2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
110 import java.net.URLEncoder;
111 import java.util.Arrays;
112 import java.util.Deque;
113 import java.util.HashMap;
114 import java.util.List;
115 import java.util.Map;
116 import java.util.StringTokenizer;
117 import java.util.Vector;
119 import org.jmol.viewer.Viewer;
121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
122 ItemListener, KeyListener, AlignViewControllerGuiI
124 public AlignViewControllerI avc;
126 public AlignmentPanel alignPanel;
128 public AlignViewport viewport;
130 // width and height may be overridden by applet parameters
131 int frameWidth = 700;
133 int frameHeight = 500;
135 String jalviewServletURL;
138 * Flag for showing autocalculated consensus above or below other consensus
141 private boolean showAutoCalculatedAbove;
143 private SequenceAnnotationOrder annotationSortOrder;
146 * Constructor that creates the frame and adds it to the display.
153 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156 this(al, applet, title, embedded, true);
160 * Constructor that optionally allows the frame to be displayed or only
167 * @param addToDisplay
169 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
170 boolean embedded, boolean addToDisplay)
172 this(al, null, null, applet, title, embedded, addToDisplay);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 HiddenColumns hidden, JalviewLite applet,
177 String title, boolean embedded)
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet,
184 String title, boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
238 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
239 followMouseOverFlag.setState(viewport.isFollowHighlight());
240 showGroupConsensus.setState(viewport.isShowGroupConsensus());
241 showGroupConservation.setState(viewport.isShowGroupConservation());
242 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
243 showSequenceLogo.setState(viewport.isShowSequenceLogo());
244 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
245 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
246 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
247 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
248 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showAlignmentAnnotations.setState(true);
250 showSequenceAnnotations.setState(false);
252 seqLimits.setState(viewport.getShowJVSuffix());
256 String param = applet.getParameter("sortBy");
259 if (param.equalsIgnoreCase("Id"))
261 sortIDMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Pairwise Identity"))
265 sortPairwiseMenuItem_actionPerformed();
267 else if (param.equalsIgnoreCase("Length"))
269 sortLengthMenuItem_actionPerformed();
273 param = applet.getParameter("wrap");
276 if (param.equalsIgnoreCase("true"))
278 wrapMenuItem.setState(true);
279 wrapMenuItem_actionPerformed();
282 param = applet.getParameter("centrecolumnlabels");
285 centreColumnLabelFlag.setState(true);
286 centreColumnLabelFlag_stateChanged();
290 if (viewport.getAlignment().isNucleotide())
292 conservationMenuItem.setEnabled(false);
293 clustalColour.setEnabled(false);
294 BLOSUM62Colour.setEnabled(false);
295 zappoColour.setEnabled(false);
296 taylorColour.setEnabled(false);
297 hydrophobicityColour.setEnabled(false);
298 helixColour.setEnabled(false);
299 strandColour.setEnabled(false);
300 turnColour.setEnabled(false);
301 buriedColour.setEnabled(false);
302 viewport.updateStrucConsensus(alignPanel);
303 if (viewport.getAlignment().hasRNAStructure())
305 RNAHelixColour.setEnabled(true);
309 RNAHelixColour.setEnabled(false);
314 RNAHelixColour.setEnabled(false);
315 purinePyrimidineColour.setEnabled(false);
316 nucleotideColour.setEnabled(false);
318 // Some JVMS send keyevents to Top frame or lowest panel,
319 // Havent worked out why yet. So add to both this frame and seqCanvas for
321 this.addKeyListener(this);
322 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
323 alignPanel.idPanel.idCanvas.addKeyListener(this);
324 alignPanel.scalePanel.addKeyListener(this);
325 alignPanel.annotationPanel.addKeyListener(this);
326 alignPanel.annotationPanelHolder.addKeyListener(this);
327 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
328 alignPanel.alabels.addKeyListener(this);
330 setAnnotationsVisibility();
334 addToDisplay(embedded);
341 public void addToDisplay(boolean embedded)
343 createAlignFrameWindow(embedded);
345 alignPanel.adjustAnnotationHeight();
346 alignPanel.paintAlignment(true);
349 public AlignViewport getAlignViewport()
354 public SeqCanvas getSeqcanvas()
356 return alignPanel.seqPanel.seqCanvas;
360 * Load a features file onto the alignment
363 * file URL, content, or other resolvable path
365 * is protocol for accessing data referred to by file
368 public boolean parseFeaturesFile(String file, DataSourceType type)
370 return parseFeaturesFile(file, type, true);
374 * Load a features file onto the alignment
377 * file URL, content, or other resolvable path
379 * is protocol for accessing data referred to by file
380 * @param autoenabledisplay
381 * when true, display features flag will be automatically enabled if
382 * features are loaded
383 * @return true if data parsed as a features file
385 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
386 boolean autoenabledisplay)
388 boolean featuresFile = false;
391 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
392 .getFeatureRenderer().getFeatureColours();
393 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
394 "relaxedidmatch", false);
395 featuresFile = new FeaturesFile(file, sourceType).parse(
396 viewport.getAlignment(), colours, true, relaxedIdMatching);
397 } catch (Exception ex)
399 ex.printStackTrace();
404 if (autoenabledisplay)
406 viewport.setShowSequenceFeatures(true);
407 sequenceFeatures.setState(true);
409 if (alignPanel.seqPanel.seqCanvas.fr != null)
411 // update the min/max ranges where necessary
412 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
414 if (viewport.featureSettings != null)
416 viewport.featureSettings.refreshTable();
418 alignPanel.paintAlignment(true);
419 statusBar.setText(MessageManager
420 .getString("label.successfully_added_features_alignment"));
426 public void keyPressed(KeyEvent evt)
428 ViewportRanges ranges = viewport.getRanges();
430 if (viewport.cursorMode
431 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
432 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
433 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
434 && Character.isDigit(evt.getKeyChar()))
436 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
439 switch (evt.getKeyCode())
441 case 27: // escape key
442 deselectAllSequenceMenuItem_actionPerformed();
444 alignPanel.alabels.cancelDrag();
447 if (evt.isControlDown() || evt.isMetaDown())
449 cut_actionPerformed();
453 if (viewport.cursorMode && !evt.isControlDown())
455 alignPanel.seqPanel.setCursorColumn();
457 if (evt.isControlDown() || evt.isMetaDown())
459 copy_actionPerformed();
463 if (evt.isControlDown())
465 paste(evt.isShiftDown());
469 if (evt.isControlDown() || evt.isMetaDown())
471 selectAllSequenceMenuItem_actionPerformed();
474 case KeyEvent.VK_DOWN:
475 if (viewport.cursorMode)
477 alignPanel.seqPanel.moveCursor(0, 1);
481 moveSelectedSequences(false);
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.moveCursor(0, -1);
492 moveSelectedSequences(true);
496 case KeyEvent.VK_LEFT:
497 if (evt.isAltDown() || !viewport.cursorMode)
499 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
503 alignPanel.seqPanel.moveCursor(-1, 0);
507 case KeyEvent.VK_RIGHT:
508 if (evt.isAltDown() || !viewport.cursorMode)
510 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
514 alignPanel.seqPanel.moveCursor(1, 0);
518 case KeyEvent.VK_SPACE:
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
522 || evt.isShiftDown() || evt.isAltDown());
526 case KeyEvent.VK_DELETE:
527 case KeyEvent.VK_BACK_SPACE:
528 if (viewport.cursorMode)
530 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
531 || evt.isShiftDown() || evt.isAltDown());
535 cut_actionPerformed();
536 alignPanel.seqPanel.seqCanvas.repaint();
541 if (viewport.cursorMode)
543 alignPanel.seqPanel.setCursorRow();
547 if (viewport.cursorMode)
549 alignPanel.seqPanel.setCursorPosition();
553 case KeyEvent.VK_ENTER:
554 case KeyEvent.VK_COMMA:
555 if (viewport.cursorMode)
557 alignPanel.seqPanel.setCursorRowAndColumn();
562 if (viewport.cursorMode)
564 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
568 if (viewport.cursorMode)
570 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
575 viewport.cursorMode = !viewport.cursorMode;
576 statusBar.setText(MessageManager.formatMessage(
577 "label.keyboard_editing_mode",
578 new String[] { (viewport.cursorMode ? "on" : "off") }));
579 if (viewport.cursorMode)
581 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
582 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
587 if (evt.isControlDown())
589 findMenuItem_actionPerformed();
595 boolean toggleSeqs = !evt.isControlDown();
596 boolean toggleCols = !evt.isShiftDown();
597 toggleHiddenRegions(toggleSeqs, toggleCols);
601 case KeyEvent.VK_PAGE_UP:
605 case KeyEvent.VK_PAGE_DOWN:
610 if (evt.isControlDown())
612 undoMenuItem_actionPerformed();
617 if (evt.isControlDown())
619 redoMenuItem_actionPerformed();
624 if (evt.isControlDown())
631 if (evt.isControlDown())
633 trimAlignment(false);
638 if (evt.isControlDown())
640 if (evt.isShiftDown())
642 this.removeAllGapsMenuItem_actionPerformed();
646 removeGappedColumnMenuItem_actionPerformed();
651 if (evt.isControlDown())
655 invertColSel_actionPerformed();
659 invertSequenceMenuItem_actionPerformed();
665 if (evt.isControlDown())
667 if (evt.isShiftDown())
669 this.unGroup_actionPerformed();
673 this.createGroup_actionPerformed();
679 if (evt.isControlDown())
681 this.deleteGroups_actionPerformed();
686 if (evt.isControlDown())
693 alignPanel.paintAlignment(true);
697 * called by key handler and the hide all/show all menu items
702 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
704 boolean hide = false;
705 SequenceGroup sg = viewport.getSelectionGroup();
706 if (!toggleSeqs && !toggleCols)
708 // Hide everything by the current selection - this is a hack - we do the
709 // invert and then hide
710 // first check that there will be visible columns after the invert.
711 if (viewport.hasSelectedColumns()
712 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
715 // now invert the sequence set, if required - empty selection implies
716 // that no hiding is required.
719 invertSequenceMenuItem_actionPerformed();
720 sg = viewport.getSelectionGroup();
724 viewport.expandColSelection(sg, true);
725 // finally invert the column selection and get the new sequence
726 // selection and indicate it should be hidden.
