hideSelectedColumns();
1168 alignPanel.paintAlignment(true);
1169 viewport.sendSelection();
1171 else if (source == showAllHidden)
1173 viewport.showAllHiddenColumns();
1174 viewport.showAllHiddenSeqs();
1175 alignPanel.paintAlignment(true);
1176 viewport.sendSelection();
1178 else if (source == showGroupConsensus)
1180 showGroupConsensus_actionPerformed();
1182 else if (source == showGroupConservation)
1184 showGroupConservation_actionPerformed();
1186 else if (source == showSequenceLogo)
1188 showSequenceLogo_actionPerformed();
1190 else if (source == normSequenceLogo)
1192 normSequenceLogo_actionPerformed();
1194 else if (source == showConsensusHistogram)
1196 showConsensusHistogram_actionPerformed();
1198 else if (source == applyAutoAnnotationSettings)
1200 applyAutoAnnotationSettings_actionPerformed();
1202 else if (source == featureSettings)
1204 new FeatureSettings(alignPanel);
1206 else if (source == alProperties)
1208 StringBuffer contents = new jalview.io.AlignmentProperties(
1209 viewport.getAlignment()).formatAsString();
1210 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1211 cap.setText(contents.toString());
1212 Frame frame = new Frame();
1214 jalview.bin.JalviewLite.addFrame(frame, MessageManager
1215 .formatMessage("label.alignment_properties", new String[]
1216 { getTitle() }), 400, 250);
1218 else if (source == overviewMenuItem)
1220 overviewMenuItem_actionPerformed();
1222 else if (source == noColourmenuItem)
1226 else if (source == clustalColour)
1228 abovePIDThreshold.setState(false);
1229 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1231 else if (source == zappoColour)
1233 changeColour(new ZappoColourScheme());
1235 else if (source == taylorColour)
1237 changeColour(new TaylorColourScheme());
1239 else if (source == hydrophobicityColour)
1241 changeColour(new HydrophobicColourScheme());
1243 else if (source == helixColour)
1245 changeColour(new HelixColourScheme());
1247 else if (source == strandColour)
1249 changeColour(new StrandColourScheme());
1251 else if (source == turnColour)
1253 changeColour(new TurnColourScheme());
1255 else if (source == buriedColour)
1257 changeColour(new BuriedColourScheme());
1259 else if (source == nucleotideColour)
1261 changeColour(new NucleotideColourScheme());
1263 else if (source == purinePyrimidineColour)
1265 changeColour(new PurinePyrimidineColourScheme());
1267 // else if (source == RNAInteractionColour)
1269 // changeColour(new RNAInteractionColourScheme());
1271 else if (source == RNAHelixColour)
1273 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1274 // new RNAHelicesColourChooser(viewport, alignPanel);
1276 else if (source == modifyPID)
1278 modifyPID_actionPerformed();
1280 else if (source == modifyConservation)
1282 modifyConservation_actionPerformed();
1284 else if (source == userDefinedColour)
1286 new UserDefinedColours(alignPanel, null);
1288 else if (source == PIDColour)
1290 changeColour(new PIDColourScheme());
1292 else if (source == BLOSUM62Colour)
1294 changeColour(new Blosum62ColourScheme());
1296 else if (source == tcoffeeColour)
1298 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1300 else if (source == annotationColour)
1302 new AnnotationColourChooser(viewport, alignPanel);
1304 else if (source == annotationColumnSelection)
1306 new AnnotationColumnChooser(viewport, alignPanel);
1308 else if (source == sortPairwiseMenuItem)
1310 sortPairwiseMenuItem_actionPerformed();
1312 else if (source == sortIDMenuItem)
1314 sortIDMenuItem_actionPerformed();
1316 else if (source == sortLengthMenuItem)
1318 sortLengthMenuItem_actionPerformed();
1320 else if (source == sortGroupMenuItem)
1322 sortGroupMenuItem_actionPerformed();
1324 else if (source == removeRedundancyMenuItem)
1326 removeRedundancyMenuItem_actionPerformed();
1328 else if (source == pairwiseAlignmentMenuItem)
1330 pairwiseAlignmentMenuItem_actionPerformed();
1332 else if (source == PCAMenuItem)
1334 PCAMenuItem_actionPerformed();
1336 else if (source == averageDistanceTreeMenuItem)
1338 averageDistanceTreeMenuItem_actionPerformed();
1340 else if (source == neighbourTreeMenuItem)
1342 neighbourTreeMenuItem_actionPerformed();
1344 else if (source == njTreeBlosumMenuItem)
1346 njTreeBlosumMenuItem_actionPerformed();
1348 else if (source == avDistanceTreeBlosumMenuItem)
1350 avTreeBlosumMenuItem_actionPerformed();
1352 else if (source == documentation)
1354 documentation_actionPerformed();
1356 else if (source == about)
1358 about_actionPerformed();
1363 public void inputText_actionPerformed()
1365 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1366 Frame frame = new Frame();
1368 jalview.bin.JalviewLite.addFrame(frame,
1369 MessageManager.getString("label.input_cut_paste"), 500, 500);
1372 protected void outputText_actionPerformed(ActionEvent e)
1374 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1375 Frame frame = new Frame();
1377 JalviewLite.addFrame(frame, MessageManager
1378 .formatMessage("label.alignment_output_command", new Object[]
1379 { e.getActionCommand() }), 600, 500);
1381 FileFormatI fileFormat = FileFormats.getInstance()
1382 .forName(e.getActionCommand());
1384 new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1385 viewport.getAlignment(), viewport.getShowJVSuffix()));
1388 public void loadAnnotations()
1390 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1391 cap.setText(MessageManager
1392 .getString("label.paste_features_annotations_Tcoffee_here"));
1393 cap.setAnnotationImport();
1394 Frame frame = new Frame();
1396 jalview.bin.JalviewLite.addFrame(frame,
1397 MessageManager.getString("action.paste_annotations"), 400, 300);
1401 public String outputAnnotations(boolean displayTextbox)
1403 String annotation = new AnnotationFile()
1404 .printAnnotationsForView(viewport);
1408 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1409 Frame frame = new Frame();
1411 jalview.bin.JalviewLite.addFrame(frame,
1412 MessageManager.getString("label.annotations"), 600, 500);
1413 cap.setText(annotation);
1419 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1421 if (alignPanel.getFeatureRenderer() != null
1422 && viewport.getFeaturesDisplayed() != null)
1424 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1430 public String outputFeatures(boolean displayTextbox, String format)
1433 FeaturesFile formatter = new FeaturesFile();
1434 if (format.equalsIgnoreCase("Jalview"))
1436 features = formatter.printJalviewFormat(
1437 viewport.getAlignment().getSequencesArray(),
1438 getDisplayedFeatureCols());
1442 features = formatter.printGffFormat(
1443 viewport.getAlignment().getSequencesArray(),
1444 getDisplayedFeatureCols());
1449 boolean frimport = false;
1450 if (features == null || features.equals("No Features Visible"))
1452 features = "# No features visible - paste some and import them here.";
1456 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1459 cap.setAnnotationImport();
1461 Frame frame = new Frame();
1463 jalview.bin.JalviewLite.addFrame(frame,
1464 MessageManager.getString("label.features"), 600, 500);
1465 cap.setText(features);
1469 if (features == null)
1478 void launchFullApplication()
1480 StringBuffer url = new StringBuffer(jalviewServletURL);
1482 // allow servlet parameters to be passed in applet parameter
1483 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1485 url.append(firstSep);
1488 "open=" + appendProtocol(viewport.applet.getParameter("file")));
1490 if (viewport.applet.getParameter("features") != null)
1492 url.append("&features=");
1493 url.append(appendProtocol(viewport.applet.getParameter("features")));
1496 if (viewport.applet.getParameter("annotations") != null)
1498 url.append("&annotations=");
1500 appendProtocol(viewport.applet.getParameter("annotations")));
1503 if (viewport.applet.getParameter("jnetfile") != null
1504 || viewport.applet.getParameter("jpredfile") != null)
1506 url.append("&annotations=");
1507 url.append(appendProtocol(
1508 viewport.applet.getParameter("jnetfile") != null
1509 ? viewport.applet.getParameter("jnetfile")
1510 : viewport.applet.getParameter("jpredfile")));
1513 if (viewport.applet.getParameter("defaultColour") != null)
1515 url.append("&colour=" + removeWhiteSpace(
1516 viewport.applet.getParameter("defaultColour")));
1519 if (viewport.applet.getParameter("userDefinedColour") != null)
1521 url.append("&colour=" + removeWhiteSpace(
1522 viewport.applet.getParameter("userDefinedColour")));
1524 if (viewport.applet.getParameter("tree") != null)
1527 + appendProtocol(viewport.applet.getParameter("tree")));
1529 if (viewport.applet.getParameter("treeFile") != null)
1532 + appendProtocol(viewport.applet.getParameter("treeFile")));
1535 showURL(url.toString(), "FULL_APP");
1538 String removeWhiteSpace(String colour)
1540 StringBuffer sb = new StringBuffer();
1541 for (int i = 0; i < colour.length(); i++)
1543 if (Character.isWhitespace(colour.charAt(i)))
1549 sb.append(colour.charAt(i));
1553 return sb.toString();
1556 String appendProtocol(String url)
1561 url = URLEncoder.encode(url);
1564 * When we finally deprecate 1.1 compatibility, we can start to use
1565 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1566 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1567 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1568 * ex.printStackTrace(); }
1570 catch (java.net.MalformedURLException ex)
1572 url = viewport.applet.getCodeBase() + url;
1577 public void closeMenuItem_actionPerformed()
1579 PaintRefresher.RemoveComponent(alignPanel);
1580 if (alignPanel.seqPanel != null
1581 && alignPanel.seqPanel.seqCanvas != null)
1583 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1585 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1587 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1590 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1605 void updateEditMenuBar()
1608 if (viewport.getHistoryList().size() > 0)
1610 undoMenuItem.setEnabled(true);
1611 CommandI command = viewport.getHistoryList().peek();
1612 undoMenuItem.setLabel(MessageManager
1613 .formatMessage("label.undo_command", new Object[]
1614 { command.getDescription() }));
1618 undoMenuItem.setEnabled(false);
1619 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1622 if (viewport.getRedoList().size() > 0)
1624 redoMenuItem.setEnabled(true);
1626 CommandI command = viewport.getRedoList().peek();
1627 redoMenuItem.setLabel(MessageManager
1628 .formatMessage("label.redo_command", new Object[]
1629 { command.getDescription() }));
1633 redoMenuItem.setEnabled(false);
1634 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1642 public void addHistoryItem(CommandI command)
1644 if (command.getSize() > 0)
1646 viewport.addToHistoryList(command);
1647 viewport.clearRedoList();
1648 updateEditMenuBar();
1649 viewport.updateHiddenColumns();
1654 * TODO: JAL-1104 DOCUMENT ME!
