#useDynLib(Rolexa, .registration=TRUE)

import(mclust)

importClassesFrom(ShortRead, SFastqQuality, ShortRead, ShortReadQ, SolexaIntensity, SolexaIntensityInfo, SolexaPath)
importMethodsFrom(ShortRead, experimentPath, readFastq, readIntensities, readPrb, SFastqQuality, writeFastq)
importFrom(ShortRead, baseCallPath, id, intensity, readInfo, readXStringColumns, sread)

importMethodsFrom(Biostrings, quality)
importFrom(Biostrings, BStringSet, DNAStringSet, DNA_ALPHABET, IUPAC_CODE_MAP)

importMethodsFrom(IRanges, as.matrix, cor, median, nchar)

importClassesFrom(methods, array, character, integer, logical, numeric)
importFrom(methods, "@<-", as, new)
importFrom(graphics, abline, boxplot, hist, image, lines, par, plot, points, text, title)
importFrom(grDevices, heat.colors)
importFrom(stats, density, loess, loess.control, optim, predict)

exportClassPattern("^[^\\.]")
exportPattern("^[^\\.]")