727 invertColSel_actionPerformed();
734 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
737 viewport.hideAllSelectedSeqs();
739 else if (!(toggleCols && viewport.hasSelectedColumns()))
741 viewport.showAllHiddenSeqs();
747 if (viewport.hasSelectedColumns())
749 viewport.hideSelectedColumns();
752 viewport.setSelectionGroup(sg);
757 viewport.showAllHiddenColumns();
759 viewport.sendSelection();
764 public void keyReleased(KeyEvent evt)
769 public void keyTyped(KeyEvent evt)
774 public void itemStateChanged(ItemEvent evt)
776 final Object source = evt.getSource();
777 if (source == displayNonconservedMenuItem)
779 displayNonconservedMenuItem_actionPerformed();
781 else if (source == colourTextMenuItem)
783 colourTextMenuItem_actionPerformed();
785 else if (source == wrapMenuItem)
787 wrapMenuItem_actionPerformed();
789 else if (source == scaleAbove)
791 viewport.setScaleAboveWrapped(scaleAbove.getState());
793 else if (source == scaleLeft)
795 viewport.setScaleLeftWrapped(scaleLeft.getState());
797 else if (source == scaleRight)
799 viewport.setScaleRightWrapped(scaleRight.getState());
801 else if (source == seqLimits)
803 seqLimits_itemStateChanged();
805 else if (source == viewBoxesMenuItem)
807 viewport.setShowBoxes(viewBoxesMenuItem.getState());
809 else if (source == viewTextMenuItem)
811 viewport.setShowText(viewTextMenuItem.getState());
813 else if (source == renderGapsMenuItem)
815 viewport.setRenderGaps(renderGapsMenuItem.getState());
817 else if (source == annotationPanelMenuItem)
819 boolean showAnnotations = annotationPanelMenuItem.getState();
820 showAlignmentAnnotations.setEnabled(showAnnotations);
821 showSequenceAnnotations.setEnabled(showAnnotations);
822 viewport.setShowAnnotation(showAnnotations);
823 alignPanel.setAnnotationVisible(showAnnotations);
825 else if (source == sequenceFeatures)
827 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
828 alignPanel.seqPanel.seqCanvas.repaint();
830 else if (source == showAlignmentAnnotations)
832 setAnnotationsVisibility();
834 else if (source == showSequenceAnnotations)
836 setAnnotationsVisibility();
838 else if (source == sortAnnBySequence)
840 boolean newState = sortAnnBySequence.getState();
841 sortAnnByLabel.setState(false);
842 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
843 : SequenceAnnotationOrder.NONE);
844 setViewportAnnotationOrder();
846 else if (source == sortAnnByLabel)
848 boolean newState = sortAnnByLabel.getState();
849 sortAnnBySequence.setState(false);
850 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
851 : SequenceAnnotationOrder.NONE);
852 setViewportAnnotationOrder();
854 else if (source == showAutoFirst)
856 showAutoLast.setState(!showAutoFirst.getState());
857 setShowAutoCalculatedAbove(showAutoFirst.getState());
858 setViewportAnnotationOrder();
860 else if (source == showAutoLast)
862 showAutoFirst.setState(!showAutoLast.getState());
863 setShowAutoCalculatedAbove(showAutoFirst.getState());
864 setViewportAnnotationOrder();
866 else if (source == conservationMenuItem)
868 conservationMenuItem_actionPerformed();
870 else if (source == abovePIDThreshold)
872 abovePIDThreshold_actionPerformed();
874 else if (source == applyToAllGroups)
876 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
878 else if (source == autoCalculate)
880 viewport.autoCalculateConsensus = autoCalculate.getState();
882 else if (source == sortByTree)
884 viewport.sortByTree = sortByTree.getState();
886 else if (source == this.centreColumnLabelFlag)
888 centreColumnLabelFlag_stateChanged();
890 else if (source == this.followMouseOverFlag)
892 mouseOverFlag_stateChanged();
894 else if (source == showGroupConsensus)
896 showGroupConsensus_actionPerformed();
898 else if (source == showGroupConservation)
900 showGroupConservation_actionPerformed();
902 else if (source == showSequenceLogo)
904 showSequenceLogo_actionPerformed();
906 else if (source == normSequenceLogo)
908 normSequenceLogo_actionPerformed();
910 else if (source == showConsensusHistogram)
912 showConsensusHistogram_actionPerformed();
914 else if (source == applyAutoAnnotationSettings)
916 applyAutoAnnotationSettings_actionPerformed();
918 alignPanel.paintAlignment(true);
922 * Set the visibility state of sequence-related and/or alignment-related
923 * annotations depending on checkbox selections, and repaint.
927 private void setAnnotationsVisibility()
929 boolean showForAlignment = showAlignmentAnnotations.getState();
930 boolean showForSequences = showSequenceAnnotations.getState();
931 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
933 for (AlignmentAnnotation aa : alignPanel.getAlignment()
934 .getAlignmentAnnotation())
936 boolean visible = (aa.sequenceRef == null ? showForAlignment
938 aa.visible = visible;
941 alignPanel.validateAnnotationDimensions(true);
946 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
948 this.annotationSortOrder = order;
952 * Set flags on the viewport that control annotation ordering
954 private void setViewportAnnotationOrder()
956 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
958 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
961 private void setShowAutoCalculatedAbove(boolean showAbove)
963 this.showAutoCalculatedAbove = showAbove;
966 private void mouseOverFlag_stateChanged()
968 viewport.setFollowHighlight(followMouseOverFlag.getState());
969 // TODO: could kick the scrollTo mechanism to reset view for current
973 private void centreColumnLabelFlag_stateChanged()
975 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
976 this.alignPanel.annotationPanel.repaint();
980 public void actionPerformed(ActionEvent evt)
982 viewport.applet.currentAlignFrame = this;
984 Object source = evt.getSource();
986 if (source == inputText)
988 inputText_actionPerformed();
990 else if (source == loadTree)
992 loadTree_actionPerformed();
994 else if (source == loadApplication)
996 launchFullApplication();
998 else if (source == loadAnnotations)
1002 else if (source == outputAnnotations)
1004 outputAnnotations(true);
1006 else if (source == outputFeatures)
1008 outputFeatures(true, "Jalview");
1010 else if (source == closeMenuItem)
1012 closeMenuItem_actionPerformed();
1014 else if (source == copy)
1016 copy_actionPerformed();
1018 else if (source == undoMenuItem)
1020 undoMenuItem_actionPerformed();
1022 else if (source == redoMenuItem)
1024 redoMenuItem_actionPerformed();
1026 else if (source == inputText)
1028 inputText_actionPerformed();
1030 else if (source == closeMenuItem)
1032 closeMenuItem_actionPerformed();
1034 else if (source == undoMenuItem)
1036 undoMenuItem_actionPerformed();
1038 else if (source == redoMenuItem)
1040 redoMenuItem_actionPerformed();
1042 else if (source == copy)
1044 copy_actionPerformed();
1046 else if (source == pasteNew)
1048 pasteNew_actionPerformed();
1050 else if (source == pasteThis)
1052 pasteThis_actionPerformed();
1054 else if (source == cut)
1056 cut_actionPerformed();
1058 else if (source == delete)
1060 delete_actionPerformed();
1062 else if (source == createGroup)
1064 createGroup_actionPerformed();
1066 else if (source == unGroup)
1068 unGroup_actionPerformed();
1070 else if (source == grpsFromSelection)
1072 makeGrpsFromSelection_actionPerformed();
1074 else if (source == deleteGroups)
1076 deleteGroups_actionPerformed();
1078 else if (source == selectAllSequenceMenuItem)
1080 selectAllSequenceMenuItem_actionPerformed();
1082 else if (source == deselectAllSequenceMenuItem)
1084 deselectAllSequenceMenuItem_actionPerformed();
1086 else if (source == invertSequenceMenuItem)
1088 invertSequenceMenuItem_actionPerformed();
1089 // uncomment to slave sequence selections in split frame
1090 // viewport.sendSelection();
1092 else if (source == invertColSel)
1094 viewport.invertColumnSelection();
1095 alignPanel.paintAlignment(true);
1096 viewport.sendSelection();
1098 else if (source == remove2LeftMenuItem)
1100 trimAlignment(true);
1102 else if (source == remove2RightMenuItem)
1104 trimAlignment(false);
1106 else if (source == removeGappedColumnMenuItem)
1108 removeGappedColumnMenuItem_actionPerformed();
1110 else if (source == removeAllGapsMenuItem)
1112 removeAllGapsMenuItem_actionPerformed();
1114 else if (source == findMenuItem)
1116 findMenuItem_actionPerformed();
1118 else if (source == font)
1120 new FontChooser(alignPanel);
1122 else if (source == newView)
1126 else if (source == showColumns)
1128 viewport.showAllHiddenColumns();
1129 alignPanel.paintAlignment(true);
1130 viewport.sendSelection();
1132 else if (source == showSeqs)
1134 viewport.showAllHiddenSeqs();
1135 alignPanel.paintAlignment(true);
1136 // uncomment if we want to slave sequence selections in split frame
1137 // viewport.sendSelection();
1139 else if (source == hideColumns)
1141 viewport.hideSelectedColumns();
1142 alignPanel.paintAlignment(true);
1143 viewport.sendSelection();
1145 else if (source == hideSequences
1146 && viewport.getSelectionGroup() != null)
1148 viewport.hideAllSelectedSeqs();
1149 alignPanel.paintAlignment(true);
1150 // uncomment if we want to slave sequence selections in split frame
1151 // viewport.sendSelection();
1153 else if (source == hideAllButSelection)
1155 toggleHiddenRegions(false, false);
1156 alignPanel.paintAlignment(true);
1157 viewport.sendSelection();
1159 else if (source == hideAllSelection)
1161 SequenceGroup sg = viewport.getSelectionGroup();
1162 viewport.expandColSelection(sg, false);
1163 viewport.hideAllSelectedSeqs();
1164 viewport.hideSelectedColumns();
1165 alignPanel.paintAlignment(true);
1166 viewport.sendSelection();
1168 else if (source == showAllHidden)
1170 viewport.showAllHiddenColumns();
1171 viewport.showAllHiddenSeqs();
1172 alignPanel.paintAlignment(true);
1173 viewport.sendSelection();
1175 else if (source == showGroupConsensus)
1177 showGroupConsensus_actionPerformed();
1179 else if (source == showGroupConservation)
1181 showGroupConservation_actionPerformed();
1183 else if (source == showSequenceLogo)
1185 showSequenceLogo_actionPerformed();
1187 else if (source == normSequenceLogo)
1189 normSequenceLogo_actionPerformed();
1191 else if (source == showConsensusHistogram)
1193 showConsensusHistogram_actionPerformed();
1195 else if (source == applyAutoAnnotationSettings)
1197 applyAutoAnnotationSettings_actionPerformed();
1199 else if (source == featureSettings)
1201 new FeatureSettings(alignPanel);
1203 else if (source == alProperties)
1205 StringBuffer contents = new jalview.io.AlignmentProperties(
1206 viewport.getAlignment()).formatAsString();
1207 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1208 cap.setText(contents.toString());
1209 Frame frame = new Frame();
1211 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1212 "label.alignment_properties", new String[] { getTitle() }),
1215 else if (source == overviewMenuItem)
1217 overviewMenuItem_actionPerformed();
1219 else if (source == noColourmenuItem)
1223 else if (source == clustalColour)
1225 abovePIDThreshold.setState(false);
1226 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1228 else if (source == zappoColour)
1230 changeColour(new ZappoColourScheme());
1232 else if (source == taylorColour)
1234 changeColour(new TaylorColourScheme());
1236 else if (source == hydrophobicityColour)
1238 changeColour(new HydrophobicColourScheme());
1240 else if (source == helixColour)
1242 changeColour(new HelixColourScheme());
1244 else if (source == strandColour)
1246 changeColour(new StrandColourScheme());
1248 else if (source == turnColour)
1250 changeColour(new TurnColourScheme());
1252 else if (source == buriedColour)
1254 changeColour(new BuriedColourScheme());
1256 else if (source == nucleotideColour)
1258 changeColour(new NucleotideColourScheme());
1260 else if (source == purinePyrimidineColour)
1262 changeColour(new PurinePyrimidineColourScheme());
1264 // else if (source == RNAInteractionColour)
1266 // changeColour(new RNAInteractionColourScheme());
1268 else if (source == RNAHelixColour)
1270 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1271 // new RNAHelicesColourChooser(viewport, alignPanel);
1273 else if (source == modifyPID)
1275 modifyPID_actionPerformed();
1277 else if (source == modifyConservation)
1279 modifyConservation_actionPerformed();
1281 else if (source == userDefinedColour)
1283 new UserDefinedColours(alignPanel, null);
1285 else if (source == PIDColour)
1287 changeColour(new PIDColourScheme());
1289 else if (source == BLOSUM62Colour)
1291 changeColour(new Blosum62ColourScheme());
1293 else if (source == tcoffeeColour)
1295 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1297 else if (source == annotationColour)
1299 new AnnotationColourChooser(viewport, alignPanel);
1301 else if (source == annotationColumnSelection)
1303 new AnnotationColumnChooser(viewport, alignPanel);
1305 else if (source == sortPairwiseMenuItem)
1307 sortPairwiseMenuItem_actionPerformed();
1309 else if (source == sortIDMenuItem)
1311 sortIDMenuItem_actionPerformed();
1313 else if (source == sortLengthMenuItem)
