NAMESPACE

useDynLib(qrqc, .registration=TRUE)

importClassesFrom(methods, character, data.frame, integer, list,
                  logical, numeric)
importMethodsFrom(Biostrings, quality)
importMethodsFrom(methods, show)
import(biovizBase)
import(ggplot2)
import(reshape)
importFrom(graphics, abline, axis, layout, lines, par, plot.new,
           plot.window, points, title)
importFrom(methods, new)
importFrom(plyr, count)

importFrom(stats, approxfun, lowess, weighted.mean)

# common between ggplot2 rewrite and older version
export(readSeqFile)
export(makeReport)
exportClassPattern("^.*$")

# new plotting functions
export(getBase)
export(getKmer)
export(getBaseProp)
export(getQual)
export(getGC)
export(getMCQual)
export(getSeqlen)
export(basePlot)
export(qualPlot)
export(seqlenPlot)
export(gcPlot)
export(geom_qlinerange)
export(list2df)
export(scale_color_iupac)
export(scale_color_dna)
export(kmerKLPlot)
export(kmerEntropyPlot)
export(calcKL)

# deprecated
export(plotQuals)
export(plotBases)
export(plotSeqLengths)
export(plotGC)