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JnetAnnotationMaker GffHelperBase Conservation MappedFeatures JustifyLeftOrRightCommand ScoreMatrixFile Rna MSFfile FeatureAttributes.AttributeData JalviewFileChooser.recentlyOpenedCellRenderer TreePanel.TreeLoader AlignmentAnnotationUtils FeatureRendererSettings PileUpfile AAFrequency RemoveGapColCommand FeatureColourFinder CigarBase Grouping AverageDistanceEngine

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1.	0.3370544333.7%	jalview.gui 8653
2.	0.5958177459.6%	jalview.io 3440
3.	0.737062773.7%	jalview.datamodel 3438
4.	0.00%	jalview.appletgui 3050
5.	0.158080415.8%	com.stevesoft.pat 3038

1.	0.00278551530.3%	CaseMgr 1433
2.	0.754305175.4%	Jalview2XML 869
3.	0.3171571831.7%	AlignFrame 835
4.	0.00%	AlignFrame 570
5.	0.7606557676.1%	AlignmentViewport 531

1.	0.00%	Bits.letter_f() : void 1
2.	0.00%	AlignFrame.jbInit() : void 2
3.	0.00%	AlignFrame.actionPerformed(ActionEvent) : void 87
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%	SeqPanel.editSequence(boolean,int) : void 72
8.	0.00%	AlignFrame.paste(boolean) : void 48
9.	0.00%	AlignFrame.keyPressed(KeyEvent) : void 76
10.	0.00%	AppletParams.addParam(List<String>,String,Object,AppletParams,String) : void 77
11.	0.00%	Launcher.main(String[]) : void 48
12.	0.00%	JSONParser.parse(Reader,ContentHandler,boolean) : void 50
13.	0.00%	JSONML.parse(XMLTokener,boolean,JSONArray,boolean) : Object 48
14.	0.00%	Preferences.ok_actionPerformed(ActionEvent) : void 19
15.	0.00%	XML.parse(XMLTokener,JSONObject,String,boolean) : boolean 37
16.	0.00%	AnnotationLabels.mousePressed(MouseEvent) : void 31
17.	0.00%	SimpleBlastFile.parse() : void 43
18.	0.00%	VamsasAppDatastore.getjAlignmentAnnotation(jalview.datamodel.AlignmentI,uk.ac.vamsas.objects.core.RangeAnnotation) : jalview.datamodel.AlignmentAnnotation 43
19.	0.00%	GroupUrlLink.makeUrlsIf(boolean,Hashtable,boolean) : Object[] 42
20.	0.00%	ccAnalysis.run() : MatrixI 21