1315 sortLengthMenuItem_actionPerformed();
1317 else if (source == sortGroupMenuItem)
1319 sortGroupMenuItem_actionPerformed();
1321 else if (source == removeRedundancyMenuItem)
1323 removeRedundancyMenuItem_actionPerformed();
1325 else if (source == pairwiseAlignmentMenuItem)
1327 pairwiseAlignmentMenuItem_actionPerformed();
1329 else if (source == PCAMenuItem)
1331 PCAMenuItem_actionPerformed();
1333 else if (source == averageDistanceTreeMenuItem)
1335 averageDistanceTreeMenuItem_actionPerformed();
1337 else if (source == neighbourTreeMenuItem)
1339 neighbourTreeMenuItem_actionPerformed();
1341 else if (source == njTreeBlosumMenuItem)
1343 njTreeBlosumMenuItem_actionPerformed();
1345 else if (source == avDistanceTreeBlosumMenuItem)
1347 avTreeBlosumMenuItem_actionPerformed();
1349 else if (source == documentation)
1351 documentation_actionPerformed();
1353 else if (source == about)
1355 about_actionPerformed();
1360 public void inputText_actionPerformed()
1362 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1363 Frame frame = new Frame();
1365 jalview.bin.JalviewLite.addFrame(frame,
1366 MessageManager.getString("label.input_cut_paste"), 500, 500);
1369 protected void outputText_actionPerformed(ActionEvent e)
1371 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1372 Frame frame = new Frame();
1374 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1375 "label.alignment_output_command",
1376 new Object[] { e.getActionCommand() }), 600, 500);
1378 FileFormatI fileFormat = FileFormats.getInstance().forName(
1379 e.getActionCommand());
1380 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1381 fileFormat, viewport.getAlignment(),
1382 viewport.getShowJVSuffix()));
1385 public void loadAnnotations()
1387 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388 cap.setText(MessageManager
1389 .getString("label.paste_features_annotations_Tcoffee_here"));
1390 cap.setAnnotationImport();
1391 Frame frame = new Frame();
1393 jalview.bin.JalviewLite.addFrame(frame,
1394 MessageManager.getString("action.paste_annotations"), 400, 300);
1398 public String outputAnnotations(boolean displayTextbox)
1400 String annotation = new AnnotationFile()
1401 .printAnnotationsForView(viewport);
1405 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1406 Frame frame = new Frame();
1408 jalview.bin.JalviewLite.addFrame(frame,
1409 MessageManager.getString("label.annotations"), 600, 500);
1410 cap.setText(annotation);
1416 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1418 if (alignPanel.getFeatureRenderer() != null
1419 && viewport.getFeaturesDisplayed() != null)
1421 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1427 public String outputFeatures(boolean displayTextbox, String format)
1430 FeaturesFile formatter = new FeaturesFile();
1431 if (format.equalsIgnoreCase("Jalview"))
1433 features = formatter.printJalviewFormat(viewport.getAlignment()
1434 .getSequencesArray(), getDisplayedFeatureCols());
1438 features = formatter.printGffFormat(viewport.getAlignment()
1439 .getSequencesArray(), getDisplayedFeatureCols());
1444 boolean frimport = false;
1445 if (features == null || features.equals("No Features Visible"))
1447 features = "# No features visible - paste some and import them here.";
1451 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1454 cap.setAnnotationImport();
1456 Frame frame = new Frame();
1458 jalview.bin.JalviewLite.addFrame(frame,
1459 MessageManager.getString("label.features"), 600, 500);
1460 cap.setText(features);
1464 if (features == null)
1473 void launchFullApplication()
1475 StringBuffer url = new StringBuffer(jalviewServletURL);
1477 // allow servlet parameters to be passed in applet parameter
1478 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1480 url.append(firstSep);
1483 + appendProtocol(viewport.applet.getParameter("file")));
1485 if (viewport.applet.getParameter("features") != null)
1487 url.append("&features=");
1488 url.append(appendProtocol(viewport.applet.getParameter("features")));
1491 if (viewport.applet.getParameter("annotations") != null)
1493 url.append("&annotations=");
1494 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1497 if (viewport.applet.getParameter("jnetfile") != null
1498 || viewport.applet.getParameter("jpredfile") != null)
1500 url.append("&annotations=");
1501 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1502 .getParameter("jnetfile") : viewport.applet
1503 .getParameter("jpredfile")));
1506 if (viewport.applet.getParameter("defaultColour") != null)
1508 url.append("&colour="
1509 + removeWhiteSpace(viewport.applet
1510 .getParameter("defaultColour")));
1513 if (viewport.applet.getParameter("userDefinedColour") != null)
1515 url.append("&colour="
1516 + removeWhiteSpace(viewport.applet
1517 .getParameter("userDefinedColour")));
1519 if (viewport.applet.getParameter("tree") != null)
1522 + appendProtocol(viewport.applet.getParameter("tree")));
1524 if (viewport.applet.getParameter("treeFile") != null)
1527 + appendProtocol(viewport.applet.getParameter("treeFile")));
1530 showURL(url.toString(), "FULL_APP");
1533 String removeWhiteSpace(String colour)
1535 StringBuffer sb = new StringBuffer();
1536 for (int i = 0; i < colour.length(); i++)
1538 if (Character.isWhitespace(colour.charAt(i)))
1544 sb.append(colour.charAt(i));
1548 return sb.toString();
1551 String appendProtocol(String url)
1556 url = URLEncoder.encode(url);
1559 * When we finally deprecate 1.1 compatibility, we can start to use
1560 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1561 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1562 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1563 * ex.printStackTrace(); }
1565 catch (java.net.MalformedURLException ex)
1567 url = viewport.applet.getCodeBase() + url;
1572 public void closeMenuItem_actionPerformed()
1574 PaintRefresher.RemoveComponent(alignPanel);
1575 if (alignPanel.seqPanel != null
1576 && alignPanel.seqPanel.seqCanvas != null)
1578 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1580 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1582 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1585 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1600 void updateEditMenuBar()
1603 if (viewport.getHistoryList().size() > 0)
1605 undoMenuItem.setEnabled(true);
1606 CommandI command = viewport.getHistoryList().peek();
1607 undoMenuItem.setLabel(MessageManager.formatMessage(
1608 "label.undo_command",
1609 new Object[] { command.getDescription() }));
1613 undoMenuItem.setEnabled(false);
1614 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1617 if (viewport.getRedoList().size() > 0)
1619 redoMenuItem.setEnabled(true);
1621 CommandI command = viewport.getRedoList().peek();
1622 redoMenuItem.setLabel(MessageManager.formatMessage(
1623 "label.redo_command",
1624 new Object[] { command.getDescription() }));
1628 redoMenuItem.setEnabled(false);
1629 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1637 public void addHistoryItem(CommandI command)
1639 if (command.getSize() > 0)
1641 viewport.addToHistoryList(command);
1642 viewport.clearRedoList();
1643 updateEditMenuBar();
1644 viewport.updateHiddenColumns();
1649 * TODO: JAL-1104 DOCUMENT ME!
1654 protected void undoMenuItem_actionPerformed()
1656 if (viewport.getHistoryList().isEmpty())
1661 CommandI command = viewport.getHistoryList().pop();
1662 viewport.addToRedoList(command);
1663 command.undoCommand(null);
1665 AlignmentViewport originalSource = getOriginatingSource(command);
1667 if (originalSource != viewport)
1670 .println("Warning: Viewport object mismatch whilst undoing");
1672 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1673 // viewport.getColumnSelection().getHiddenColumns()
1675 updateEditMenuBar();
1676 originalSource.firePropertyChange("alignment", null, originalSource
1677 .getAlignment().getSequences());
1681 * TODO: JAL-1104 DOCUMENT ME!
1686 protected void redoMenuItem_actionPerformed()
1688 if (viewport.getRedoList().isEmpty())
1693 CommandI command = viewport.getRedoList().pop();
1694 viewport.addToHistoryList(command);
1695 command.doCommand(null);
1697 AlignmentViewport originalSource = getOriginatingSource(command);
1699 if (originalSource != viewport)
1702 .println("Warning: Viewport object mismatch whilst re-doing");
1704 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1705 // viewport.getColumnSelection().getHiddenColumns()
1708 updateEditMenuBar();
1709 originalSource.firePropertyChange("alignment", null, originalSource
1710 .getAlignment().getSequences());
1713 AlignmentViewport getOriginatingSource(CommandI command)
1715 AlignmentViewport originalSource = null;
1716 // For sequence removal and addition, we need to fire
1717 // the property change event FROM the viewport where the
1718 // original alignment was altered
1719 AlignmentI al = null;
1720 if (command instanceof EditCommand)
1722 EditCommand editCommand = (EditCommand) command;
1723 al = editCommand.getAlignment();
1724 Vector comps = (Vector) PaintRefresher.components.get(viewport
1725 .getSequenceSetId());
1726 for (int i = 0; i < comps.size(); i++)
1728 if (comps.elementAt(i) instanceof AlignmentPanel)
1730 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1732 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1739 if (originalSource == null)
1741 // The original view is closed, we must validate
1742 // the current view against the closed view first
1745 PaintRefresher.validateSequences(al, viewport.getAlignment());
1748 originalSource = viewport;
1751 return originalSource;
1755 * Move the currently selected sequences up or down one position in the
1760 public void moveSelectedSequences(boolean up)
1762 SequenceGroup sg = viewport.getSelectionGroup();
1767 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1768 up ? null : viewport.getHiddenRepSequences(), up);
1769 alignPanel.paintAlignment(true);
1772 * Also move cDNA/protein complement sequences
1774 AlignViewportI complement = viewport.getCodingComplement();
1775 if (complement != null)
1777 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1778 viewport, complement);
1779 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1780 up ? null : complement.getHiddenRepSequences(), up);
1781 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1785 synchronized void slideSequences(boolean right, int size)
1787 List<SequenceI> sg = new Vector<>();
1788 if (viewport.cursorMode)
1790 sg.add(viewport.getAlignment().getSequenceAt(
1791 alignPanel.seqPanel.seqCanvas.cursorY));
1793 else if (viewport.getSelectionGroup() != null
1794 && viewport.getSelectionGroup().getSize() != viewport
1795 .getAlignment().getHeight())
1797 sg = viewport.getSelectionGroup().getSequences(
1798 viewport.getHiddenRepSequences());
1806 Vector<SequenceI> invertGroup = new Vector();
1808 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1810 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1812 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1816 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1818 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1820 for (int i = 0; i < invertGroup.size(); i++)
1822 seqs2[i] = invertGroup.elementAt(i);
1825 SlideSequencesCommand ssc;
1828 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1829 size, viewport.getGapCharacter());
1833 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1834 size, viewport.getGapCharacter());
1837 int groupAdjustment = 0;
1838 if (ssc.getGapsInsertedBegin() && right)
1840 if (viewport.cursorMode)
1842 alignPanel.seqPanel.moveCursor(size, 0);
1846 groupAdjustment = size;
1849 else if (!ssc.getGapsInsertedBegin() && !right)
1851 if (viewport.cursorMode)
1853 alignPanel.seqPanel.moveCursor(-size, 0);
1857 groupAdjustment = -size;
1861 if (groupAdjustment != 0)
1863 viewport.getSelectionGroup().setStartRes(
1864 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1865 viewport.getSelectionGroup().setEndRes(
1866 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1869 boolean appendHistoryItem = false;
1870 Deque<CommandI> historyList = viewport.getHistoryList();
1871 if (historyList != null && historyList.size() > 0
1872 && historyList.peek() instanceof SlideSequencesCommand)
1874 appendHistoryItem = ssc
1875 .appendSlideCommand((SlideSequencesCommand) historyList
1879 if (!appendHistoryItem)
1881 addHistoryItem(ssc);
1887 static StringBuffer copiedSequences;
1889 static Vector<int[]> copiedHiddenColumns;
1891 protected void copy_actionPerformed()
1893 if (viewport.getSelectionGroup() == null)
1898 SequenceGroup sg = viewport.getSelectionGroup();
1899 copiedSequences = new StringBuffer();
1900 Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1901 for (int i = 0; i < sg.getSize(); i++)
1903 SequenceI seq = sg.getSequenceAt(i);
1904 int index = viewport.getAlignment().findIndex(seq);
1905 orderedSeqs.put(index, seq);
1908 int index = 0, startRes, endRes;
