NAMESPACE

import(methods)
importFrom(stats4, summary)

import(BiocGenerics)
import(S4Vectors)
import(IRanges)  # for CompressedList


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### Export non-generic functions
###

export(
    ## rankSeqlevels.R:
    orderSeqlevels,
    rankSeqlevels,

    ## fetchExtendedChromInfoFromUCSC.R:
    fetchExtendedChromInfoFromUCSC,

    ## seqlevelsStyle.R:
    genomeStyles,
    extractSeqlevels,
    extractSeqlevelsByGroup,
    mapSeqlevels,
    seqlevelsInGroup,

    ## seqlevels-wrappers.R:
    keepSeqlevels, dropSeqlevels, renameSeqlevels, restoreSeqlevels,
    keepStandardChromosomes,

    ## Seqinfo-class.R:
    Seqinfo,

    ## GenomeDescription-classR:
    GenomeDescription
)


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### Export S4 classes
###

exportClasses(
    Seqinfo,
    GenomeDescription
)


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### Export S3 methods
###

S3method(summary, Seqinfo)

### We also export them thru the export() directive so that (a) they can be
### called directly, (b) tab-completion on the name of the generic shows them,
### and (c) methods() doesn't asterisk them.
export(
    summary.Seqinfo
)


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### Export S4 methods for generics not defined in GenomeInfoDb
###

exportMethods(
    length,
    names, "names<-",
    "[",
    as.data.frame,
    show,
    merge,

    ## Generics defined in the stats4 package:
    summary,

    ## Generics defined in the BiocGenerics package:
    intersect, organism, species
)


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### Export S4 generics defined in GenomeInfoDb + export corresponding methods
###

export(
    ## seqinfo.R:
    seqinfo, "seqinfo<-",
    seqnames, "seqnames<-",
    seqlevels, "seqlevels<-",
    sortSeqlevels,
    seqlevelsInUse,
    seqlevels0,
    seqlengths, "seqlengths<-",
    isCircular, "isCircular<-",
    genome, "genome<-",

    ## seqlevelsStyle.R:
    seqlevelsStyle, "seqlevelsStyle<-",

    ## GenomeDescription-class.R:
    commonName, provider, providerVersion,
    releaseDate, releaseName, bsgenomeName,
    available.species
)

exportMethods(
    seqinfo,
    seqnames, "seqnames<-",
    seqlevels, "seqlevels<-",
    sortSeqlevels,
    seqlevelsInUse,
    seqlengths, "seqlengths<-",
    isCircular, "isCircular<-",
    genome, "genome<-",
    seqlevelsStyle, "seqlevelsStyle<-",
    commonName, provider, providerVersion,
    releaseDate, releaseName, bsgenomeName
)