1659 protected void undoMenuItem_actionPerformed()
1661 if (viewport.getHistoryList().isEmpty())
1666 CommandI command = viewport.getHistoryList().pop();
1667 viewport.addToRedoList(command);
1668 command.undoCommand(null);
1670 AlignmentViewport originalSource = getOriginatingSource(command);
1672 if (originalSource != viewport)
1675 .println("Warning: Viewport object mismatch whilst undoing");
1677 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1678 // viewport.getColumnSelection().getHiddenColumns()
1680 updateEditMenuBar();
1681 originalSource.firePropertyChange("alignment", null,
1682 originalSource.getAlignment().getSequences());
1686 * TODO: JAL-1104 DOCUMENT ME!
1691 protected void redoMenuItem_actionPerformed()
1693 if (viewport.getRedoList().isEmpty())
1698 CommandI command = viewport.getRedoList().pop();
1699 viewport.addToHistoryList(command);
1700 command.doCommand(null);
1702 AlignmentViewport originalSource = getOriginatingSource(command);
1704 if (originalSource != viewport)
1707 .println("Warning: Viewport object mismatch whilst re-doing");
1709 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1710 // viewport.getColumnSelection().getHiddenColumns()
1713 updateEditMenuBar();
1714 originalSource.firePropertyChange("alignment", null,
1715 originalSource.getAlignment().getSequences());
1718 AlignmentViewport getOriginatingSource(CommandI command)
1720 AlignmentViewport originalSource = null;
1721 // For sequence removal and addition, we need to fire
1722 // the property change event FROM the viewport where the
1723 // original alignment was altered
1724 AlignmentI al = null;
1725 if (command instanceof EditCommand)
1727 EditCommand editCommand = (EditCommand) command;
1728 al = editCommand.getAlignment();
1729 Vector comps = (Vector) PaintRefresher.components
1730 .get(viewport.getSequenceSetId());
1731 for (int i = 0; i < comps.size(); i++)
1733 if (comps.elementAt(i) instanceof AlignmentPanel)
1735 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1737 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1744 if (originalSource == null)
1746 // The original view is closed, we must validate
1747 // the current view against the closed view first
1750 PaintRefresher.validateSequences(al, viewport.getAlignment());
1753 originalSource = viewport;
1756 return originalSource;
1760 * Move the currently selected sequences up or down one position in the
1765 public void moveSelectedSequences(boolean up)
1767 SequenceGroup sg = viewport.getSelectionGroup();
1772 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1773 up ? null : viewport.getHiddenRepSequences(), up);
1774 alignPanel.paintAlignment(true);
1777 * Also move cDNA/protein complement sequences
1779 AlignViewportI complement = viewport.getCodingComplement();
1780 if (complement != null)
1782 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1783 viewport, complement);
1784 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1785 up ? null : complement.getHiddenRepSequences(), up);
1786 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1790 synchronized void slideSequences(boolean right, int size)
1792 List<SequenceI> sg = new Vector<>();
1793 if (viewport.cursorMode)
1795 sg.add(viewport.getAlignment()
1796 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1798 else if (viewport.getSelectionGroup() != null
1799 && viewport.getSelectionGroup().getSize() != viewport
1800 .getAlignment().getHeight())
1802 sg = viewport.getSelectionGroup()
1803 .getSequences(viewport.getHiddenRepSequences());
1811 Vector<SequenceI> invertGroup = new Vector();
1813 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1815 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1817 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1821 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1823 SequenceI[] seqs2 = invertGroup
1824 .toArray(new SequenceI[invertGroup.size()]);
1825 for (int i = 0; i < invertGroup.size(); i++)
1827 seqs2[i] = invertGroup.elementAt(i);
1830 SlideSequencesCommand ssc;
1833 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1834 viewport.getGapCharacter());
1838 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1839 viewport.getGapCharacter());
1842 int groupAdjustment = 0;
1843 if (ssc.getGapsInsertedBegin() && right)
1845 if (viewport.cursorMode)
1847 alignPanel.seqPanel.moveCursor(size, 0);
1851 groupAdjustment = size;
1854 else if (!ssc.getGapsInsertedBegin() && !right)
1856 if (viewport.cursorMode)
1858 alignPanel.seqPanel.moveCursor(-size, 0);
1862 groupAdjustment = -size;
1866 if (groupAdjustment != 0)
1868 viewport.getSelectionGroup().setStartRes(
1869 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1870 viewport.getSelectionGroup().setEndRes(
1871 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1874 boolean appendHistoryItem = false;
1875 Deque<CommandI> historyList = viewport.getHistoryList();
1876 if (historyList != null && historyList.size() > 0
1877 && historyList.peek() instanceof SlideSequencesCommand)
1879 appendHistoryItem = ssc.appendSlideCommand(
1880 (SlideSequencesCommand) historyList.peek());
1883 if (!appendHistoryItem)
1885 addHistoryItem(ssc);
1891 static StringBuffer copiedSequences;
1893 static Vector<int[]> copiedHiddenColumns;
1895 protected void copy_actionPerformed()
1897 if (viewport.getSelectionGroup() == null)
1902 SequenceGroup sg = viewport.getSelectionGroup();
1903 copiedSequences = new StringBuffer();
1904 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1905 for (int i = 0; i < sg.getSize(); i++)
1907 SequenceI seq = sg.getSequenceAt(i);
1908 int index = viewport.getAlignment().findIndex(seq);
1909 orderedSeqs.put(index, seq);
1912 int index = 0, startRes, endRes;
1915 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1917 copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1918 .getHiddenColumns().getHiddenColumnsCopy());
1919 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1920 for (int[] region : copiedHiddenColumns)
1922 region[0] = region[0] - hiddenOffset;
1923 region[1] = region[1] - hiddenOffset;
1928 copiedHiddenColumns = null;
1931 for (int i = 0; i < sg.getSize(); i++)
1933 SequenceI seq = null;
1937 if (orderedSeqs.containsKey(index))
1939 seq = orderedSeqs.get(index);
1950 // Returns residue following index if gap
1951 startRes = seq.findPosition(sg.getStartRes());
1954 // Need to find the residue preceeding index if gap
1957 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1959 ch = seq.getCharAt(j);
1960 if (!jalview.util.Comparison.isGap((ch)))
1968 endRes += seq.getStart() - 1;
1971 copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1972 + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1979 protected void pasteNew_actionPerformed()
1984 protected void pasteThis_actionPerformed()
1989 void paste(boolean newAlignment)
1994 if (copiedSequences == null)
1999 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2000 Vector seqs = new Vector();
2001 while (st.hasMoreElements())
2003 String name = st.nextToken();
2004 int start = Integer.parseInt(st.nextToken());
2005 int end = Integer.parseInt(st.nextToken());
2006 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2008 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2009 for (int i = 0; i < seqs.size(); i++)
2011 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2016 String newtitle = MessageManager
2017 .getString("label.copied_sequences");
2018 if (getTitle().startsWith(
2019 MessageManager.getString("label.copied_sequences")))
2021 newtitle = getTitle();
2025 newtitle = newtitle.concat(MessageManager
2026 .formatMessage("label.from_msname", new String[]
2029 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2030 viewport.applet, newtitle, false);
2031 if (copiedHiddenColumns != null)
2033 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2035 int[] region = copiedHiddenColumns.elementAt(i);
2036 af.viewport.hideColumns(region[0], region[1]);
2040 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2045 addSequences(newSeqs);
2048 } catch (Exception ex)
2050 } // could be anything being pasted in here
2054 void addSequences(SequenceI[] seqs)
2056 for (int i = 0; i < seqs.length; i++)
2058 viewport.getAlignment().addSequence(seqs[i]);
2062 addHistoryItem(new EditCommand(
2063 MessageManager.getString("label.add_sequences"), Action.PASTE,
2064 seqs, 0, viewport.getAlignment().getWidth(),
2065 viewport.getAlignment()));
2067 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2068 viewport.getAlignment().getWidth();
2069 viewport.firePropertyChange("alignment", null,
2070 viewport.getAlignment().getSequences());
2074 protected void cut_actionPerformed()
2076 copy_actionPerformed();
2077 delete_actionPerformed();
2080 protected void delete_actionPerformed()
2083 SequenceGroup sg = viewport.getSelectionGroup();
2089 Vector seqs = new Vector();
2091 for (int i = 0; i < sg.getSize(); i++)
2093 seq = sg.getSequenceAt(i);
2094 seqs.addElement(seq);
2098 * If the cut affects all sequences, warn, remove highlighted columns
2100 if (sg.getSize() == viewport.getAlignment().getHeight())
2102 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2103 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2104 if (isEntireAlignWidth)
2106 String title = MessageManager.getString("label.delete_all");
2107 Panel infoPanel = new Panel();
2108 infoPanel.setLayout(new FlowLayout());
2110 new Label(MessageManager.getString("warn.delete_all")));
2112 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2113 dialog.setMainPanel(infoPanel);
2114 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2115 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2116 dialog.setVisible(true);
2123 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2124 sg.getEndRes() + 1);
2127 SequenceI[] cut = new SequenceI[seqs.size()];
2128 for (int i = 0; i < seqs.size(); i++)
2130 cut[i] = (SequenceI) seqs.elementAt(i);
2134 * //ADD HISTORY ITEM
2136 addHistoryItem(new EditCommand(
2137 MessageManager.getString("label.cut_sequences"), Action.CUT,
2138 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2139 viewport.getAlignment()));
2141 viewport.setSelectionGroup(null);
2142 viewport.getAlignment().deleteGroup(sg);
2144 viewport.firePropertyChange("alignment", null,
2145 viewport.getAlignment().getSequences());
2147 if (viewport.getAlignment().getHeight() < 1)
2149 this.setVisible(false);
2151 viewport.sendSelection();
2155 * group consensus toggled
2158 protected void showGroupConsensus_actionPerformed()
2160 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2161 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2166 * group conservation toggled.