1911 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1913 copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1914 .getHiddenColumns().getHiddenColumnsCopy());
1915 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1916 for (int[] region : copiedHiddenColumns)
1918 region[0] = region[0] - hiddenOffset;
1919 region[1] = region[1] - hiddenOffset;
1924 copiedHiddenColumns = null;
1927 for (int i = 0; i < sg.getSize(); i++)
1929 SequenceI seq = null;
1933 if (orderedSeqs.containsKey(index))
1935 seq = orderedSeqs.get(index);
1946 // Returns residue following index if gap
1947 startRes = seq.findPosition(sg.getStartRes());
1950 // Need to find the residue preceeding index if gap
1953 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1955 ch = seq.getCharAt(j);
1956 if (!jalview.util.Comparison.isGap((ch)))
1964 endRes += seq.getStart() - 1;
1967 copiedSequences.append(seq.getName()
1973 + seq.getSequenceAsString(sg.getStartRes(),
1974 sg.getEndRes() + 1) + "\n");
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.formatMessage(
2026 "label.from_msname", new String[] { getTitle() }));
2028 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2029 viewport.applet, newtitle, false);
2030 if (copiedHiddenColumns != null)
2032 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2034 int[] region = copiedHiddenColumns.elementAt(i);
2035 af.viewport.hideColumns(region[0], region[1]);
2039 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2044 addSequences(newSeqs);
2047 } catch (Exception ex)
2049 } // could be anything being pasted in here
2053 void addSequences(SequenceI[] seqs)
2055 for (int i = 0; i < seqs.length; i++)
2057 viewport.getAlignment().addSequence(seqs[i]);
2061 addHistoryItem(new EditCommand(
2062 MessageManager.getString("label.add_sequences"), Action.PASTE,
2063 seqs, 0, viewport.getAlignment().getWidth(),
2064 viewport.getAlignment()));
2066 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2067 viewport.getAlignment().getWidth();
2068 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2073 protected void cut_actionPerformed()
2075 copy_actionPerformed();
2076 delete_actionPerformed();
2079 protected void delete_actionPerformed()
2082 SequenceGroup sg = viewport.getSelectionGroup();
2088 Vector seqs = new Vector();
2090 for (int i = 0; i < sg.getSize(); i++)
2092 seq = sg.getSequenceAt(i);
2093 seqs.addElement(seq);
2097 * If the cut affects all sequences, warn, remove highlighted columns
2099 if (sg.getSize() == viewport.getAlignment().getHeight())
2101 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2102 .getAlignment().getWidth()) ? true : false;
2103 if (isEntireAlignWidth)
2105 String title = MessageManager.getString("label.delete_all");
2106 Panel infoPanel = new Panel();
2107 infoPanel.setLayout(new FlowLayout());
2109 .add(new Label(MessageManager.getString("warn.delete_all")));
2111 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2112 dialog.setMainPanel(infoPanel);
2113 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2114 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2115 dialog.setVisible(true);
2122 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2123 sg.getEndRes() + 1);
2126 SequenceI[] cut = new SequenceI[seqs.size()];
2127 for (int i = 0; i < seqs.size(); i++)
2129 cut[i] = (SequenceI) seqs.elementAt(i);
2133 * //ADD HISTORY ITEM
2135 addHistoryItem(new EditCommand(
2136 MessageManager.getString("label.cut_sequences"), Action.CUT,
2137 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2138 viewport.getAlignment()));
2140 viewport.setSelectionGroup(null);
2141 viewport.getAlignment().deleteGroup(sg);
2143 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2146 if (viewport.getAlignment().getHeight() < 1)
2148 this.setVisible(false);
2150 viewport.sendSelection();
2154 * group consensus toggled
2157 protected void showGroupConsensus_actionPerformed()
2159 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2160 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2165 * group conservation toggled.
2167 protected void showGroupConservation_actionPerformed()
2169 viewport.setShowGroupConservation(showGroupConservation.getState());
2170 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2178 * .event.ActionEvent)
2180 protected void showConsensusHistogram_actionPerformed()
2182 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2183 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2191 * .event.ActionEvent)
2193 protected void showSequenceLogo_actionPerformed()
2195 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2196 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2199 protected void normSequenceLogo_actionPerformed()
2201 showSequenceLogo.setState(true);
2202 viewport.setShowSequenceLogo(true);
2203 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2204 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2207 protected void applyAutoAnnotationSettings_actionPerformed()
2209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2212 protected void makeGrpsFromSelection_actionPerformed()
2214 if (avc.makeGroupsFromSelection())
2216 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2217 alignPanel.updateAnnotation();
2218 alignPanel.paintAlignment(true);
2222 protected void createGroup_actionPerformed()
2227 protected void unGroup_actionPerformed()
2231 alignPanel.alignmentChanged();
2235 protected void deleteGroups_actionPerformed()
2237 if (avc.deleteGroups())
2239 alignPanel.alignmentChanged();
2243 public void selectAllSequenceMenuItem_actionPerformed()
2245 SequenceGroup sg = new SequenceGroup();
2246 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2248 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2250 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2251 viewport.setSelectionGroup(sg);
2252 // JAL-2034 - should delegate to
2253 // alignPanel to decide if overview needs
2255 alignPanel.paintAlignment(false);
2256 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257 viewport.sendSelection();
2260 public void deselectAllSequenceMenuItem_actionPerformed()
2262 if (viewport.cursorMode)
2264 alignPanel.seqPanel.keyboardNo1 = null;
2265 alignPanel.seqPanel.keyboardNo2 = null;
2267 viewport.setSelectionGroup(null);
2268 viewport.getColumnSelection().clear();
2269 viewport.setSelectionGroup(null);
2270 alignPanel.idPanel.idCanvas.searchResults = null;
2271 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2272 // JAL-2034 - should delegate to
2273 // alignPanel to decide if overview needs
2275 alignPanel.paintAlignment(false);
2276 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277 viewport.sendSelection();
2280 public void invertSequenceMenuItem_actionPerformed()
2282 SequenceGroup sg = viewport.getSelectionGroup();
2283 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2285 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2288 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289 viewport.sendSelection();
2292 public void invertColSel_actionPerformed()
2294 viewport.invertColumnSelection();
2295 alignPanel.paintAlignment(true);
2296 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297 viewport.sendSelection();
2300 void trimAlignment(boolean trimLeft)
2302 AlignmentI al = viewport.getAlignment();
2303 ViewportRanges ranges = viewport.getRanges();
2304 ColumnSelection colSel = viewport.getColumnSelection();
2307 if (!colSel.isEmpty())
2311 column = colSel.getMin();
2315 column = colSel.getMax();
2319 if (viewport.getSelectionGroup() != null)
2321 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2322 viewport.getHiddenRepSequences());
2326 seqs = al.getSequencesArray();
2329 TrimRegionCommand trimRegion;
2332 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2334 ranges.setStartRes(0);
2338 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2342 statusBar.setText(MessageManager.formatMessage(
2343 "label.removed_columns",
2344 new String[] { Integer.valueOf(trimRegion.getSize())
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().getSequencesAsArray(
2372 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.formatMessage(
2388 "label.removed_empty_columns",
2389 new String[] { Integer.valueOf(removeGapCols.getSize())
2392 // This is to maintain viewport position on first residue
2393 // of first sequence
2394 SequenceI seq = al.getSequenceAt(0);
2395 int startRes = seq.findPosition(ranges.getStartRes());
2396 // ShiftList shifts;
2397 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2398 // edit.alColumnChanges=shifts.getInverse();
2399 // if (viewport.hasHiddenColumns)
2400 // viewport.getColumnSelection().compensateForEdits(shifts);
2401 ranges.setStartRes(seq.findIndex(startRes) - 1);
2402 viewport.firePropertyChange("alignment", null, al.getSequences());
2406 public void removeAllGapsMenuItem_actionPerformed()
2408 AlignmentI al = viewport.getAlignment();
2409 ViewportRanges ranges = viewport.getRanges();
2411 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2414 if (viewport.getSelectionGroup() != null)
2416 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2417 viewport.getHiddenRepSequences());
2418 start = viewport.getSelectionGroup().getStartRes();
2419 end = viewport.getSelectionGroup().getEndRes();
2423 seqs = viewport.getAlignment().getSequencesArray();
2426 // This is to maintain viewport position on first residue
2427 // of first sequence
2428 SequenceI seq = al.getSequenceAt(0);
2429 int startRes = seq.findPosition(ranges.getStartRes());
2431 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2434 ranges.setStartRes(seq.findIndex(startRes) - 1);
2436 viewport.firePropertyChange("alignment", null, al.getSequences());
2440 public void findMenuItem_actionPerformed()
2442 new Finder(alignPanel);
2446 * create a new view derived from the current view
2449 * @return frame for the new view
2451 public AlignFrame newView(String viewtitle)
2454 if (viewport.hasHiddenRows())
2456 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2457 .getFullAlignment().getSequencesArray());
2461 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2464 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2466 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2468 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2470 newal.addAnnotation(viewport.getAlignment()
2471 .getAlignmentAnnotation()[i]);
2476 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2478 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2479 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2480 PaintRefresher.Register(newaf.alignPanel,
2481 newaf.alignPanel.av.getSequenceSetId());
2483 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2484 newaf.alignPanel.av.getSequenceSetId());
2485 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2486 newaf.alignPanel.av.getSequenceSetId());
2488 Vector comps = (Vector) PaintRefresher.components.get(viewport
2489 .getSequenceSetId());
2491 for (int i = 0; i < comps.size(); i++)
2493 if (comps.elementAt(i) instanceof AlignmentPanel)
2499 String title = new String(this.getTitle());
2500 if (viewtitle != null)
2502 title = viewtitle + " ( " + title + ")";
2506 if (title.indexOf("(View") > -1)
2508 title = title.substring(0, title.indexOf("(View"));
2510 title += "(View " + viewSize + ")";
2513 newaf.setTitle(title.toString());
2515 newaf.viewport.setHistoryList(viewport.getHistoryList());
2516 newaf.viewport.setRedoList(viewport.getRedoList());
2522 * @return list of feature groups on the view
2524 public String[] getFeatureGroups()
2526 FeatureRenderer fr = null;
2527 if (alignPanel != null
2528 && (fr = alignPanel.getFeatureRenderer()) != null)
2530 List<String> gps = fr.getFeatureGroups();
2531 String[] _gps = gps.toArray(new String[gps.size()]);
2538 * get sequence feature groups that are hidden or shown
2544 public String[] getFeatureGroupsOfState(boolean visible)
2546 FeatureRenderer fr = null;
2547 if (alignPanel != null
2548 && (fr = alignPanel.getFeatureRenderer()) != null)
2550 List<String> gps = fr.getGroups(visible);
2551 String[] _gps = gps.toArray(new String[gps.size()]);
2558 * Change the display state for the given feature groups
2561 * list of group strings
2563 * visible or invisible
2565 public void setFeatureGroupState(String[] groups, boolean state)
2567 FeatureRenderer fr = null;
2568 this.sequenceFeatures.setState(true);
2569 viewport.setShowSequenceFeatures(true);
2570 if (alignPanel != null
2571 && (fr = alignPanel.getFeatureRenderer()) != null)
2574 fr.setGroupVisibility(Arrays.asList(groups), state);
2575 alignPanel.seqPanel.seqCanvas.repaint();
2576 if (alignPanel.overviewPanel != null)
2578 alignPanel.overviewPanel.updateOverviewImage();
2583 public void seqLimits_itemStateChanged()
2585 viewport.setShowJVSuffix(seqLimits.getState());
2586 alignPanel.fontChanged();
2587 alignPanel.paintAlignment(true);
2590 protected void colourTextMenuItem_actionPerformed()
2592 viewport.setColourText(colourTextMenuItem.getState());
2593 alignPanel.paintAlignment(true);
2596 protected void displayNonconservedMenuItem_actionPerformed()
