useDynLib(ShortRead, .registration=TRUE)

importClassesFrom(Biobase, AnnotatedDataFrame, Versioned,
                  ScalarCharacter)

importClassesFrom(Biostrings, BStringSet, DNAStringSet)

importFrom(Biobase, selectSome, phenoData, featureData, sampleNames,
           mkScalar)

importFrom(IRanges, coverage, width, strand)

importFrom(Biostrings, BStringSet, DNAStringSet,
           alphabetFrequency, alphabet,
           quality, pairwiseAlignment)

exportClasses(SRError, SRWarn, SRList, SRVector, SRFilter,
              QualityScore, IntegerQuality, NumericQuality, MatrixQuality,
              FastqQuality, SFastqQuality,
              ShortRead, ShortReadQ,
              AlignedDataFrame, AlignedRead,
              SolexaPath, SolexaSet, SolexaExportQA,
              SRSet, RochePath, RocheSet)

exportMethods(show, length, "[", "[[",
              alphabetFrequency, alphabet, coverage,
              strand, width)

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