2168 protected void showGroupConservation_actionPerformed()
2170 viewport.setShowGroupConservation(showGroupConservation.getState());
2171 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2178 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2179 * .event.ActionEvent)
2181 protected void showConsensusHistogram_actionPerformed()
2183 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2184 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2191 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2192 * .event.ActionEvent)
2194 protected void showSequenceLogo_actionPerformed()
2196 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2197 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200 protected void normSequenceLogo_actionPerformed()
2202 showSequenceLogo.setState(true);
2203 viewport.setShowSequenceLogo(true);
2204 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2205 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2208 protected void applyAutoAnnotationSettings_actionPerformed()
2210 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2213 protected void makeGrpsFromSelection_actionPerformed()
2215 if (avc.makeGroupsFromSelection())
2217 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2218 alignPanel.updateAnnotation();
2219 alignPanel.paintAlignment(true);
2223 protected void createGroup_actionPerformed()
2228 protected void unGroup_actionPerformed()
2232 alignPanel.alignmentChanged();
2236 protected void deleteGroups_actionPerformed()
2238 if (avc.deleteGroups())
2240 alignPanel.alignmentChanged();
2244 public void selectAllSequenceMenuItem_actionPerformed()
2246 SequenceGroup sg = new SequenceGroup();
2247 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2249 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2251 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2252 viewport.setSelectionGroup(sg);
2253 // JAL-2034 - should delegate to
2254 // alignPanel to decide if overview needs
2256 alignPanel.paintAlignment(false);
2257 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2258 viewport.sendSelection();
2261 public void deselectAllSequenceMenuItem_actionPerformed()
2263 if (viewport.cursorMode)
2265 alignPanel.seqPanel.keyboardNo1 = null;
2266 alignPanel.seqPanel.keyboardNo2 = null;
2268 viewport.setSelectionGroup(null);
2269 viewport.getColumnSelection().clear();
2270 viewport.setSelectionGroup(null);
2271 alignPanel.idPanel.idCanvas.searchResults = null;
2272 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2273 // JAL-2034 - should delegate to
2274 // alignPanel to decide if overview needs
2276 alignPanel.paintAlignment(false);
2277 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2278 viewport.sendSelection();
2281 public void invertSequenceMenuItem_actionPerformed()
2283 SequenceGroup sg = viewport.getSelectionGroup();
2284 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2286 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2289 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2290 viewport.sendSelection();
2293 public void invertColSel_actionPerformed()
2295 viewport.invertColumnSelection();
2296 alignPanel.paintAlignment(true);
2297 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2298 viewport.sendSelection();
2301 void trimAlignment(boolean trimLeft)
2303 AlignmentI al = viewport.getAlignment();
2304 ViewportRanges ranges = viewport.getRanges();
2305 ColumnSelection colSel = viewport.getColumnSelection();
2308 if (!colSel.isEmpty())
2312 column = colSel.getMin();
2316 column = colSel.getMax();
2320 if (viewport.getSelectionGroup() != null)
2322 seqs = viewport.getSelectionGroup()
2323 .getSequencesAsArray(viewport.getHiddenRepSequences());
2327 seqs = al.getSequencesArray();
2330 TrimRegionCommand trimRegion;
2333 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2335 ranges.setStartRes(0);
2339 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2343 statusBar.setText(MessageManager
2344 .formatMessage("label.removed_columns", new String[]
2345 { Integer.valueOf(trimRegion.getSize()).toString() }));
2346 addHistoryItem(trimRegion);
2348 for (SequenceGroup sg : al.getGroups())
2350 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2351 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2357 viewport.firePropertyChange("alignment", null, al.getSequences());
2361 public void removeGappedColumnMenuItem_actionPerformed()
2363 AlignmentI al = viewport.getAlignment();
2364 ViewportRanges ranges = viewport.getRanges();
2366 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2369 if (viewport.getSelectionGroup() != null)
2371 seqs = viewport.getSelectionGroup()
2372 .getSequencesAsArray(viewport.getHiddenRepSequences());
2373 start = viewport.getSelectionGroup().getStartRes();
2374 end = viewport.getSelectionGroup().getEndRes();
2378 seqs = viewport.getAlignment().getSequencesArray();
2381 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2382 "Remove Gapped Columns", seqs, start, end,
2383 viewport.getAlignment());
2385 addHistoryItem(removeGapCols);
2387 statusBar.setText(MessageManager
2388 .formatMessage("label.removed_empty_columns", new String[]
2389 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2391 // This is to maintain viewport position on first residue
2392 // of first sequence
2393 SequenceI seq = al.getSequenceAt(0);
2394 int startRes = seq.findPosition(ranges.getStartRes());
2395 // ShiftList shifts;
2396 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2397 // edit.alColumnChanges=shifts.getInverse();
2398 // if (viewport.hasHiddenColumns)
2399 // viewport.getColumnSelection().compensateForEdits(shifts);
2400 ranges.setStartRes(seq.findIndex(startRes) - 1);
2401 viewport.firePropertyChange("alignment", null, al.getSequences());
2405 public void removeAllGapsMenuItem_actionPerformed()
2407 AlignmentI al = viewport.getAlignment();
2408 ViewportRanges ranges = viewport.getRanges();
2410 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2413 if (viewport.getSelectionGroup() != null)
2415 seqs = viewport.getSelectionGroup()
2416 .getSequencesAsArray(viewport.getHiddenRepSequences());
2417 start = viewport.getSelectionGroup().getStartRes();
2418 end = viewport.getSelectionGroup().getEndRes();
2422 seqs = viewport.getAlignment().getSequencesArray();
2425 // This is to maintain viewport position on first residue
2426 // of first sequence
2427 SequenceI seq = al.getSequenceAt(0);
2428 int startRes = seq.findPosition(ranges.getStartRes());
2431 new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2433 ranges.setStartRes(seq.findIndex(startRes) - 1);
2435 viewport.firePropertyChange("alignment", null, al.getSequences());
2439 public void findMenuItem_actionPerformed()
2441 new Finder(alignPanel);
2445 * create a new view derived from the current view
2448 * @return frame for the new view
2450 public AlignFrame newView(String viewtitle)
2453 if (viewport.hasHiddenRows())
2455 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2456 .getFullAlignment().getSequencesArray());
2460 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2463 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2465 for (int i = 0; i < viewport.getAlignment()
2466 .getAlignmentAnnotation().length; i++)
2468 if (!viewport.getAlignment()
2469 .getAlignmentAnnotation()[i].autoCalculated)
2471 newal.addAnnotation(
2472 viewport.getAlignment().getAlignmentAnnotation()[i]);
2477 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2479 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2480 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2481 PaintRefresher.Register(newaf.alignPanel,
2482 newaf.alignPanel.av.getSequenceSetId());
2484 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2485 newaf.alignPanel.av.getSequenceSetId());
2486 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2487 newaf.alignPanel.av.getSequenceSetId());
2489 Vector comps = (Vector) PaintRefresher.components
2490 .get(viewport.getSequenceSetId());
2492 for (int i = 0; i < comps.size(); i++)
2494 if (comps.elementAt(i) instanceof AlignmentPanel)
2500 String title = new String(this.getTitle());
2501 if (viewtitle != null)
2503 title = viewtitle + " ( " + title + ")";
2507 if (title.indexOf("(View") > -1)
2509 title = title.substring(0, title.indexOf("(View"));
2511 title += "(View " + viewSize + ")";
2514 newaf.setTitle(title.toString());
2516 newaf.viewport.setHistoryList(viewport.getHistoryList());
2517 newaf.viewport.setRedoList(viewport.getRedoList());
2523 * @return list of feature groups on the view
2525 public String[] getFeatureGroups()
2527 FeatureRenderer fr = null;
2528 if (alignPanel != null
2529 && (fr = alignPanel.getFeatureRenderer()) != null)
2531 List<String> gps = fr.getFeatureGroups();
2532 String[] _gps = gps.toArray(new String[gps.size()]);
2539 * get sequence feature groups that are hidden or shown
2545 public String[] getFeatureGroupsOfState(boolean visible)
2547 FeatureRenderer fr = null;
2548 if (alignPanel != null
2549 && (fr = alignPanel.getFeatureRenderer()) != null)
2551 List<String> gps = fr.getGroups(visible);
2552 String[] _gps = gps.toArray(new String[gps.size()]);
2559 * Change the display state for the given feature groups
2562 * list of group strings
2564 * visible or invisible
2566 public void setFeatureGroupState(String[] groups, boolean state)
2568 FeatureRenderer fr = null;
2569 this.sequenceFeatures.setState(true);
2570 viewport.setShowSequenceFeatures(true);
2571 if (alignPanel != null
2572 && (fr = alignPanel.getFeatureRenderer()) != null)
2575 fr.setGroupVisibility(Arrays.asList(groups), state);
2576 alignPanel.seqPanel.seqCanvas.repaint();
2577 if (alignPanel.overviewPanel != null)
2579 alignPanel.overviewPanel.updateOverviewImage();
2584 public void seqLimits_itemStateChanged()
