BatchAnalysis	Plots1
BatchAnalysis,RolexaRun-method	Plots1
ChannelHistogram	Plots2
ChannelHistogram,SolexaIntensity-method	Plots2
CombinedPlot	Plots2
CombinedPlot,RolexaRun-method	Plots2
CombineFastQ	Files
CombineFastQ,RolexaRun,SolexaPath-method	Files
CombineReads	Files
CombineReads,RolexaRun,SolexaPath-method	Files
DeCorrelateChannels	Model1
DeCorrelateChannels,array-method	Model1
DeCorrelateChannels,SolexaIntensity-method	Model1
DeCorrelateCycles	Model1
DeCorrelateCycles,array-method	Model1
DeCorrelateCycles,SolexaIntensity-method	Model1
FilterResults	Model2
FilterResults,RolexaRun-method	Model2
ForkBatch	Batch
GetModel	AllClasses
OneBatch	Batch
OneBatch,RolexaRun-method	Batch
OptimizeAngle	Model1
OptimizeAngle,SolexaIntensity-method	Model1
OptimizeRate	Model1
OptimizeRate,SolexaIntensity-method	Model1
PlotCycles	Plots1
PlotCycles,RolexaRun-method	Plots1
QualityBoxPlots	Plots1
RolexaRun	AllClasses
RolexaRun-class	AllClasses
SaveResults	Files
SaveResults,RolexaRun-method	Files
SeqScore	Model3
SeqScore,RolexaRun-method	Model3
SetModel	AllClasses
TileImage	Plots3
TileImage,SolexaIntensity-method	Plots3
TileNormalize	Model1
TileNormalize,RolexaRun-method	Model1