2598 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2599 alignPanel.paintAlignment(true);
2602 protected void wrapMenuItem_actionPerformed()
2604 viewport.setWrapAlignment(wrapMenuItem.getState());
2605 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2606 scaleAbove.setEnabled(wrapMenuItem.getState());
2607 scaleLeft.setEnabled(wrapMenuItem.getState());
2608 scaleRight.setEnabled(wrapMenuItem.getState());
2609 alignPanel.paintAlignment(true);
2612 public void overviewMenuItem_actionPerformed()
2614 if (alignPanel.overviewPanel != null)
2619 Frame frame = new Frame();
2620 final OverviewPanel overview = new OverviewPanel(alignPanel);
2621 frame.add(overview);
2622 // +50 must allow for applet frame window
2623 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2624 "label.overview_params", new String[] { this.getTitle() }),
2625 overview.getPreferredSize().width,
2626 overview.getPreferredSize().height + 50);
2629 final AlignmentPanel ap = alignPanel;
2630 frame.addWindowListener(new WindowAdapter()
2633 public void windowClosing(WindowEvent e)
2638 ap.setOverviewPanel(null);
2643 alignPanel.setOverviewPanel(overview);
2648 public void changeColour(ColourSchemeI cs)
2650 viewport.setGlobalColourScheme(cs);
2652 alignPanel.paintAlignment(true);
2655 protected void modifyPID_actionPerformed()
2657 if (viewport.getAbovePIDThreshold()
2658 && viewport.getGlobalColourScheme() != null)
2660 SliderPanel.setPIDSliderSource(alignPanel,
2661 viewport.getResidueShading(), alignPanel.getViewName());
2662 SliderPanel.showPIDSlider();
2666 protected void modifyConservation_actionPerformed()
2668 if (viewport.getConservationSelected()
2669 && viewport.getGlobalColourScheme() != null)
2671 SliderPanel.setConservationSlider(alignPanel,
2672 viewport.getResidueShading(), alignPanel.getViewName());
2673 SliderPanel.showConservationSlider();
2677 protected void conservationMenuItem_actionPerformed()
2679 boolean selected = conservationMenuItem.getState();
2680 modifyConservation.setEnabled(selected);
2681 viewport.setConservationSelected(selected);
2682 viewport.getResidueShading().setConservationApplied(selected);
2684 changeColour(viewport.getGlobalColourScheme());
2688 modifyConservation_actionPerformed();
2692 SliderPanel.hideConservationSlider();
2696 public void abovePIDThreshold_actionPerformed()
2698 boolean selected = abovePIDThreshold.getState();
2699 modifyPID.setEnabled(selected);
2700 viewport.setAbovePIDThreshold(selected);
2703 viewport.getResidueShading().setThreshold(0,
2704 viewport.isIgnoreGapsConsensus());
2707 changeColour(viewport.getGlobalColourScheme());
2711 modifyPID_actionPerformed();
2715 SliderPanel.hidePIDSlider();
2719 public void sortPairwiseMenuItem_actionPerformed()
2721 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2722 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2723 .getAlignment().getSequenceAt(0));
2725 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2726 viewport.getAlignment()));
2727 alignPanel.paintAlignment(true);
2730 public void sortIDMenuItem_actionPerformed()
2732 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2733 AlignmentSorter.sortByID(viewport.getAlignment());
2734 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2735 viewport.getAlignment()));
2736 alignPanel.paintAlignment(true);
2739 public void sortLengthMenuItem_actionPerformed()
2741 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2742 AlignmentSorter.sortByLength(viewport.getAlignment());
2743 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2744 viewport.getAlignment()));
2745 alignPanel.paintAlignment(true);
2748 public void sortGroupMenuItem_actionPerformed()
2750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2751 AlignmentSorter.sortByGroup(viewport.getAlignment());
2752 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2753 viewport.getAlignment()));
2754 alignPanel.paintAlignment(true);
2758 public void removeRedundancyMenuItem_actionPerformed()
2760 new RedundancyPanel(alignPanel);
2763 public void pairwiseAlignmentMenuItem_actionPerformed()
2765 if (viewport.getSelectionGroup() != null
2766 && viewport.getSelectionGroup().getSize() > 1)
2768 Frame frame = new Frame();
2769 frame.add(new PairwiseAlignPanel(alignPanel));
2770 jalview.bin.JalviewLite.addFrame(frame,
2771 MessageManager.getString("action.pairwise_alignment"), 600,
2776 public void PCAMenuItem_actionPerformed()
2778 // are the sequences aligned?
2779 if (!viewport.getAlignment().isAligned(false))
2782 int Width = viewport.getAlignment().getWidth();
2784 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2786 current = viewport.getAlignment().getSequenceAt(i);
2788 if (current.getLength() < Width)
2790 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2793 alignPanel.paintAlignment(true);
2796 if ((viewport.getSelectionGroup() != null
2797 && viewport.getSelectionGroup().getSize() < 4 && viewport
2798 .getSelectionGroup().getSize() > 0)
2799 || viewport.getAlignment().getHeight() < 4)
2806 new PCAPanel(viewport);
2807 } catch (java.lang.OutOfMemoryError ex)
2813 public void averageDistanceTreeMenuItem_actionPerformed()
2815 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2816 "Average distance tree using PID");
2819 public void neighbourTreeMenuItem_actionPerformed()
2821 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2822 "Neighbour joining tree using PID");
2825 protected void njTreeBlosumMenuItem_actionPerformed()
2827 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2828 .getBlosum62().getName(),
2829 "Neighbour joining tree using BLOSUM62");
2832 protected void avTreeBlosumMenuItem_actionPerformed()
2834 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2835 .getBlosum62().getName(),
2836 "Average distance tree using BLOSUM62");
2839 void newTreePanel(String type, String pwType, String title)
2841 // are the sequences aligned?
2842 if (!viewport.getAlignment().isAligned(false))
2845 int Width = viewport.getAlignment().getWidth();
2847 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2849 current = viewport.getAlignment().getSequenceAt(i);
2851 if (current.getLength() < Width)
2853 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2856 alignPanel.paintAlignment(true);
2860 if ((viewport.getSelectionGroup() != null && viewport
2861 .getSelectionGroup().getSize() > 1)
2862 || (viewport.getAlignment().getHeight() > 1))
2864 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2866 addTreeMenuItem(tp, title);
2868 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2872 void loadTree_actionPerformed()
2874 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2875 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2876 cap.setTreeImport();
2877 Frame frame = new Frame();
2879 jalview.bin.JalviewLite.addFrame(frame,
2880 MessageManager.getString("label.paste_newick_file"), 400, 300);
2883 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2885 TreePanel tp = new TreePanel(alignPanel, treeFile,
2886 MessageManager.getString("label.load_tree_from_file"), tree);
2887 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2888 addTreeMenuItem(tp, treeFile);
2892 * sort the alignment using the given treePanel
2895 * tree used to sort view
2897 * string used for undo event name
2899 public void sortByTree(TreePanel treePanel, String title)
2901 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2903 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2904 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2905 // HistoryItem.SORT));
2906 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2907 "label.order_by_params", new String[] { title }), oldOrder,
2908 viewport.getAlignment()));
2909 alignPanel.paintAlignment(true);
2913 * Do any automatic reordering of the alignment and add the necessary bits to
2914 * the menu structure for the new tree
2919 protected void addTreeMenuItem(final TreePanel treePanel,
2922 final MenuItem item = new MenuItem(title);
2923 sortByTreeMenu.add(item);
2924 item.addActionListener(new java.awt.event.ActionListener()
2927 public void actionPerformed(ActionEvent evt)
2929 sortByTree(treePanel, title); // treePanel.getTitle());
2933 treePanel.addWindowListener(new WindowAdapter()
2936 public void windowOpened(WindowEvent e)
2938 if (viewport.sortByTree)
2940 sortByTree(treePanel, title);
2942 super.windowOpened(e);
2946 public void windowClosing(WindowEvent e)
2948 sortByTreeMenu.remove(item);
2953 public boolean sortBy(AlignmentOrder alorder, String undoname)
2955 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2956 if (viewport.applet.debug)
2958 System.err.println("Sorting " + alorder.getOrder().size()
2959 + " in alignment '" + getTitle() + "'");
2961 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2962 if (undoname != null)
2964 addHistoryItem(new OrderCommand(undoname, oldOrder,
2965 viewport.getAlignment()));
2967 alignPanel.paintAlignment(true);
2971 protected void documentation_actionPerformed()
2973 alignPanel.av.applet.openJalviewHelpUrl();
2976 protected void about_actionPerformed()
2979 class AboutPanel extends Canvas
2985 public AboutPanel(String version, String builddate)
2987 this.version = version;
2988 this.builddate = builddate;
2992 public void paint(Graphics g)
2994 g.setColor(Color.white);
2995 g.fillRect(0, 0, getSize().width, getSize().height);
2996 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2997 FontMetrics fm = g.getFontMetrics();
2998 int fh = fm.getHeight();
3000 g.setColor(Color.black);
3001 // TODO: update this text for each release or centrally store it for
3002 // lite and application
3003 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3004 g.drawString(MessageManager.formatMessage(
3005 "label.jalviewLite_release", new String[] { version }), x,
3007 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3008 g.drawString(MessageManager.formatMessage(
3009 "label.jaview_build_date", new String[] { builddate }), x,
3011 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3012 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3014 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3015 x + 50, y += fh + 8);
3017 MessageManager.getString("label.jalview_dev_managers"), x,
3019 g.drawString(MessageManager
3020 .getString("label.jalview_distribution_lists"), x, y += fh);
3021 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3024 MessageManager.getString("label.jalview_cite_1_authors"),
3027 MessageManager.getString("label.jalview_cite_1_title"), x,
3029 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3034 Frame frame = new Frame();
3035 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3037 jalview.bin.JalviewLite.addFrame(frame,
3038 MessageManager.getString("label.jalview"), 580, 220);
3042 public void showURL(String url, String target)
3044 if (viewport.applet == null)
3046 System.out.println("Not running as applet - no browser available.");
3050 viewport.applet.showURL(url, target);
3054 // ////////////////////////////////////////////////////////////////////////////////
3055 // JBuilder Graphics here
3057 MenuBar alignFrameMenuBar = new MenuBar();
3059 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3061 MenuItem loadApplication = new MenuItem(
3062 MessageManager.getString("label.view_full_application"));
3064 MenuItem loadTree = new MenuItem(
3065 MessageManager.getString("label.load_associated_tree"));
3067 MenuItem loadAnnotations = new MenuItem(
3068 MessageManager.getString("label.load_features_annotations"));
3070 MenuItem outputFeatures = new MenuItem(
3071 MessageManager.getString("label.export_features"));
3073 MenuItem outputAnnotations = new MenuItem(
3074 MessageManager.getString("label.export_annotations"));
3076 MenuItem closeMenuItem = new MenuItem(
3077 MessageManager.getString("action.close"));
3079 MenuItem selectAllSequenceMenuItem = new MenuItem(
3080 MessageManager.getString("action.select_all"));
3082 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3083 MessageManager.getString("action.deselect_all"));
3085 MenuItem invertSequenceMenuItem = new MenuItem(
3086 MessageManager.getString("action.invert_selection"));
3088 MenuItem remove2LeftMenuItem = new MenuItem();
3090 MenuItem remove2RightMenuItem = new MenuItem();
3092 MenuItem removeGappedColumnMenuItem = new MenuItem();
3094 MenuItem removeAllGapsMenuItem = new MenuItem();
3096 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3098 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3100 MenuItem sortPairwiseMenuItem = new MenuItem();
3102 MenuItem sortIDMenuItem = new MenuItem();
3104 MenuItem sortLengthMenuItem = new MenuItem();
3106 MenuItem sortGroupMenuItem = new MenuItem();
3108 MenuItem removeRedundancyMenuItem = new MenuItem();
3110 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3112 MenuItem PCAMenuItem = new MenuItem();
3114 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3116 MenuItem neighbourTreeMenuItem = new MenuItem();
3118 BorderLayout borderLayout1 = new BorderLayout();