2586 viewport.setShowJVSuffix(seqLimits.getState());
2587 alignPanel.fontChanged();
2588 alignPanel.paintAlignment(true);
2591 protected void colourTextMenuItem_actionPerformed()
2593 viewport.setColourText(colourTextMenuItem.getState());
2594 alignPanel.paintAlignment(true);
2597 protected void displayNonconservedMenuItem_actionPerformed()
2599 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2600 alignPanel.paintAlignment(true);
2603 protected void wrapMenuItem_actionPerformed()
2605 viewport.setWrapAlignment(wrapMenuItem.getState());
2606 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2607 scaleAbove.setEnabled(wrapMenuItem.getState());
2608 scaleLeft.setEnabled(wrapMenuItem.getState());
2609 scaleRight.setEnabled(wrapMenuItem.getState());
2610 alignPanel.paintAlignment(true);
2613 public void overviewMenuItem_actionPerformed()
2615 if (alignPanel.overviewPanel != null)
2620 Frame frame = new Frame();
2621 final OverviewPanel overview = new OverviewPanel(alignPanel);
2622 frame.add(overview);
2623 // +50 must allow for applet frame window
2624 jalview.bin.JalviewLite.addFrame(frame, MessageManager
2625 .formatMessage("label.overview_params", new String[]
2626 { this.getTitle() }), overview.getPreferredSize().width,
2627 overview.getPreferredSize().height + 50);
2630 final AlignmentPanel ap = alignPanel;
2631 frame.addWindowListener(new WindowAdapter()
2634 public void windowClosing(WindowEvent e)
2639 ap.setOverviewPanel(null);
2644 alignPanel.setOverviewPanel(overview);
2649 public void changeColour(ColourSchemeI cs)
2651 viewport.setGlobalColourScheme(cs);
2653 alignPanel.paintAlignment(true);
2656 protected void modifyPID_actionPerformed()
2658 if (viewport.getAbovePIDThreshold()
2659 && viewport.getGlobalColourScheme() != null)
2661 SliderPanel.setPIDSliderSource(alignPanel,
2662 viewport.getResidueShading(), alignPanel.getViewName());
2663 SliderPanel.showPIDSlider();
2667 protected void modifyConservation_actionPerformed()
2669 if (viewport.getConservationSelected()
2670 && viewport.getGlobalColourScheme() != null)
2672 SliderPanel.setConservationSlider(alignPanel,
2673 viewport.getResidueShading(), alignPanel.getViewName());
2674 SliderPanel.showConservationSlider();
2678 protected void conservationMenuItem_actionPerformed()
2680 boolean selected = conservationMenuItem.getState();
2681 modifyConservation.setEnabled(selected);
2682 viewport.setConservationSelected(selected);
2683 viewport.getResidueShading().setConservationApplied(selected);
2685 changeColour(viewport.getGlobalColourScheme());
2689 modifyConservation_actionPerformed();
2693 SliderPanel.hideConservationSlider();
2697 public void abovePIDThreshold_actionPerformed()
2699 boolean selected = abovePIDThreshold.getState();
2700 modifyPID.setEnabled(selected);
2701 viewport.setAbovePIDThreshold(selected);
2704 viewport.getResidueShading().setThreshold(0,
2705 viewport.isIgnoreGapsConsensus());
2708 changeColour(viewport.getGlobalColourScheme());
2712 modifyPID_actionPerformed();
2716 SliderPanel.hidePIDSlider();
2720 public void sortPairwiseMenuItem_actionPerformed()
2722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723 AlignmentSorter.sortByPID(viewport.getAlignment(),
2724 viewport.getAlignment().getSequenceAt(0));
2726 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2727 viewport.getAlignment()));
2728 alignPanel.paintAlignment(true);
2731 public void sortIDMenuItem_actionPerformed()
2733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734 AlignmentSorter.sortByID(viewport.getAlignment());
2736 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2737 alignPanel.paintAlignment(true);
2740 public void sortLengthMenuItem_actionPerformed()
2742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2743 AlignmentSorter.sortByLength(viewport.getAlignment());
2744 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2745 viewport.getAlignment()));
2746 alignPanel.paintAlignment(true);
2749 public void sortGroupMenuItem_actionPerformed()
2751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752 AlignmentSorter.sortByGroup(viewport.getAlignment());
2753 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2754 viewport.getAlignment()));
2755 alignPanel.paintAlignment(true);
2759 public void removeRedundancyMenuItem_actionPerformed()
2761 new RedundancyPanel(alignPanel);
2764 public void pairwiseAlignmentMenuItem_actionPerformed()
2766 if (viewport.getSelectionGroup() != null
2767 && viewport.getSelectionGroup().getSize() > 1)
2769 Frame frame = new Frame();
2770 frame.add(new PairwiseAlignPanel(alignPanel));
2771 jalview.bin.JalviewLite.addFrame(frame,
2772 MessageManager.getString("action.pairwise_alignment"), 600,
2777 public void PCAMenuItem_actionPerformed()
2779 // are the sequences aligned?
2780 if (!viewport.getAlignment().isAligned(false))
2783 int Width = viewport.getAlignment().getWidth();
2785 for (int i = 0; i < viewport.getAlignment().getSequences()
2788 current = viewport.getAlignment().getSequenceAt(i);
2790 if (current.getLength() < Width)
2792 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2795 alignPanel.paintAlignment(true);
2798 if ((viewport.getSelectionGroup() != null
2799 && viewport.getSelectionGroup().getSize() < 4
2800 && viewport.getSelectionGroup().getSize() > 0)
2801 || viewport.getAlignment().getHeight() < 4)
2808 new PCAPanel(viewport);
2809 } catch (java.lang.OutOfMemoryError ex)
2815 public void averageDistanceTreeMenuItem_actionPerformed()
2817 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2818 "Average distance tree using PID");
2821 public void neighbourTreeMenuItem_actionPerformed()
2823 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2824 "Neighbour joining tree using PID");
2827 protected void njTreeBlosumMenuItem_actionPerformed()
2829 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2830 ScoreModels.getInstance().getBlosum62().getName(),
2831 "Neighbour joining tree using BLOSUM62");
2834 protected void avTreeBlosumMenuItem_actionPerformed()
2836 newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2837 ScoreModels.getInstance().getBlosum62().getName(),
2838 "Average distance tree using BLOSUM62");
2841 void newTreePanel(String type, String pwType, String title)
2843 // are the sequences aligned?
2844 if (!viewport.getAlignment().isAligned(false))
2847 int Width = viewport.getAlignment().getWidth();
2849 for (int i = 0; i < viewport.getAlignment().getSequences()
2852 current = viewport.getAlignment().getSequenceAt(i);
2854 if (current.getLength() < Width)
2856 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2859 alignPanel.paintAlignment(true);
2863 if ((viewport.getSelectionGroup() != null
2864 && viewport.getSelectionGroup().getSize() > 1)
2865 || (viewport.getAlignment().getHeight() > 1))
2867 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2869 addTreeMenuItem(tp, title);
2871 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2875 void loadTree_actionPerformed()
2877 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2878 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2879 cap.setTreeImport();
2880 Frame frame = new Frame();
2882 jalview.bin.JalviewLite.addFrame(frame,
2883 MessageManager.getString("label.paste_newick_file"), 400, 300);
2886 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2888 TreePanel tp = new TreePanel(alignPanel, treeFile,
2889 MessageManager.getString("label.load_tree_from_file"), tree);
2890 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2891 addTreeMenuItem(tp, treeFile);
2895 * sort the alignment using the given treePanel
2898 * tree used to sort view
2900 * string used for undo event name
2902 public void sortByTree(TreePanel treePanel, String title)
2904 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2905 AlignmentSorter.sortByTree(viewport.getAlignment(),
2906 treePanel.getTree());
2907 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2908 // HistoryItem.SORT));
2909 addHistoryItem(new OrderCommand(MessageManager
2910 .formatMessage("label.order_by_params", new String[]
2911 { title }), oldOrder, viewport.getAlignment()));
2912 alignPanel.paintAlignment(true);
2916 * Do any automatic reordering of the alignment and add the necessary bits to
2917 * the menu structure for the new tree
2922 protected void addTreeMenuItem(final TreePanel treePanel,
2925 final MenuItem item = new MenuItem(title);
2926 sortByTreeMenu.add(item);
2927 item.addActionListener(new java.awt.event.ActionListener()
2930 public void actionPerformed(ActionEvent evt)
2932 sortByTree(treePanel, title); // treePanel.getTitle());
2936 treePanel.addWindowListener(new WindowAdapter()
2939 public void windowOpened(WindowEvent e)
2941 if (viewport.sortByTree)
2943 sortByTree(treePanel, title);
2945 super.windowOpened(e);
2949 public void windowClosing(WindowEvent e)
2951 sortByTreeMenu.remove(item);
2956 public boolean sortBy(AlignmentOrder alorder, String undoname)
2958 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2959 if (viewport.applet.debug)
2961 System.err.println("Sorting " + alorder.getOrder().size()
2962 + " in alignment '" + getTitle() + "'");
2964 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2965 if (undoname != null)
2967 addHistoryItem(new OrderCommand(undoname, oldOrder,
2968 viewport.getAlignment()));
2970 alignPanel.paintAlignment(true);
2974 protected void documentation_actionPerformed()
2976 alignPanel.av.applet.openJalviewHelpUrl();
2979 protected void about_actionPerformed()
2982 class AboutPanel extends Canvas
2988 public AboutPanel(String version, String builddate)
2990 this.version = version;
2991 this.builddate = builddate;
2995 public void paint(Graphics g)
2997 g.setColor(Color.white);
2998 g.fillRect(0, 0, getSize().width, getSize().height);
