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JustifyLeftOrRightCommand MSFfile JalviewFileChooser.recentlyOpenedCellRenderer ScoreMatrixFile Conservation AlignmentAnnotationUtils RemoveGapColCommand CigarBase PileUpfile AAFrequency MappedFeatures FeatureColourFinder StockholmFile IdentifyFile SequenceAnnotationReport Grouping AverageDistanceEngine AlignmentUtils ClustalFile RegOpt

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1.	0.2527156525.3%	jalview.gui 8223
2.	0.647588964.8%	jalview.datamodel 3271
3.	0.4296144243%	jalview.io 3203
4.	0.00%	jalview.appletgui 3048
5.	0.1538966315.4%	com.stevesoft.pat 3038

1.	0.00278551530.3%	CaseMgr 1433
2.	0.451424245.1%	Jalview2XML 827
3.	0.273972627.4%	AlignFrame 745
4.	0.00%	AlignFrame 566
5.	0.667372966.7%	AlignmentViewport 486

1.	0.00%	Bits.letter_f() : void 1
2.	0.00%	AlignFrame.jbInit() : void 2
3.	0.00%	AlignFrame.actionPerformed(ActionEvent) : void 85
4.	0.00%	RestJobThread.realiseResults(boolean) : void 57
5.	0.00%	VamsasAppDatastore.storeVAMSAS(AlignViewport,String) : boolean 57
6.	0.00%	GPreferences.initVisualTab() : JPanel 2
7.	0.00%	AnnotationFile.printAnnotations(AlignmentAnnotation[],List<SequenceGroup>,Hashtable,HiddenColumns,AlignmentI,ViewDef) : String 62
8.	0.00%	VamsasAppDatastore.updateToJalview() : int 50
9.	0.00%	Preferences.Preferences() 21
10.	0.00%	SeqPanel.editSequence(boolean,int) : void 72
11.	0.00%	AlignFrame.paste(boolean) : void 48
12.	0.00%	AlignFrame.keyPressed(KeyEvent) : void 76
13.	0.00%	Launcher.main(String[]) : void 48
14.	0.00%	JSONParser.parse(Reader,ContentHandler,boolean) : void 50
15.	0.00%	JSONML.parse(XMLTokener,boolean,JSONArray,boolean) : Object 48
16.	0.00%	GPreferences.initConnTabProxyPanel() : JPanel 2
17.	0.00%	XML.parse(XMLTokener,JSONObject,String,boolean) : boolean 37
18.	0.00%	AnnotationLabels.mousePressed(MouseEvent) : void 31
19.	0.00%	SimpleBlastFile.parse() : void 43
20.	0.00%	VamsasAppDatastore.getjAlignmentAnnotation(jalview.datamodel.AlignmentI,uk.ac.vamsas.objects.core.RangeAnnotation) : jalview.datamodel.AlignmentAnnotation 43