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ScaleRenderer AlignmentAnnotationUtils GffHelperBase Conservation MSFfile ScoreMatrixFile Rna MappedFeatures MemorySetting FeatureRendererSettings FeatureAttributes.AttributeData AlignmentUtils RemoveGapColCommand PileUpfile StringUtils CigarBase FeatureColourFinder ColorUtils AAFrequency Grouping

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1.	0.2829166428.3%	jalview.gui 7054
2.	0.00%	jalview.appletgui 3046
3.	0.1573420815.7%	com.stevesoft.pat 3038
4.	0.5388086453.9%	jalview.io 2898
5.	0.734025973.4%	jalview.datamodel 2798

1.	0.00278551530.3%	CaseMgr 1433
2.	0.7461738674.6%	Jalview2XML 747
3.	0.3023715330.2%	AlignFrame 661
4.	0.00%	AlignFrame 566
5.	0.7497921675%	AlignmentViewport 423

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%	VamsasAppDatastore.updateToJalview() : int 50
7.	0.00%	GPreferences.initVisualTab() : JPanel 2
8.	0.00%	SeqPanel.editSequence(boolean,int) : void 72
9.	0.00%	AlignFrame.keyPressed(KeyEvent) : void 76
10.	0.00%	AlignFrame.paste(boolean) : void 47
11.	0.00%	JSONParser.parse(Reader,ContentHandler,boolean) : void 50
12.	0.00%	Preferences.Preferences() 17
13.	0.00%	JSONML.parse(XMLTokener,boolean,JSONArray,boolean) : Object 48
14.	0.00%	XML.parse(XMLTokener,JSONObject,String,boolean) : boolean 37
15.	0.00%	AnnotationLabels.mousePressed(MouseEvent) : void 31
16.	0.00%	SimpleBlastFile.parse() : void 43
17.	0.00%	VamsasAppDatastore.getjAlignmentAnnotation(jalview.datamodel.AlignmentI,uk.ac.vamsas.objects.core.RangeAnnotation) : jalview.datamodel.AlignmentAnnotation 43
18.	0.00%	GroupUrlLink.makeUrlsIf(boolean,Hashtable,boolean) : Object[] 42
19.	0.00%	AlignmentView.getUpdatedView(SequenceI[][],AlignmentOrder[],char) : Object[] 38
20.	0.00%	FeatureRenderer.amendFeatures(List<SequenceI>,List<SequenceFeature>,boolean,AlignmentPanel) : boolean 21