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CaseMgr Launcher JnetAnnotationMaker RegOpt ParsePackedSet JobStateSummary AnnotationRenderer CodonComparator StructureFrequency ColourSchemeMapper AnnotationFile GetdownLauncherUpdate parsePerl IdentifyFile VarnaCommands StockholmFile JalviewFileChooser.recentlyOpenedCellRenderer JustifyLeftOrRightCommand AppJmol.RenderPanel AlignmentAnnotationUtils

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1.	0.00%	jalview.gui 8104
2.	0.00%	jalview.datamodel 3242
3.	0.00%	jalview.io 3201
4.	0.00%	jalview.appletgui 3048
5.	0.00%	com.stevesoft.pat 3038

1.	0.00%	CaseMgr 1433
2.	0.00%	Jalview2XML 817
3.	0.00%	AlignFrame 730
4.	0.00%	AlignFrame 566
5.	0.00%	Desktop 470

1.	0.00%	Bits.letter_f() : void 1
2.	0.00%	CaseMgr.toLowerCase(char) : char 706
3.	0.00%	CaseMgr.toUpperCase(char) : char 675
4.	0.00%	ResidueProperties.<clinit>, line 1105() 1
5.	0.00%	Jalview2XML.saveState(AlignmentPanel,String,boolean,JarOutputStream,List<String>) : JalviewModel 106
6.	0.00%	GAlignFrame.jbInit() : void 7
7.	0.00%	Jalview.doMain(String[]) : void 146
8.	0.00%	AnnotationRenderer.drawComponent(AwtRenderPanelI,AlignViewportI,Graphics,int,int,int) : boolean 226
9.	0.00%	Jalview2XML.loadFromObject(JalviewModel,String,boolean,jarInputStreamProvider) : AlignFrame 118
10.	0.00%	Commands.processLinked(String) : boolean 94
11.	0.00%	AlignFrame.jbInit() : void 2
12.	0.00%	Regex.compile1(StrPos,Rthings) : void 95
13.	0.00%	AlignFrame.actionPerformed(ActionEvent) : void 85
14.	0.00%	AnnotationFile.parseAnnotationFrom(AlignmentI,HiddenColumns,BufferedReader) : boolean 68
15.	0.00%	RestJobThread.realiseResults(boolean) : void 57
16.	0.00%	StockholmFile.parse() : void 60
17.	0.00%	VamsasAppDatastore.storeVAMSAS(AlignViewport,String) : boolean 57
18.	0.00%	AnnotationLabels.drawLabels(Graphics,boolean,int,boolean,boolean,FontMetrics,boolean) : int 83
19.	0.00%	Jalview2XML.loadViewport(String,List<JSeq>,List<SequenceI>,AlignmentI,JalviewModel,Viewport,String,String,List<JvAnnotRow>) : AlignFrame 42
20.	0.00%	ArgParser.parse(List<String>,boolean,boolean) : void 83