2999 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3000 FontMetrics fm = g.getFontMetrics();
3001 int fh = fm.getHeight();
3003 g.setColor(Color.black);
3004 // TODO: update this text for each release or centrally store it for
3005 // lite and application
3006 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3007 g.drawString(MessageManager
3008 .formatMessage("label.jalviewLite_release", new String[]
3009 { version }), x, y += fh);
3010 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3011 g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3013 { builddate }), x, y += fh);
3014 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3015 g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3017 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3018 x + 50, y += fh + 8);
3019 g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3021 g.drawString(MessageManager
3022 .getString("label.jalview_distribution_lists"), x, y += fh);
3023 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3026 MessageManager.getString("label.jalview_cite_1_authors"), x,
3028 g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3030 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3035 Frame frame = new Frame();
3036 frame.add(new AboutPanel(JalviewLite.getVersion(),
3037 JalviewLite.getBuildDate()));
3038 jalview.bin.JalviewLite.addFrame(frame,
3039 MessageManager.getString("label.jalview"), 580, 220);
3043 public void showURL(String url, String target)
3045 if (viewport.applet == null)
3047 System.out.println("Not running as applet - no browser available.");
3051 viewport.applet.showURL(url, target);
3055 // ////////////////////////////////////////////////////////////////////////////////
3056 // JBuilder Graphics here
3058 MenuBar alignFrameMenuBar = new MenuBar();
3060 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3062 MenuItem loadApplication = new MenuItem(
3063 MessageManager.getString("label.view_full_application"));
3065 MenuItem loadTree = new MenuItem(
3066 MessageManager.getString("label.load_associated_tree"));
3068 MenuItem loadAnnotations = new MenuItem(
3069 MessageManager.getString("label.load_features_annotations"));
3071 MenuItem outputFeatures = new MenuItem(
3072 MessageManager.getString("label.export_features"));
3074 MenuItem outputAnnotations = new MenuItem(
3075 MessageManager.getString("label.export_annotations"));
3077 MenuItem closeMenuItem = new MenuItem(
3078 MessageManager.getString("action.close"));
3080 MenuItem selectAllSequenceMenuItem = new MenuItem(
3081 MessageManager.getString("action.select_all"));
3083 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3084 MessageManager.getString("action.deselect_all"));
3086 MenuItem invertSequenceMenuItem = new MenuItem(
3087 MessageManager.getString("action.invert_selection"));
3089 MenuItem remove2LeftMenuItem = new MenuItem();
3091 MenuItem remove2RightMenuItem = new MenuItem();
3093 MenuItem removeGappedColumnMenuItem = new MenuItem();
3095 MenuItem removeAllGapsMenuItem = new MenuItem();
3097 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3099 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3101 MenuItem sortPairwiseMenuItem = new MenuItem();
3103 MenuItem sortIDMenuItem = new MenuItem();
3105 MenuItem sortLengthMenuItem = new MenuItem();
3107 MenuItem sortGroupMenuItem = new MenuItem();
3109 MenuItem removeRedundancyMenuItem = new MenuItem();
3111 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3113 MenuItem PCAMenuItem = new MenuItem();
3115 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3117 MenuItem neighbourTreeMenuItem = new MenuItem();
3119 BorderLayout borderLayout1 = new BorderLayout();
3121 public Label statusBar = new Label();
3123 MenuItem clustalColour = new MenuItem();
3125 MenuItem zappoColour = new MenuItem();
3127 MenuItem taylorColour = new MenuItem();
3129 MenuItem hydrophobicityColour = new MenuItem();
3131 MenuItem helixColour = new MenuItem();
3133 MenuItem strandColour = new MenuItem();
3135 MenuItem turnColour = new MenuItem();
3137 MenuItem buriedColour = new MenuItem();
3139 MenuItem purinePyrimidineColour = new MenuItem();
3141 // MenuItem RNAInteractionColour = new MenuItem();
3143 MenuItem RNAHelixColour = new MenuItem();
3145 MenuItem userDefinedColour = new MenuItem();
3147 MenuItem PIDColour = new MenuItem();
3149 MenuItem BLOSUM62Colour = new MenuItem();
3151 MenuItem tcoffeeColour = new MenuItem();
3153 MenuItem njTreeBlosumMenuItem = new MenuItem();
3155 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3157 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3159 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3161 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3163 MenuItem alProperties = new MenuItem(
3164 MessageManager.getString("label.alignment_props"));
3166 MenuItem overviewMenuItem = new MenuItem();
3168 MenuItem undoMenuItem = new MenuItem();
3170 MenuItem redoMenuItem = new MenuItem();
3172 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3174 MenuItem noColourmenuItem = new MenuItem();
3176 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3178 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3180 MenuItem findMenuItem = new MenuItem();
3182 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3184 MenuItem nucleotideColour = new MenuItem();
3186 MenuItem deleteGroups = new MenuItem();
3188 MenuItem grpsFromSelection = new MenuItem();
3190 MenuItem createGroup = new MenuItem();
3192 MenuItem unGroup = new MenuItem();
3194 MenuItem delete = new MenuItem();
3196 MenuItem copy = new MenuItem();
3198 MenuItem cut = new MenuItem();
3200 Menu pasteMenu = new Menu();
3202 MenuItem pasteNew = new MenuItem();
3204 MenuItem pasteThis = new MenuItem();
3206 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3208 MenuItem font = new MenuItem();
3210 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3212 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3214 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3216 MenuItem modifyPID = new MenuItem();
3218 MenuItem modifyConservation = new MenuItem();
3220 CheckboxMenuItem autoCalculate = null;
3222 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3223 "Sort Alignment With New Tree", true);
3225 Menu sortByTreeMenu = new Menu();
3227 MenuItem inputText = new MenuItem();
3229 MenuItem documentation = new MenuItem();
3231 MenuItem about = new MenuItem();
3233 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3235 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3237 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3239 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3241 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3243 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3245 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3247 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3249 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3252 * Initialise menus and other items
3256 private void jbInit() throws Exception
3258 setMenuBar(alignFrameMenuBar);
3261 * Configure File menu items and actions
3264 .setLabel(MessageManager.getString("label.input_from_textbox"));
3265 inputText.addActionListener(this);
3266 Menu outputTextboxMenu = new Menu(
3267 MessageManager.getString("label.out_to_textbox"));
3268 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3270 MenuItem item = new MenuItem(ff);
3272 item.addActionListener(new java.awt.event.ActionListener()
3275 public void actionPerformed(ActionEvent e)
3277 outputText_actionPerformed(e);
3281 outputTextboxMenu.add(item);
3283 closeMenuItem.addActionListener(this);
3284 loadApplication.addActionListener(this);
3285 loadTree.addActionListener(this);
3286 loadAnnotations.addActionListener(this);
3287 outputFeatures.addActionListener(this);
3288 outputAnnotations.addActionListener(this);
3291 * Configure Edit menu items and actions
3293 undoMenuItem.setEnabled(false);
3294 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3295 undoMenuItem.addActionListener(this);
3296 redoMenuItem.setEnabled(false);
3297 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3298 redoMenuItem.addActionListener(this);
3299 copy.setLabel(MessageManager.getString("action.copy"));
3300 copy.addActionListener(this);
3301 cut.setLabel(MessageManager.getString("action.cut"));
3302 cut.addActionListener(this);
3303 delete.setLabel(MessageManager.getString("action.delete"));
3304 delete.addActionListener(this);
3305 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3306 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3307 pasteNew.addActionListener(this);
3308 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3309 pasteThis.addActionListener(this);
3311 .setLabel(MessageManager.getString("action.remove_left"));
3312 remove2LeftMenuItem.addActionListener(this);
3313 remove2RightMenuItem
3314 .setLabel(MessageManager.getString("action.remove_right"));
3315 remove2RightMenuItem.addActionListener(this);
3316 removeGappedColumnMenuItem.setLabel(
3317 MessageManager.getString("action.remove_empty_columns"));
3318 removeGappedColumnMenuItem.addActionListener(this);
3319 removeAllGapsMenuItem
3320 .setLabel(MessageManager.getString("action.remove_all_gaps"));
3321 removeAllGapsMenuItem.addActionListener(this);
3322 removeRedundancyMenuItem
3323 .setLabel(MessageManager.getString("action.remove_redundancy"));
3324 removeRedundancyMenuItem.addActionListener(this);
3327 * Configure Select menu items and actions
3329 findMenuItem.setLabel(MessageManager.getString("action.find"));
3330 findMenuItem.addActionListener(this);
3331 selectAllSequenceMenuItem.addActionListener(this);
3332 deselectAllSequenceMenuItem.addActionListener(this);
3333 invertSequenceMenuItem.setLabel(