3120 public Label statusBar = new Label();
3122 MenuItem clustalColour = new MenuItem();
3124 MenuItem zappoColour = new MenuItem();
3126 MenuItem taylorColour = new MenuItem();
3128 MenuItem hydrophobicityColour = new MenuItem();
3130 MenuItem helixColour = new MenuItem();
3132 MenuItem strandColour = new MenuItem();
3134 MenuItem turnColour = new MenuItem();
3136 MenuItem buriedColour = new MenuItem();
3138 MenuItem purinePyrimidineColour = new MenuItem();
3140 // MenuItem RNAInteractionColour = new MenuItem();
3142 MenuItem RNAHelixColour = new MenuItem();
3144 MenuItem userDefinedColour = new MenuItem();
3146 MenuItem PIDColour = new MenuItem();
3148 MenuItem BLOSUM62Colour = new MenuItem();
3150 MenuItem tcoffeeColour = new MenuItem();
3152 MenuItem njTreeBlosumMenuItem = new MenuItem();
3154 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3156 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3158 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3160 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3162 MenuItem alProperties = new MenuItem(
3163 MessageManager.getString("label.alignment_props"));
3165 MenuItem overviewMenuItem = new MenuItem();
3167 MenuItem undoMenuItem = new MenuItem();
3169 MenuItem redoMenuItem = new MenuItem();
3171 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3173 MenuItem noColourmenuItem = new MenuItem();
3175 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3177 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3179 MenuItem findMenuItem = new MenuItem();
3181 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3183 MenuItem nucleotideColour = new MenuItem();
3185 MenuItem deleteGroups = new MenuItem();
3187 MenuItem grpsFromSelection = new MenuItem();
3189 MenuItem createGroup = new MenuItem();
3191 MenuItem unGroup = new MenuItem();
3193 MenuItem delete = new MenuItem();
3195 MenuItem copy = new MenuItem();
3197 MenuItem cut = new MenuItem();
3199 Menu pasteMenu = new Menu();
3201 MenuItem pasteNew = new MenuItem();
3203 MenuItem pasteThis = new MenuItem();
3205 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3207 MenuItem font = new MenuItem();
3209 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3211 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3213 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3215 MenuItem modifyPID = new MenuItem();
3217 MenuItem modifyConservation = new MenuItem();
3219 CheckboxMenuItem autoCalculate = null;
3221 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3222 "Sort Alignment With New Tree", true);
3224 Menu sortByTreeMenu = new Menu();
3226 MenuItem inputText = new MenuItem();
3228 MenuItem documentation = new MenuItem();
3230 MenuItem about = new MenuItem();
3232 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3234 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3236 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3238 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3240 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3242 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3244 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3246 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3248 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3251 * Initialise menus and other items
3255 private void jbInit() throws Exception
3257 setMenuBar(alignFrameMenuBar);
3260 * Configure File menu items and actions
3263 .setLabel(MessageManager.getString("label.input_from_textbox"));
3264 inputText.addActionListener(this);
3265 Menu outputTextboxMenu = new Menu(
3266 MessageManager.getString("label.out_to_textbox"));
3267 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3269 MenuItem item = new MenuItem(ff);
3271 item.addActionListener(new java.awt.event.ActionListener()
3274 public void actionPerformed(ActionEvent e)
3276 outputText_actionPerformed(e);
3280 outputTextboxMenu.add(item);
3282 closeMenuItem.addActionListener(this);
3283 loadApplication.addActionListener(this);
3284 loadTree.addActionListener(this);
3285 loadAnnotations.addActionListener(this);
3286 outputFeatures.addActionListener(this);
3287 outputAnnotations.addActionListener(this);
3290 * Configure Edit menu items and actions
3292 undoMenuItem.setEnabled(false);
3293 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3294 undoMenuItem.addActionListener(this);
3295 redoMenuItem.setEnabled(false);
3296 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3297 redoMenuItem.addActionListener(this);
3298 copy.setLabel(MessageManager.getString("action.copy"));
3299 copy.addActionListener(this);
3300 cut.setLabel(MessageManager.getString("action.cut"));
3301 cut.addActionListener(this);
3302 delete.setLabel(MessageManager.getString("action.delete"));
3303 delete.addActionListener(this);
3304 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3305 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3306 pasteNew.addActionListener(this);
3307 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3308 pasteThis.addActionListener(this);
3309 remove2LeftMenuItem.setLabel(MessageManager
3310 .getString("action.remove_left"));
3311 remove2LeftMenuItem.addActionListener(this);
3312 remove2RightMenuItem.setLabel(MessageManager
3313 .getString("action.remove_right"));
3314 remove2RightMenuItem.addActionListener(this);
3315 removeGappedColumnMenuItem.setLabel(MessageManager
3316 .getString("action.remove_empty_columns"));
3317 removeGappedColumnMenuItem.addActionListener(this);
3318 removeAllGapsMenuItem.setLabel(MessageManager
3319 .getString("action.remove_all_gaps"));
3320 removeAllGapsMenuItem.addActionListener(this);
3321 removeRedundancyMenuItem.setLabel(MessageManager
3322 .getString("action.remove_redundancy"));
3323 removeRedundancyMenuItem.addActionListener(this);
3326 * Configure Select menu items and actions
3328 findMenuItem.setLabel(MessageManager.getString("action.find"));
3329 findMenuItem.addActionListener(this);
3330 selectAllSequenceMenuItem.addActionListener(this);
3331 deselectAllSequenceMenuItem.addActionListener(this);
3332 invertSequenceMenuItem.setLabel(MessageManager
3333 .getString("action.invert_sequence_selection"));
3334 invertSequenceMenuItem.addActionListener(this);
3335 invertColSel.setLabel(MessageManager
3336 .getString("action.invert_column_selection"));
3337 invertColSel.addActionListener(this);
3338 deleteGroups.setLabel(MessageManager
3339 .getString("action.undefine_groups"));
3340 deleteGroups.addActionListener(this);
3341 grpsFromSelection.setLabel(MessageManager
3342 .getString("action.make_groups_selection"));
3343 grpsFromSelection.addActionListener(this);
3344 createGroup.setLabel(MessageManager.getString("action.create_group"));
3345 createGroup.addActionListener(this);
3346 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3347 unGroup.addActionListener(this);
3349 annotationColumnSelection.setLabel(MessageManager
3350 .getString("action.select_by_annotation"));
3351 annotationColumnSelection.addActionListener(this);
3354 * Configure View menu items and actions
3356 newView.setLabel(MessageManager.getString("action.new_view"));
3357 newView.addActionListener(this);
3358 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3359 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3360 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3361 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3363 .setLabel(MessageManager.getString("label.selected_columns"));
3364 hideSequences.setLabel(MessageManager
3365 .getString("label.selected_sequences"));
3366 hideAllButSelection.setLabel(MessageManager
3367 .getString("label.all_but_selected_region"));
3368 hideAllSelection.setLabel(MessageManager
3369 .getString("label.selected_region"));
3370 showAllHidden.setLabel(MessageManager
3371 .getString("label.all_sequences_columns"));
3372 showColumns.addActionListener(this);
3373 showSeqs.addActionListener(this);
3374 hideColumns.addActionListener(this);
3375 hideSequences.addActionListener(this);
3376 hideAllButSelection.addActionListener(this);
3377 hideAllSelection.addActionListener(this);
3378 showAllHidden.addActionListener(this);
3379 featureSettings.setLabel(MessageManager
3380 .getString("action.feature_settings"));
3381 featureSettings.addActionListener(this);
3382 sequenceFeatures.setLabel(MessageManager
3383 .getString("label.show_sequence_features"));
3384 sequenceFeatures.addItemListener(this);
3385 sequenceFeatures.setState(false);
3386 followMouseOverFlag.setLabel(MessageManager
3387 .getString("label.automatic_scrolling"));
3388 followMouseOverFlag.addItemListener(this);
3389 alProperties.addActionListener(this);
3390 overviewMenuItem.setLabel(MessageManager
3391 .getString("label.overview_window"));
3392 overviewMenuItem.addActionListener(this);
3395 * Configure Annotations menu items and actions
3397 annotationPanelMenuItem.setLabel(MessageManager
3398 .getString("label.show_annotations"));
3399 annotationPanelMenuItem.addItemListener(this);
3400 showGroupConsensus.setLabel(MessageManager
3401 .getString("label.group_consensus"));
3402 showGroupConservation.setLabel(MessageManager
3403 .getString("label.group_conservation"));
3404 showConsensusHistogram.setLabel(MessageManager
3405 .getString("label.show_consensus_histogram"));
3406 showSequenceLogo.setLabel(MessageManager
3407 .getString("label.show_consensus_logo"));
3408 normSequenceLogo.setLabel(MessageManager
3409 .getString("label.norm_consensus_logo"));
3410 applyAutoAnnotationSettings.setLabel(MessageManager
3411 .getString("label.apply_all_groups"));
3412 applyAutoAnnotationSettings.setState(true);
3413 Menu autoAnnMenu = new Menu(
3414 MessageManager.getString("label.autocalculated_annotation"));
3415 showGroupConsensus.addItemListener(this);
3416 showGroupConservation.addItemListener(this);
3417 showConsensusHistogram.addItemListener(this);
3418 showSequenceLogo.addItemListener(this);
3419 normSequenceLogo.addItemListener(this);
3420 applyAutoAnnotationSettings.addItemListener(this);
3421 showAlignmentAnnotations = new CheckboxMenuItem(
3422 MessageManager.getString("label.show_all_al_annotations"));
3423 showSequenceAnnotations = new CheckboxMenuItem(
3424 MessageManager.getString("label.show_all_seq_annotations"));
3425 sortAnnBySequence = new CheckboxMenuItem(
3426 MessageManager.getString("label.sort_annotations_by_sequence"));
3427 sortAnnByLabel = new CheckboxMenuItem(
3428 MessageManager.getString("label.sort_annotations_by_label"));
3429 showAutoFirst = new CheckboxMenuItem(
3430 MessageManager.getString("label.show_first"));
3431 showAutoFirst.setState(false); // pending applet parameter
3432 setShowAutoCalculatedAbove(showAutoFirst.getState());
3433 showAutoLast = new CheckboxMenuItem(
3434 MessageManager.getString("label.show_last"));
3435 showAutoLast.setState(!showAutoFirst.getState());
3436 showAlignmentAnnotations.addItemListener(this);
3437 showSequenceAnnotations.addItemListener(this);
3438 sortAnnBySequence.addItemListener(this);
3439 sortAnnByLabel.addItemListener(this);
3440 showAutoFirst.addItemListener(this);
3441 showAutoLast.addItemListener(this);
3444 * Configure Format menu items and actions
3446 font.setLabel(MessageManager.getString("action.font"));
3447 font.addActionListener(this);
3448 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3449 scaleAbove.setState(true);
3450 scaleAbove.setEnabled(false);
3451 scaleAbove.addItemListener(this);
3452 scaleLeft.setEnabled(false);
3453 scaleLeft.setState(true);
3454 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3455 scaleLeft.addItemListener(this);
3456 scaleRight.setEnabled(false);
3457 scaleRight.setState(true);
3458 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3459 scaleRight.addItemListener(this);
3460 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3461 viewBoxesMenuItem.setState(true);
3462 viewBoxesMenuItem.addItemListener(this);
3463 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3464 viewTextMenuItem.setState(true);
3465 viewTextMenuItem.addItemListener(this);
3466 colourTextMenuItem.setLabel(MessageManager
3467 .getString("label.colour_text"));
3468 colourTextMenuItem.addItemListener(this);
3469 displayNonconservedMenuItem.setLabel(MessageManager
3470 .getString("label.show_non_conserved"));
3471 displayNonconservedMenuItem.addItemListener(this);
3472 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3473 wrapMenuItem.addItemListener(this);
3474 renderGapsMenuItem.setLabel(MessageManager
3475 .getString("action.show_gaps"));
3476 renderGapsMenuItem.setState(true);
3477 renderGapsMenuItem.addItemListener(this);
3478 centreColumnLabelFlag.setLabel(MessageManager
3479 .getString("label.centre_column_labels"));
3480 centreColumnLabelFlag.addItemListener(this);
3481 seqLimits.setState(true);
3482 seqLimits.setLabel(MessageManager
3483 .getString("label.show_sequence_limits"));
3484 seqLimits.addItemListener(this);
3487 * Configure Colour menu items and actions
3489 applyToAllGroups.setLabel(MessageManager
