useDynLib(ShortRead, .registration=TRUE)

importClassesFrom(Biobase, AnnotatedDataFrame, Versioned,
                  ScalarCharacter)

importClassesFrom(Biostrings, BStringSet, DNAStringSet,
                  PairwiseAlignedXStringSet)

importFrom(Biobase, selectSome, subListExtract, copySubstitute,
           "dimLabels<-",
           pData, phenoData, varLabels, varMetadata, sampleNames,
           mkScalar)

importFrom(IRanges, append, coverage, narrow, score, start, Views,
           width)

importFrom(BSgenome, strand)

importFrom(Biostrings, BStringSet, DNAStringSet,
           alphabetFrequency, alphabet, DNA_ALPHABET,
           quality, pairwiseAlignment, pattern,
           trimLRPatterns, unaligned)

importFrom(hwriter, hwrite, hwriteImage)

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

exportMethods(show, coerce, dim, length, "[", "[[", alphabetFrequency,
              alphabet, coverage, narrow, strand, trimLRPatterns,
              width, append)
export(pData, phenoData, varLabels, varMetadata)

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