3334 MessageManager.getString("action.invert_sequence_selection"));
3335 invertSequenceMenuItem.addActionListener(this);
3336 invertColSel.setLabel(
3337 MessageManager.getString("action.invert_column_selection"));
3338 invertColSel.addActionListener(this);
3340 .setLabel(MessageManager.getString("action.undefine_groups"));
3341 deleteGroups.addActionListener(this);
3342 grpsFromSelection.setLabel(
3343 MessageManager.getString("action.make_groups_selection"));
3344 grpsFromSelection.addActionListener(this);
3345 createGroup.setLabel(MessageManager.getString("action.create_group"));
3346 createGroup.addActionListener(this);
3347 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3348 unGroup.addActionListener(this);
3350 annotationColumnSelection.setLabel(
3351 MessageManager.getString("action.select_by_annotation"));
3352 annotationColumnSelection.addActionListener(this);
3355 * Configure View menu items and actions
3357 newView.setLabel(MessageManager.getString("action.new_view"));
3358 newView.addActionListener(this);
3359 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3360 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3361 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3362 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3364 .setLabel(MessageManager.getString("label.selected_columns"));
3366 .setLabel(MessageManager.getString("label.selected_sequences"));
3367 hideAllButSelection.setLabel(
3368 MessageManager.getString("label.all_but_selected_region"));
3370 .setLabel(MessageManager.getString("label.selected_region"));
3371 showAllHidden.setLabel(
3372 MessageManager.getString("label.all_sequences_columns"));
3373 showColumns.addActionListener(this);
3374 showSeqs.addActionListener(this);
3375 hideColumns.addActionListener(this);
3376 hideSequences.addActionListener(this);
3377 hideAllButSelection.addActionListener(this);
3378 hideAllSelection.addActionListener(this);
3379 showAllHidden.addActionListener(this);
3381 .setLabel(MessageManager.getString("action.feature_settings"));
3382 featureSettings.addActionListener(this);
3383 sequenceFeatures.setLabel(
3384 MessageManager.getString("label.show_sequence_features"));
3385 sequenceFeatures.addItemListener(this);
3386 sequenceFeatures.setState(false);
3387 followMouseOverFlag.setLabel(
3388 MessageManager.getString("label.automatic_scrolling"));
3389 followMouseOverFlag.addItemListener(this);
3390 alProperties.addActionListener(this);
3392 .setLabel(MessageManager.getString("label.overview_window"));
3393 overviewMenuItem.addActionListener(this);
3396 * Configure Annotations menu items and actions
3398 annotationPanelMenuItem
3399 .setLabel(MessageManager.getString("label.show_annotations"));
3400 annotationPanelMenuItem.addItemListener(this);
3402 .setLabel(MessageManager.getString("label.group_consensus"));
3403 showGroupConservation
3404 .setLabel(MessageManager.getString("label.group_conservation"));
3405 showConsensusHistogram.setLabel(
3406 MessageManager.getString("label.show_consensus_histogram"));
3407 showSequenceLogo.setLabel(
3408 MessageManager.getString("label.show_consensus_logo"));
3409 normSequenceLogo.setLabel(
3410 MessageManager.getString("label.norm_consensus_logo"));
3411 applyAutoAnnotationSettings
3412 .setLabel(MessageManager.getString("label.apply_all_groups"));
3413 applyAutoAnnotationSettings.setState(true);
3414 Menu autoAnnMenu = new Menu(
3415 MessageManager.getString("label.autocalculated_annotation"));
3416 showGroupConsensus.addItemListener(this);
3417 showGroupConservation.addItemListener(this);
3418 showConsensusHistogram.addItemListener(this);
3419 showSequenceLogo.addItemListener(this);
3420 normSequenceLogo.addItemListener(this);
3421 applyAutoAnnotationSettings.addItemListener(this);
3422 showAlignmentAnnotations = new CheckboxMenuItem(
3423 MessageManager.getString("label.show_all_al_annotations"));
3424 showSequenceAnnotations = new CheckboxMenuItem(
3425 MessageManager.getString("label.show_all_seq_annotations"));
3426 sortAnnBySequence = new CheckboxMenuItem(
3427 MessageManager.getString("label.sort_annotations_by_sequence"));
3428 sortAnnByLabel = new CheckboxMenuItem(
3429 MessageManager.getString("label.sort_annotations_by_label"));
3430 showAutoFirst = new CheckboxMenuItem(
3431 MessageManager.getString("label.show_first"));
3432 showAutoFirst.setState(false); // pending applet parameter
3433 setShowAutoCalculatedAbove(showAutoFirst.getState());
3434 showAutoLast = new CheckboxMenuItem(
3435 MessageManager.getString("label.show_last"));
3436 showAutoLast.setState(!showAutoFirst.getState());
3437 showAlignmentAnnotations.addItemListener(this);
3438 showSequenceAnnotations.addItemListener(this);
3439 sortAnnBySequence.addItemListener(this);
3440 sortAnnByLabel.addItemListener(this);
3441 showAutoFirst.addItemListener(this);
3442 showAutoLast.addItemListener(this);
3445 * Configure Format menu items and actions
3447 font.setLabel(MessageManager.getString("action.font"));
3448 font.addActionListener(this);
3449 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3450 scaleAbove.setState(true);
3451 scaleAbove.setEnabled(false);
3452 scaleAbove.addItemListener(this);
3453 scaleLeft.setEnabled(false);
3454 scaleLeft.setState(true);
3455 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3456 scaleLeft.addItemListener(this);
3457 scaleRight.setEnabled(false);
3458 scaleRight.setState(true);
3459 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3460 scaleRight.addItemListener(this);
3461 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3462 viewBoxesMenuItem.setState(true);
3463 viewBoxesMenuItem.addItemListener(this);
3464 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3465 viewTextMenuItem.setState(true);
3466 viewTextMenuItem.addItemListener(this);
3468 .setLabel(MessageManager.getString("label.colour_text"));
3469 colourTextMenuItem.addItemListener(this);
3470 displayNonconservedMenuItem
3471 .setLabel(MessageManager.getString("label.show_non_conserved"));
3472 displayNonconservedMenuItem.addItemListener(this);
3473 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3474 wrapMenuItem.addItemListener(this);
3476 .setLabel(MessageManager.getString("action.show_gaps"));
3477 renderGapsMenuItem.setState(true);
3478 renderGapsMenuItem.addItemListener(this);
3479 centreColumnLabelFlag.setLabel(
3480 MessageManager.getString("label.centre_column_labels"));
3481 centreColumnLabelFlag.addItemListener(this);
3482 seqLimits.setState(true);
3484 MessageManager.getString("label.show_sequence_limits"));
3485 seqLimits.addItemListener(this);
3488 * Configure Colour menu items and actions
3490 applyToAllGroups.setLabel(
3491 MessageManager.getString("label.apply_colour_to_all_groups"));
3492 applyToAllGroups.setState(true);
3493 applyToAllGroups.addItemListener(this);
3494 clustalColour.setLabel(
3495 MessageManager.getString("label.colourScheme_clustal"));
3496 clustalColour.addActionListener(this);
3498 .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3499 zappoColour.addActionListener(this);
3500 taylorColour.setLabel(
3501 MessageManager.getString("label.colourScheme_taylor"));
3502 taylorColour.addActionListener(this);
3503 hydrophobicityColour.setLabel(
3504 MessageManager.getString("label.colourScheme_hydrophobic"));
3505 hydrophobicityColour.addActionListener(this);
3506 helixColour.setLabel(MessageManager
3507 .getString("label.colourScheme_helix_propensity"));
3508 helixColour.addActionListener(this);
3509 strandColour.setLabel(MessageManager
3510 .getString("label.colourScheme_strand_propensity"));
3511 strandColour.addActionListener(this);
3512 turnColour.setLabel(
3513 MessageManager.getString("label.colourScheme_turn_propensity"));
3514 turnColour.addActionListener(this);
3515 buriedColour.setLabel(
3516 MessageManager.getString("label.colourScheme_buried_index"));
3517 buriedColour.addActionListener(this);
3518 purinePyrimidineColour.setLabel(MessageManager
3519 .getString("label.colourScheme_purine/pyrimidine"));
3520 purinePyrimidineColour.addActionListener(this);
3521 // RNAInteractionColour.setLabel(MessageManager
3522 // .getString("label.rna_interaction"));
3523 // RNAInteractionColour.addActionListener(this);
3524 RNAHelixColour.setLabel(
3525 MessageManager.getString("label.colourScheme_rna_helices"));
3526 RNAHelixColour.addActionListener(this);
3528 .setLabel(MessageManager.getString("action.user_defined"));
3529 userDefinedColour.addActionListener(this);
3531 MessageManager.getString("label.colourScheme_%_identity"));
3532 PIDColour.addActionListener(this);
3533 BLOSUM62Colour.setLabel(
3534 MessageManager.getString("label.colourScheme_blosum62"));
3535 BLOSUM62Colour.addActionListener(this);
3536 tcoffeeColour.setLabel(
3537 MessageManager.getString("label.colourScheme_t-coffee_scores"));
3538 // it will be enabled only if a score file is provided
3539 tcoffeeColour.setEnabled(false);
3540 tcoffeeColour.addActionListener(this);
3541 conservationMenuItem
3542 .setLabel(MessageManager.getString("action.by_conservation"));
3543 conservationMenuItem.addItemListener(this);
3544 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3545 noColourmenuItem.addActionListener(this);
3546 abovePIDThreshold.setLabel(
3547 MessageManager.getString("label.above_identity_threshold"));
3548 abovePIDThreshold.addItemListener(this);
3549 nucleotideColour.setLabel(
3550 MessageManager.getString("label.colourScheme_nucleotide"));
3551 nucleotideColour.addActionListener(this);
3553 MessageManager.getString("label.modify_identity_threshold"));
3554 modifyPID.setEnabled(abovePIDThreshold.getState());
3555 modifyPID.addActionListener(this);
3556 modifyConservation.setLabel(MessageManager
3557 .getString("label.modify_conservation_threshold"));