3490 .getString("label.apply_colour_to_all_groups"));
3491 applyToAllGroups.setState(true);
3492 applyToAllGroups.addItemListener(this);
3493 clustalColour.setLabel(MessageManager
3494 .getString("label.colourScheme_clustal"));
3495 clustalColour.addActionListener(this);
3496 zappoColour.setLabel(MessageManager
3497 .getString("label.colourScheme_zappo"));
3498 zappoColour.addActionListener(this);
3499 taylorColour.setLabel(MessageManager
3500 .getString("label.colourScheme_taylor"));
3501 taylorColour.addActionListener(this);
3502 hydrophobicityColour.setLabel(MessageManager
3503 .getString("label.colourScheme_hydrophobic"));
3504 hydrophobicityColour.addActionListener(this);
3505 helixColour.setLabel(MessageManager
3506 .getString("label.colourScheme_helix_propensity"));
3507 helixColour.addActionListener(this);
3508 strandColour.setLabel(MessageManager
3509 .getString("label.colourScheme_strand_propensity"));
3510 strandColour.addActionListener(this);
3511 turnColour.setLabel(MessageManager
3512 .getString("label.colourScheme_turn_propensity"));
3513 turnColour.addActionListener(this);
3514 buriedColour.setLabel(MessageManager
3515 .getString("label.colourScheme_buried_index"));
3516 buriedColour.addActionListener(this);
3517 purinePyrimidineColour.setLabel(MessageManager
3518 .getString("label.colourScheme_purine/pyrimidine"));
3519 purinePyrimidineColour.addActionListener(this);
3520 // RNAInteractionColour.setLabel(MessageManager
3521 // .getString("label.rna_interaction"));
3522 // RNAInteractionColour.addActionListener(this);
3523 RNAHelixColour.setLabel(MessageManager
3524 .getString("label.colourScheme_rna_helices"));
3525 RNAHelixColour.addActionListener(this);
3526 userDefinedColour.setLabel(MessageManager
3527 .getString("action.user_defined"));
3528 userDefinedColour.addActionListener(this);
3529 PIDColour.setLabel(MessageManager
3530 .getString("label.colourScheme_%_identity"));
3531 PIDColour.addActionListener(this);
3532 BLOSUM62Colour.setLabel(MessageManager
3533 .getString("label.colourScheme_blosum62"));
3534 BLOSUM62Colour.addActionListener(this);
3535 tcoffeeColour.setLabel(MessageManager
3536 .getString("label.colourScheme_t-coffee_scores"));
3537 // it will be enabled only if a score file is provided
3538 tcoffeeColour.setEnabled(false);
3539 tcoffeeColour.addActionListener(this);
3540 conservationMenuItem.setLabel(MessageManager
3541 .getString("action.by_conservation"));
3542 conservationMenuItem.addItemListener(this);
3543 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3544 noColourmenuItem.addActionListener(this);
3545 abovePIDThreshold.setLabel(MessageManager
3546 .getString("label.above_identity_threshold"));
3547 abovePIDThreshold.addItemListener(this);
3548 nucleotideColour.setLabel(MessageManager
3549 .getString("label.colourScheme_nucleotide"));
3550 nucleotideColour.addActionListener(this);
3551 modifyPID.setLabel(MessageManager
3552 .getString("label.modify_identity_threshold"));
3553 modifyPID.setEnabled(abovePIDThreshold.getState());
3554 modifyPID.addActionListener(this);
3555 modifyConservation.setLabel(MessageManager
3556 .getString("label.modify_conservation_threshold"));
3557 modifyConservation.setEnabled(conservationMenuItem.getState());
3558 modifyConservation.addActionListener(this);
3559 annotationColour.setLabel(MessageManager
3560 .getString("action.by_annotation"));
3561 annotationColour.addActionListener(this);
3564 * Configure Calculate menu items and actions
3566 sortPairwiseMenuItem.setLabel(MessageManager
3567 .getString("action.by_pairwise_id"));
3568 sortPairwiseMenuItem.addActionListener(this);
3569 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3570 sortIDMenuItem.addActionListener(this);
3571 sortLengthMenuItem.setLabel(MessageManager
3572 .getString("action.by_length"));
3573 sortLengthMenuItem.addActionListener(this);
3574 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3575 sortGroupMenuItem.addActionListener(this);
3576 pairwiseAlignmentMenuItem.setLabel(MessageManager
3577 .getString("action.pairwise_alignment"));
3578 pairwiseAlignmentMenuItem.addActionListener(this);
3579 PCAMenuItem.setLabel(MessageManager
3580 .getString("label.principal_component_analysis"));
3581 PCAMenuItem.addActionListener(this);
3582 autoCalculate = new CheckboxMenuItem(
3583 MessageManager.getString("label.autocalculate_consensus"), true);
3584 averageDistanceTreeMenuItem.setLabel(MessageManager
3585 .getString("label.average_distance_identity"));
3586 averageDistanceTreeMenuItem.addActionListener(this);
3587 neighbourTreeMenuItem.setLabel(MessageManager
3588 .getString("label.neighbour_joining_identity"));
3589 neighbourTreeMenuItem.addActionListener(this);
3590 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3591 .getString("label.average_distance_blosum62"));
3592 avDistanceTreeBlosumMenuItem.addActionListener(this);
3593 njTreeBlosumMenuItem.setLabel(MessageManager
3594 .getString("label.neighbour_blosum62"));
3595 njTreeBlosumMenuItem.addActionListener(this);
3596 sortByTreeMenu.setLabel(MessageManager
3597 .getString("action.by_tree_order"));
3598 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3599 Menu calculateTreeMenu = new Menu(
3600 MessageManager.getString("action.calculate_tree"));
3601 autoCalculate.addItemListener(this);
3602 sortByTree.addItemListener(this);
3605 * Configure Help menu items and actions
3607 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3608 documentation.setLabel(MessageManager.getString("label.documentation"));
3609 documentation.addActionListener(this);
3610 about.setLabel(MessageManager.getString("label.about"));
3611 about.addActionListener(this);
3614 * Add top level menus to frame
3616 alignFrameMenuBar.add(fileMenu);
3617 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3618 alignFrameMenuBar.add(editMenu);
3619 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3620 alignFrameMenuBar.add(selectMenu);
3621 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3622 alignFrameMenuBar.add(viewMenu);
3623 Menu annotationsMenu = new Menu(
3624 MessageManager.getString("action.annotations"));
3625 alignFrameMenuBar.add(annotationsMenu);
3626 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3627 alignFrameMenuBar.add(formatMenu);
3628 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3629 alignFrameMenuBar.add(colourMenu);
3630 Menu calculateMenu = new Menu(
3631 MessageManager.getString("action.calculate"));
3632 alignFrameMenuBar.add(calculateMenu);
3633 alignFrameMenuBar.add(helpMenu);
3638 fileMenu.add(inputText);
3639 fileMenu.add(loadTree);
3640 fileMenu.add(loadAnnotations);
3641 fileMenu.addSeparator();
3642 fileMenu.add(outputTextboxMenu);
3643 fileMenu.add(outputFeatures);
3644 fileMenu.add(outputAnnotations);
3645 if (jalviewServletURL != null)
3647 fileMenu.add(loadApplication);
3649 fileMenu.addSeparator();
3650 fileMenu.add(closeMenuItem);
3655 editMenu.add(undoMenuItem);
3656 editMenu.add(redoMenuItem);
3659 pasteMenu.add(pasteNew);
3660 pasteMenu.add(pasteThis);
3661 editMenu.add(pasteMenu);
3662 editMenu.add(delete);
3663 editMenu.addSeparator();
3664 editMenu.add(remove2LeftMenuItem);
3665 editMenu.add(remove2RightMenuItem);
3666 editMenu.add(removeGappedColumnMenuItem);
3667 editMenu.add(removeAllGapsMenuItem);
3668 editMenu.add(removeRedundancyMenuItem);
3673 selectMenu.add(findMenuItem);
3674 selectMenu.addSeparator();
3675 selectMenu.add(selectAllSequenceMenuItem);
3676 selectMenu.add(deselectAllSequenceMenuItem);
3677 selectMenu.add(invertSequenceMenuItem);
3678 selectMenu.add(invertColSel);
3679 selectMenu.add(createGroup);
3680 selectMenu.add(unGroup);
3681 selectMenu.add(grpsFromSelection);
3682 selectMenu.add(deleteGroups);
3683 selectMenu.add(annotationColumnSelection);
3688 viewMenu.add(newView);
3689 viewMenu.addSeparator();
3690 showMenu.add(showColumns);
3691 showMenu.add(showSeqs);
3692 showMenu.add(showAllHidden);
3693 viewMenu.add(showMenu);
3694 hideMenu.add(hideColumns);
3695 hideMenu.add(hideSequences);
3696 hideMenu.add(hideAllSelection);
3697 hideMenu.add(hideAllButSelection);
3698 viewMenu.add(hideMenu);
3699 viewMenu.addSeparator();
3700 viewMenu.add(followMouseOverFlag);
3701 viewMenu.addSeparator();
3702 viewMenu.add(sequenceFeatures);
3703 viewMenu.add(featureSettings);
3704 viewMenu.addSeparator();
3705 viewMenu.add(alProperties);
3706 viewMenu.addSeparator();
3707 viewMenu.add(overviewMenuItem);
3712 annotationsMenu.add(annotationPanelMenuItem);
3713 annotationsMenu.addSeparator();
3714 annotationsMenu.add(showAlignmentAnnotations);
3715 annotationsMenu.add(showSequenceAnnotations);
3716 annotationsMenu.add(sortAnnBySequence);
3717 annotationsMenu.add(sortAnnByLabel);
3718 annotationsMenu.addSeparator();
3719 autoAnnMenu.add(showAutoFirst);
3720 autoAnnMenu.add(showAutoLast);
3721 autoAnnMenu.addSeparator();
3722 autoAnnMenu.add(applyAutoAnnotationSettings);
3723 autoAnnMenu.add(showConsensusHistogram);
3724 autoAnnMenu.add(showSequenceLogo);
3725 autoAnnMenu.add(normSequenceLogo);
3726 autoAnnMenu.addSeparator();
3727 autoAnnMenu.add(showGroupConservation);
3728 autoAnnMenu.add(showGroupConsensus);
3729 annotationsMenu.add(autoAnnMenu);
3734 formatMenu.add(font);
3735 formatMenu.add(seqLimits);
3736 formatMenu.add(wrapMenuItem);
3737 formatMenu.add(scaleAbove);
3738 formatMenu.add(scaleLeft);
3739 formatMenu.add(scaleRight);
3740 formatMenu.add(viewBoxesMenuItem);
3741 formatMenu.add(viewTextMenuItem);
3742 formatMenu.add(colourTextMenuItem);
3743 formatMenu.add(displayNonconservedMenuItem);
3744 formatMenu.add(renderGapsMenuItem);
3745 formatMenu.add(centreColumnLabelFlag);
3750 colourMenu.add(applyToAllGroups);
3751 colourMenu.addSeparator();
3752 colourMenu.add(noColourmenuItem);
3753 colourMenu.add(clustalColour);
3754 colourMenu.add(BLOSUM62Colour);
3755 colourMenu.add(PIDColour);
3756 colourMenu.add(zappoColour);
3757 colourMenu.add(taylorColour);
3758 colourMenu.add(hydrophobicityColour);
3759 colourMenu.add(helixColour);
3760 colourMenu.add(strandColour);
3761 colourMenu.add(turnColour);
3762 colourMenu.add(buriedColour);
3763 colourMenu.add(nucleotideColour);
3764 colourMenu.add(purinePyrimidineColour);
3765 // colourMenu.add(RNAInteractionColour);
3766 colourMenu.add(tcoffeeColour);
3767 colourMenu.add(userDefinedColour);
3768 colourMenu.addSeparator();
3769 colourMenu.add(conservationMenuItem);
3770 colourMenu.add(modifyConservation);
3771 colourMenu.add(abovePIDThreshold);
3772 colourMenu.add(modifyPID);
3773 colourMenu.add(annotationColour);
3774 colourMenu.add(RNAHelixColour);
3779 sortMenu.add(sortIDMenuItem);
3780 sortMenu.add(sortLengthMenuItem);
3781 sortMenu.add(sortByTreeMenu);
3782 sortMenu.add(sortGroupMenuItem);
3783 sortMenu.add(sortPairwiseMenuItem);
3784 calculateMenu.add(sortMenu);
3785 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3786 calculateTreeMenu.add(neighbourTreeMenuItem);
3787 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3788 calculateTreeMenu.add(njTreeBlosumMenuItem);
3789 calculateMenu.add(calculateTreeMenu);
3790 calculateMenu.addSeparator();
3791 calculateMenu.add(pairwiseAlignmentMenuItem);
3792 calculateMenu.add(PCAMenuItem);
3793 calculateMenu.add(autoCalculate);
3794 calculateMenu.add(sortByTree);
3799 helpMenu.add(documentation);
3800 helpMenu.add(about);
3805 statusBar.setBackground(Color.white);
3806 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3807 statusBar.setText(MessageManager.getString("label.status_bar"));
3808 this.add(statusBar, BorderLayout.SOUTH);
3812 public void setStatus(String string)
3814 statusBar.setText(string);
3817 MenuItem featureSettings = new MenuItem();
3819 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3821 MenuItem annotationColour = new MenuItem();
3823 MenuItem annotationColumnSelection = new MenuItem();
3825 MenuItem invertColSel = new MenuItem();
3827 MenuItem showColumns = new MenuItem();
3829 MenuItem showSeqs = new MenuItem();
3831 MenuItem hideColumns = new MenuItem();
3833 MenuItem hideSequences = new MenuItem();
3835 MenuItem hideAllButSelection = new MenuItem();
3837 MenuItem hideAllSelection = new MenuItem();
3839 MenuItem showAllHidden = new MenuItem();
3841 MenuItem newView = new MenuItem();
3843 private CheckboxMenuItem showAlignmentAnnotations;
3845 private CheckboxMenuItem showSequenceAnnotations;
3847 private CheckboxMenuItem sortAnnBySequence;
3849 private CheckboxMenuItem sortAnnByLabel;
3851 private CheckboxMenuItem showAutoFirst;
3853 private CheckboxMenuItem showAutoLast;
3855 private SplitFrame splitFrame;
3858 * Attach the alignFrame panels after embedding menus, if necessary. This used
3859 * to be called setEmbedded, but is now creates the dropdown menus in a
3860 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3862 * @param reallyEmbedded
3863 * true to attach the view to the applet area on the page rather than
3866 public void createAlignFrameWindow(boolean reallyEmbedded)
3870 embedAlignFrameInApplet(viewport.applet);
3875 // test and embed menu bar if necessary.
