useDynLib(ShortRead, .registration=TRUE)

import(zlibbioc)

importClassesFrom(Biobase, AnnotatedDataFrame, Versioned,
                  ScalarCharacter, ScalarNumeric, ScalarInteger,
                  ScalarLogical, AssayData)

importClassesFrom(Biostrings, BStringSet, DNAStringSet,
                  PairwiseAlignedXStringSet,
                  SolexaQuality, PhredQuality, XStringQuality)

importClassesFrom(IRanges, RangesList, SimpleRleList)

importFrom(grDevices, colorRampPalette)

importFrom(BiocGenerics, Filter, lapply, mapply, sapply, Map,
           cbind, rbind, strand)

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

importFrom(IRanges, append, as.list, as.vector, coverage, head,
           narrow, score, split, start, unlist, Views, width, with,
           "%in%")

importFrom(lattice, dotplot, histogram, levelplot, llines,
           panel.abline, panel.histogram, panel.levelplot,
           panel.xyplot, panel.grid, xyplot)

importFrom(methods, Ops)

importMethodsFrom(IRanges, Ops, coerce)

importFrom(GenomicRanges, GappedAlignments, left, right)

importFrom(Biostrings, BString, BStringSet, DNAString, DNAStringSet,
           alphabetFrequency, alphabet, DNA_ALPHABET,
           quality, pairwiseAlignment, pattern,
           trimLRPatterns, unaligned, detail,
           readDNAStringSet, writeXStringSet)

importFrom(hwriter, hwrite, hwriteImage)

importFrom(Rsamtools, scanBam, ScanBamParam, bamSimpleCigar, 
           bamReverseComplement, bamWhat, bamFlagTest, isOpen)

exportClassPattern("^.*$")

exportMethods(show, coerce, dim, length, "[", "[[", alphabetFrequency,
              alphabet, coverage, narrow, strand, trimLRPatterns,
              width, append, rbind, "%in%", c, lapply, sapply)

export(pData, phenoData, varLabels, varMetadata)

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