3558 modifyConservation.setEnabled(conservationMenuItem.getState());
3559 modifyConservation.addActionListener(this);
3561 .setLabel(MessageManager.getString("action.by_annotation"));
3562 annotationColour.addActionListener(this);
3565 * Configure Calculate menu items and actions
3567 sortPairwiseMenuItem
3568 .setLabel(MessageManager.getString("action.by_pairwise_id"));
3569 sortPairwiseMenuItem.addActionListener(this);
3570 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3571 sortIDMenuItem.addActionListener(this);
3573 .setLabel(MessageManager.getString("action.by_length"));
3574 sortLengthMenuItem.addActionListener(this);
3575 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3576 sortGroupMenuItem.addActionListener(this);
3577 pairwiseAlignmentMenuItem.setLabel(
3578 MessageManager.getString("action.pairwise_alignment"));
3579 pairwiseAlignmentMenuItem.addActionListener(this);
3580 PCAMenuItem.setLabel(
3581 MessageManager.getString("label.principal_component_analysis"));
3582 PCAMenuItem.addActionListener(this);
3583 autoCalculate = new CheckboxMenuItem(
3584 MessageManager.getString("label.autocalculate_consensus"),
3586 averageDistanceTreeMenuItem.setLabel(
3587 MessageManager.getString("label.average_distance_identity"));
3588 averageDistanceTreeMenuItem.addActionListener(this);
3589 neighbourTreeMenuItem.setLabel(
3590 MessageManager.getString("label.neighbour_joining_identity"));
3591 neighbourTreeMenuItem.addActionListener(this);
3592 avDistanceTreeBlosumMenuItem.setLabel(
3593 MessageManager.getString("label.average_distance_blosum62"));
3594 avDistanceTreeBlosumMenuItem.addActionListener(this);
3595 njTreeBlosumMenuItem
3596 .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3597 njTreeBlosumMenuItem.addActionListener(this);
3599 .setLabel(MessageManager.getString("action.by_tree_order"));
3600 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3601 Menu calculateTreeMenu = new Menu(
3602 MessageManager.getString("action.calculate_tree"));
3603 autoCalculate.addItemListener(this);
3604 sortByTree.addItemListener(this);
3607 * Configure Help menu items and actions
3609 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3610 documentation.setLabel(MessageManager.getString("label.documentation"));
3611 documentation.addActionListener(this);
3612 about.setLabel(MessageManager.getString("label.about"));
3613 about.addActionListener(this);
3616 * Add top level menus to frame
3618 alignFrameMenuBar.add(fileMenu);
3619 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3620 alignFrameMenuBar.add(editMenu);
3621 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3622 alignFrameMenuBar.add(selectMenu);
3623 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3624 alignFrameMenuBar.add(viewMenu);
3625 Menu annotationsMenu = new Menu(
3626 MessageManager.getString("action.annotations"));
3627 alignFrameMenuBar.add(annotationsMenu);
3628 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3629 alignFrameMenuBar.add(formatMenu);
3630 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3631 alignFrameMenuBar.add(colourMenu);
3632 Menu calculateMenu = new Menu(
3633 MessageManager.getString("action.calculate"));
3634 alignFrameMenuBar.add(calculateMenu);
3635 alignFrameMenuBar.add(helpMenu);
3640 fileMenu.add(inputText);
3641 fileMenu.add(loadTree);
3642 fileMenu.add(loadAnnotations);
3643 fileMenu.addSeparator();
3644 fileMenu.add(outputTextboxMenu);
3645 fileMenu.add(outputFeatures);
3646 fileMenu.add(outputAnnotations);
3647 if (jalviewServletURL != null)
3649 fileMenu.add(loadApplication);
3651 fileMenu.addSeparator();
3652 fileMenu.add(closeMenuItem);
3657 editMenu.add(undoMenuItem);
3658 editMenu.add(redoMenuItem);
3661 pasteMenu.add(pasteNew);
3662 pasteMenu.add(pasteThis);
3663 editMenu.add(pasteMenu);
3664 editMenu.add(delete);
3665 editMenu.addSeparator();
3666 editMenu.add(remove2LeftMenuItem);
3667 editMenu.add(remove2RightMenuItem);
3668 editMenu.add(removeGappedColumnMenuItem);
3669 editMenu.add(removeAllGapsMenuItem);
3670 editMenu.add(removeRedundancyMenuItem);
3675 selectMenu.add(findMenuItem);
3676 selectMenu.addSeparator();
3677 selectMenu.add(selectAllSequenceMenuItem);
3678 selectMenu.add(deselectAllSequenceMenuItem);
3679 selectMenu.add(invertSequenceMenuItem);
3680 selectMenu.add(invertColSel);
3681 selectMenu.add(createGroup);
3682 selectMenu.add(unGroup);
3683 selectMenu.add(grpsFromSelection);
3684 selectMenu.add(deleteGroups);
3685 selectMenu.add(annotationColumnSelection);
3690 viewMenu.add(newView);
3691 viewMenu.addSeparator();
3692 showMenu.add(showColumns);
3693 showMenu.add(showSeqs);
3694 showMenu.add(showAllHidden);
3695 viewMenu.add(showMenu);
3696 hideMenu.add(hideColumns);
3697 hideMenu.add(hideSequences);
3698 hideMenu.add(hideAllSelection);
3699 hideMenu.add(hideAllButSelection);
3700 viewMenu.add(hideMenu);
3701 viewMenu.addSeparator();
3702 viewMenu.add(followMouseOverFlag);
3703 viewMenu.addSeparator();
3704 viewMenu.add(sequenceFeatures);
3705 viewMenu.add(featureSettings);
3706 viewMenu.addSeparator();
3707 viewMenu.add(alProperties);
3708 viewMenu.addSeparator();
3709 viewMenu.add(overviewMenuItem);
3714 annotationsMenu.add(annotationPanelMenuItem);
3715 annotationsMenu.addSeparator();
3716 annotationsMenu.add(showAlignmentAnnotations);
3717 annotationsMenu.add(showSequenceAnnotations);
3718 annotationsMenu.add(sortAnnBySequence);
3719 annotationsMenu.add(sortAnnByLabel);
3720 annotationsMenu.addSeparator();
3721 autoAnnMenu.add(showAutoFirst);
3722 autoAnnMenu.add(showAutoLast);
3723 autoAnnMenu.addSeparator();
3724 autoAnnMenu.add(applyAutoAnnotationSettings);
3725 autoAnnMenu.add(showConsensusHistogram);
3726 autoAnnMenu.add(showSequenceLogo);
3727 autoAnnMenu.add(normSequenceLogo);
3728 autoAnnMenu.addSeparator();
3729 autoAnnMenu.add(showGroupConservation);
3730 autoAnnMenu.add(showGroupConsensus);
3731 annotationsMenu.add(autoAnnMenu);
3736 formatMenu.add(font);
3737 formatMenu.add(seqLimits);
3738 formatMenu.add(wrapMenuItem);
3739 formatMenu.add(scaleAbove);
3740 formatMenu.add(scaleLeft);
3741 formatMenu.add(scaleRight);
3742 formatMenu.add(viewBoxesMenuItem);
3743 formatMenu.add(viewTextMenuItem);
3744 formatMenu.add(colourTextMenuItem);
3745 formatMenu.add(displayNonconservedMenuItem);
3746 formatMenu.add(renderGapsMenuItem);
3747 formatMenu.add(centreColumnLabelFlag);
3752 colourMenu.add(applyToAllGroups);
3753 colourMenu.addSeparator();
3754 colourMenu.add(noColourmenuItem);
3755 colourMenu.add(clustalColour);
3756 colourMenu.add(BLOSUM62Colour);
3757 colourMenu.add(PIDColour);
3758 colourMenu.add(zappoColour);
3759 colourMenu.add(taylorColour);
3760 colourMenu.add(hydrophobicityColour);
3761 colourMenu.add(helixColour);
3762 colourMenu.add(strandColour);
3763 colourMenu.add(turnColour);
3764 colourMenu.add(buriedColour);
3765 colourMenu.add(nucleotideColour);
3766 colourMenu.add(purinePyrimidineColour);
3767 // colourMenu.add(RNAInteractionColour);
3768 colourMenu.add(tcoffeeColour);
3769 colourMenu.add(userDefinedColour);
3770 colourMenu.addSeparator();
3771 colourMenu.add(conservationMenuItem);
3772 colourMenu.add(modifyConservation);
3773 colourMenu.add(abovePIDThreshold);
3774 colourMenu.add(modifyPID);
3775 colourMenu.add(annotationColour);
3776 colourMenu.add(RNAHelixColour);
3781 sortMenu.add(sortIDMenuItem);
3782 sortMenu.add(sortLengthMenuItem);
3783 sortMenu.add(sortByTreeMenu);
3784 sortMenu.add(sortGroupMenuItem);
3785 sortMenu.add(sortPairwiseMenuItem);
3786 calculateMenu.add(sortMenu);
3787 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3788 calculateTreeMenu.add(neighbourTreeMenuItem);
3789 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3790 calculateTreeMenu.add(njTreeBlosumMenuItem);
3791 calculateMenu.add(calculateTreeMenu);
3792 calculateMenu.addSeparator();
3793 calculateMenu.add(pairwiseAlignmentMenuItem);
3794 calculateMenu.add(PCAMenuItem);
3795 calculateMenu.add(autoCalculate);
3796 calculateMenu.add(sortByTree);
3801 helpMenu.add(documentation);
3802 helpMenu.add(about);
3807 statusBar.setBackground(Color.white);
3808 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3809 statusBar.setText(MessageManager.getString("label.status_bar"));
3810 this.add(statusBar, BorderLayout.SOUTH);
3814 public void setStatus(String string)
3816 statusBar.setText(string);
3819 MenuItem featureSettings = new MenuItem();
3821 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3823 MenuItem annotationColour = new MenuItem();
3825 MenuItem annotationColumnSelection = new MenuItem();
3827 MenuItem invertColSel = new MenuItem();
3829 MenuItem showColumns = new MenuItem();
3831 MenuItem showSeqs = new MenuItem();
3833 MenuItem hideColumns = new MenuItem();
3835 MenuItem hideSequences = new MenuItem();
3837 MenuItem hideAllButSelection = new MenuItem();
3839 MenuItem hideAllSelection = new MenuItem();
3841 MenuItem showAllHidden = new MenuItem();
3843 MenuItem newView = new MenuItem();
3845 private CheckboxMenuItem showAlignmentAnnotations;
3847 private CheckboxMenuItem showSequenceAnnotations;
3849 private CheckboxMenuItem sortAnnBySequence;
3851 private CheckboxMenuItem sortAnnByLabel;
3853 private CheckboxMenuItem showAutoFirst;
3855 private CheckboxMenuItem showAutoLast;
3857 private SplitFrame splitFrame;
3860 * Attach the alignFrame panels after embedding menus, if necessary. This used
3861 * to be called setEmbedded, but is now creates the dropdown menus in a
3862 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3864 * @param reallyEmbedded
3865 * true to attach the view to the applet area on the page rather than
3868 public void createAlignFrameWindow(boolean reallyEmbedded)
3872 embedAlignFrameInApplet(viewport.applet);
3877 // test and embed menu bar if necessary.