3877 if (embedMenuIfNeeded(alignPanel))
3880 * adjust for status bar height too. ? pointless as overridden by layout
3883 alignPanel.setSize(getSize().width,
3884 getSize().height - statusBar.getHeight());
3886 add(statusBar, BorderLayout.SOUTH);
3887 add(alignPanel, BorderLayout.CENTER);
3888 // and register with the applet so it can pass external API calls to us
3889 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3895 * Add the components of this AlignFrame to the applet container.
3899 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3902 // Explicitly build the embedded menu panel for the on-page applet
3904 // view cannot be closed if its actually on the page
3905 fileMenu.remove(closeMenuItem);
3906 fileMenu.remove(3); // Remove Separator
3907 // construct embedded menu, using default font
3908 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3909 // and actually add the components to the applet area
3910 theApplet.setLayout(new BorderLayout());
3911 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3912 theApplet.add(statusBar, BorderLayout.SOUTH);
3913 // TODO should size be left to the layout manager?
3914 alignPanel.setSize(theApplet.getSize().width,
3915 theApplet.getSize().height - embeddedMenu.getHeight()
3916 - statusBar.getHeight());
3917 theApplet.add(alignPanel, BorderLayout.CENTER);
3918 final AlignFrame me = this;
3919 theApplet.addFocusListener(new FocusListener()
3923 public void focusLost(FocusEvent e)
3925 if (theApplet.currentAlignFrame == me)
3927 theApplet.currentAlignFrame = null;
3932 public void focusGained(FocusEvent e)
3934 theApplet.currentAlignFrame = me;
3937 theApplet.validate();
3941 * create a new binding between structures in an existing jmol viewer instance
3942 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3943 * this does not open a new Jmol window, or modify the display of the
3944 * structures in the original jmol window. Note This method doesn't work
3945 * without an additional javascript library to exchange messages between the
3946 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3949 * JmolViewer instance
3950 * @param sequenceIds
3951 * - sequence Ids to search for associations
3953 public SequenceStructureBinding addStructureViewInstance(
3954 Object jmolviewer, String[] sequenceIds)
3956 Viewer viewer = null;
3959 viewer = (Viewer) jmolviewer;
3960 } catch (ClassCastException ex)
3962 System.err.println("Unsupported viewer object :"
3963 + jmolviewer.getClass());
3967 System.err.println("Can't use this object as a structure viewer:"
3968 + jmolviewer.getClass());
3971 SequenceI[] seqs = null;
3972 if (sequenceIds == null || sequenceIds.length == 0)
3974 seqs = viewport.getAlignment().getSequencesArray();
3978 Vector sqi = new Vector();
3979 AlignmentI al = viewport.getAlignment();
3980 for (int sid = 0; sid < sequenceIds.length; sid++)
3982 SequenceI sq = al.findName(sequenceIds[sid]);
3990 seqs = new SequenceI[sqi.size()];
3991 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3993 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4001 AAStructureBindingModel jmv = null;
4002 // TODO: search for a jmv that involves viewer
4004 { // create a new viewer/jalview binding.
4005 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4012 * bind a pdb file to a sequence in the current view
4015 * - sequenceId within the dataset.
4016 * @param pdbEntryString
4017 * - the short name for the PDB file
4019 * - pdb file - either a URL or a valid PDB file.
4020 * @return true if binding was as success TODO: consider making an exception
4021 * structure for indicating when PDB parsing or sequenceId location
4024 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4027 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4028 boolean needtoadd = false;
4029 if (toaddpdb != null)
4031 Vector pdbe = toaddpdb.getAllPDBEntries();
4032 PDBEntry pdbentry = null;
4033 if (pdbe != null && pdbe.size() > 0)
4035 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4037 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4038 if (!pdbentry.getId().equals(pdbEntryString)
4039 && !pdbentry.getFile().equals(pdbFile))
4049 if (pdbentry == null)
4051 pdbentry = new PDBEntry();
4052 pdbentry.setId(pdbEntryString);
4053 pdbentry.setFile(pdbFile);
4054 needtoadd = true; // add this new entry to sequence.
4056 // resolve data source
4057 // TODO: this code should be a refactored to an io package
4058 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4059 pdbFile, FileFormat.PDB);
4060 if (protocol == null)
4066 pdbentry.setProperty("protocol", protocol);
4067 toaddpdb.addPDBId(pdbentry);
4068 alignPanel.getStructureSelectionManager()
4069 .registerPDBEntry(pdbentry);
4075 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4079 Vector sequences = new Vector();
4080 for (int i = 0; i < seqs.length; i++)
4082 if (seqs[i] != null)
4084 sequences.addElement(new Object[] { seqs[i],
4085 (chains != null) ? chains[i] : null });
4088 seqs = new SequenceI[sequences.size()];
4089 chains = new String[sequences.size()];
4090 for (int i = 0, isize = sequences.size(); i < isize; i++)
4092 Object[] oj = (Object[]) sequences.elementAt(i);
4094 seqs[i] = (SequenceI) oj[0];
4095 chains[i] = (String) oj[1];
4098 return new Object[] { seqs, chains };
4102 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4103 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4105 // Scrub any null sequences from the array
4106 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4107 seqs = (SequenceI[]) sqch[0];
4108 chains = (String[]) sqch[1];
4109 if (seqs == null || seqs.length == 0)
4112 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4114 if (protocol == null)
4116 String sourceType = (String) pdb.getProperty("protocol");
4119 protocol = DataSourceType.valueOf(sourceType);
4120 } catch (IllegalArgumentException e)
4124 if (protocol == null)
4126 System.err.println("Couldn't work out protocol to open structure: "
4131 if (applet.useXtrnalSviewer)
4133 // register the association(s) and quit, don't create any windows.
4134 if (StructureSelectionManager.getStructureSelectionManager(applet)
4135 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4137 System.err.println("Failed to map " + pdb.getFile() + " ("
4138 + protocol + ") to any sequences");
4142 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4144 // can only do alignments with Jmol
4145 // find the last jmol window assigned to this alignment
4146 AppletJmol ajm = null, tajm;
4147 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4148 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4150 tajm = (AppletJmol) jmols.elementAt(i);
4151 if (tajm.ap.alignFrame == this)
4160 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4161 // try and add the pdb structure
4166 // otherwise, create a new window
4167 if (applet.jmolAvailable)
4169 new AppletJmol(pdb, seqs, chains, alignPanel,
4171 applet.lastFrameX += 40;
4172 applet.lastFrameY += 40;
4176 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4181 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4182 SequenceI[][] seqs, String[][] chains, String[] protocols)
4184 // TODO Auto-generated method stub
4185 System.err.println("Aligned Structure View: Not yet implemented.");
4189 * modify the current selection, providing the user has not made a selection
4193 * - sequences from this alignment
4195 * - columns to be selected on the alignment
4197 public void select(SequenceGroup sel, ColumnSelection csel,
4198 HiddenColumns hidden)
4200 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4203 public void scrollTo(int row, int column)
4205 alignPanel.seqPanel.scrollTo(row, column);
4208 public void scrollToRow(int row)
4210 alignPanel.seqPanel.scrollToRow(row);
4213 public void scrollToColumn(int column)
4215 alignPanel.seqPanel.scrollToColumn(column);
4219 * @return the alignments unique ID.
4221 public String getSequenceSetId()
4223 return viewport.getSequenceSetId();
4227 * Load the (T-Coffee) score file from the specified url
4230 * File/URL/T-COFFEE score file contents
4231 * @throws IOException
4232 * @return true if alignment was annotated with data from source
4234 public boolean loadScoreFile(String source) throws IOException
4237 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4238 AppletFormatAdapter.checkProtocol(source));
4239 if (!file.isValid())
4241 // TODO: raise dialog for gui
4242 System.err.println("Problems parsing T-Coffee scores: "
4243 + file.getWarningMessage());
4244 System.err.println("Origin was:\n" + source);
4249 * check that the score matrix matches the alignment dimensions
4252 if ((aln = viewport.getAlignment()) != null
4253 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4256 // TODO: raise a dialog box here rather than bomb out.
4258 .println("The scores matrix does not match the alignment dimensions");
4262 // TODO add parameter to indicate if matching should be done
4263 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4265 alignPanel.fontChanged();
4266 tcoffeeColour.setEnabled(true);
4267 // switch to this color
4268 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4273 System.err.println("Problems resolving T-Coffee scores:");
4274 if (file.getWarningMessage() != null)
4276 System.err.println(file.getWarningMessage());
4282 public SplitFrame getSplitFrame()
4284 return this.splitFrame;
4287 public void setSplitFrame(SplitFrame sf)
4289 this.splitFrame = sf;
4292 // may not need this
4294 public void setShowSeqFeatures(boolean b)
4296 // showSeqFeatures.setSelected(b);
4297 viewport.setShowSequenceFeatures(b);
4302 public void setMenusForViewport()
4304 // setMenusFromViewport(viewport);
4309 public void refreshFeatureUI(boolean enableIfNecessary)
4311 if (enableIfNecessary)
4313 sequenceFeatures.setState(true);
4314 alignPanel.av.setShowSequenceFeatures(true);
4319 public FeatureSettingsControllerI getFeatureSettingsUI()
4321 return alignPanel.av.featureSettings;