3879 if (embedMenuIfNeeded(alignPanel))
3882 * adjust for status bar height too. ? pointless as overridden by layout
3885 alignPanel.setSize(getSize().width,
3886 getSize().height - statusBar.getHeight());
3888 add(statusBar, BorderLayout.SOUTH);
3889 add(alignPanel, BorderLayout.CENTER);
3890 // and register with the applet so it can pass external API calls to us
3891 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3897 * Add the components of this AlignFrame to the applet container.
3901 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3904 // Explicitly build the embedded menu panel for the on-page applet
3906 // view cannot be closed if its actually on the page
3907 fileMenu.remove(closeMenuItem);
3908 fileMenu.remove(3); // Remove Separator
3909 // construct embedded menu, using default font
3910 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3911 // and actually add the components to the applet area
3912 theApplet.setLayout(new BorderLayout());
3913 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3914 theApplet.add(statusBar, BorderLayout.SOUTH);
3915 // TODO should size be left to the layout manager?
3916 alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3917 - embeddedMenu.getHeight() - statusBar.getHeight());
3918 theApplet.add(alignPanel, BorderLayout.CENTER);
3919 final AlignFrame me = this;
3920 theApplet.addFocusListener(new FocusListener()
3924 public void focusLost(FocusEvent e)
3926 if (theApplet.currentAlignFrame == me)
3928 theApplet.currentAlignFrame = null;
3933 public void focusGained(FocusEvent e)
3935 theApplet.currentAlignFrame = me;
3938 theApplet.validate();
3942 * create a new binding between structures in an existing jmol viewer instance
3943 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3944 * this does not open a new Jmol window, or modify the display of the
3945 * structures in the original jmol window. Note This method doesn't work
3946 * without an additional javascript library to exchange messages between the
3947 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3950 * JmolViewer instance
3951 * @param sequenceIds
3952 * - sequence Ids to search for associations
3954 public SequenceStructureBinding addStructureViewInstance(
3955 Object jmolviewer, String[] sequenceIds)
3957 Viewer viewer = null;
3960 viewer = (Viewer) jmolviewer;
3961 } catch (ClassCastException ex)
3964 "Unsupported viewer object :" + jmolviewer.getClass());
3968 System.err.println("Can't use this object as a structure viewer:"
3969 + jmolviewer.getClass());
3972 SequenceI[] seqs = null;
3973 if (sequenceIds == null || sequenceIds.length == 0)
3975 seqs = viewport.getAlignment().getSequencesArray();
3979 Vector sqi = new Vector();
3980 AlignmentI al = viewport.getAlignment();
3981 for (int sid = 0; sid < sequenceIds.length; sid++)
3983 SequenceI sq = al.findName(sequenceIds[sid]);
3991 seqs = new SequenceI[sqi.size()];
3992 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3994 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4002 AAStructureBindingModel jmv = null;
4003 // TODO: search for a jmv that involves viewer
4005 { // create a new viewer/jalview binding.
4006 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4013 * bind a pdb file to a sequence in the current view
4016 * - sequenceId within the dataset.
4017 * @param pdbEntryString
4018 * - the short name for the PDB file
4020 * - pdb file - either a URL or a valid PDB file.
4021 * @return true if binding was as success TODO: consider making an exception
4022 * structure for indicating when PDB parsing or sequenceId location
4025 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4028 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4029 boolean needtoadd = false;
4030 if (toaddpdb != null)
4032 Vector pdbe = toaddpdb.getAllPDBEntries();
4033 PDBEntry pdbentry = null;
4034 if (pdbe != null && pdbe.size() > 0)
4036 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4038 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4039 if (!pdbentry.getId().equals(pdbEntryString)
4040 && !pdbentry.getFile().equals(pdbFile))
4050 if (pdbentry == null)
4052 pdbentry = new PDBEntry();
4053 pdbentry.setId(pdbEntryString);
4054 pdbentry.setFile(pdbFile);
4055 needtoadd = true; // add this new entry to sequence.
4057 // resolve data source
4058 // TODO: this code should be a refactored to an io package
4059 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4061 if (protocol == null)
4067 pdbentry.setProperty("protocol", protocol);
4068 toaddpdb.addPDBId(pdbentry);
4069 alignPanel.getStructureSelectionManager()
4070 .registerPDBEntry(pdbentry);
4076 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4080 Vector sequences = new Vector();
4081 for (int i = 0; i < seqs.length; i++)
4083 if (seqs[i] != null)
4086 .addElement(new Object[]
4087 { seqs[i], (chains != null) ? chains[i] : null });
4090 seqs = new SequenceI[sequences.size()];
4091 chains = new String[sequences.size()];
4092 for (int i = 0, isize = sequences.size(); i < isize; i++)
4094 Object[] oj = (Object[]) sequences.elementAt(i);
4096 seqs[i] = (SequenceI) oj[0];
4097 chains[i] = (String) oj[1];
4100 return new Object[] { seqs, chains };
4104 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4105 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4107 // Scrub any null sequences from the array
4108 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4109 seqs = (SequenceI[]) sqch[0];
4110 chains = (String[]) sqch[1];
4111 if (seqs == null || seqs.length == 0)
4114 "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4116 if (protocol == null)
4118 String sourceType = (String) pdb.getProperty("protocol");
4121 protocol = DataSourceType.valueOf(sourceType);
4122 } catch (IllegalArgumentException e)
4126 if (protocol == null)
4128 System.err.println("Couldn't work out protocol to open structure: "
4133 if (applet.useXtrnalSviewer)
4135 // register the association(s) and quit, don't create any windows.
4136 if (StructureSelectionManager.getStructureSelectionManager(applet)
4137 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4139 System.err.println("Failed to map " + pdb.getFile() + " ("
4140 + protocol + ") to any sequences");
4144 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4146 // can only do alignments with Jmol
4147 // find the last jmol window assigned to this alignment
4148 AppletJmol ajm = null, tajm;
4149 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4150 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4152 tajm = (AppletJmol) jmols.elementAt(i);
4153 if (tajm.ap.alignFrame == this)
4162 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4163 // try and add the pdb structure
4168 // otherwise, create a new window
4169 if (applet.jmolAvailable)
4171 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4172 applet.lastFrameX += 40;
4173 applet.lastFrameY += 40;
4177 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4182 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4183 SequenceI[][] seqs, String[][] chains, String[] protocols)
4185 // TODO Auto-generated method stub
4186 System.err.println("Aligned Structure View: Not yet implemented.");
4190 * modify the current selection, providing the user has not made a selection
4194 * - sequences from this alignment
4196 * - columns to be selected on the alignment
4198 public void select(SequenceGroup sel, ColumnSelection csel,
4199 HiddenColumns hidden)
4201 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4204 public void scrollTo(int row, int column)
4206 alignPanel.seqPanel.scrollTo(row, column);
4209 public void scrollToRow(int row)
4211 alignPanel.seqPanel.scrollToRow(row);
4214 public void scrollToColumn(int column)
4216 alignPanel.seqPanel.scrollToColumn(column);
4220 * @return the alignments unique ID.
4222 public String getSequenceSetId()
4224 return viewport.getSequenceSetId();
4228 * Load the (T-Coffee) score file from the specified url
4231 * File/URL/T-COFFEE score file contents
4232 * @throws IOException
4233 * @return true if alignment was annotated with data from source
4235 public boolean loadScoreFile(String source) throws IOException
4238 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4239 AppletFormatAdapter.checkProtocol(source));
4240 if (!file.isValid())
4242 // TODO: raise dialog for gui
4243 System.err.println("Problems parsing T-Coffee scores: "
4244 + file.getWarningMessage());
4245 System.err.println("Origin was:\n" + source);
4250 * check that the score matrix matches the alignment dimensions
4253 if ((aln = viewport.getAlignment()) != null
4254 && (aln.getHeight() != file.getHeight()
4255 || aln.getWidth() != file.getWidth()))
4257 // TODO: raise a dialog box here rather than bomb out.
4259 "The scores matrix does not match the alignment dimensions");
4263 // TODO add parameter to indicate if matching should be done
4264 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4266 alignPanel.fontChanged();
4267 tcoffeeColour.setEnabled(true);
4268 // switch to this color
4269 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4274 System.err.println("Problems resolving T-Coffee scores:");
4275 if (file.getWarningMessage() != null)
4277 System.err.println(file.getWarningMessage());
4283 public SplitFrame getSplitFrame()
4285 return this.splitFrame;
4288 public void setSplitFrame(SplitFrame sf)
4290 this.splitFrame = sf;
4293 // may not need this
4295 public void setShowSeqFeatures(boolean b)
4297 // showSeqFeatures.setSelected(b);
4298 viewport.setShowSequenceFeatures(b);
4303 public void setMenusForViewport()
4305 // setMenusFromViewport(viewport);
4310 public void refreshFeatureUI(boolean enableIfNecessary)
4312 if (enableIfNecessary)
4314 sequenceFeatures.setState(true);
4315 alignPanel.av.setShowSequenceFeatures(true);
4320 public FeatureSettingsControllerI getFeatureSettingsUI()
4322 return alignPanel.av.featureSettings;