NAMESPACE

import(methods)
importFrom(utils, data, download.file, read.delim, read.table, read.csv,
                  write.table, as.roman)
importFrom(stats, setNames, update)
importFrom(stats4, summary)

import(BiocGenerics)
import(S4Vectors)
import(IRanges)  # for CompressedList
import(UCSC.utils)
import(GenomeInfoDbData)


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### Export S4 classes
###

exportClasses(
    Seqinfo,
    GenomeDescription
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###

S3method(as.data.frame, Seqinfo)

S3method(merge, Seqinfo)

S3method(summary, Seqinfo)

S3method(update, 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(
    as.data.frame.Seqinfo,

    merge.Seqinfo,

    summary.Seqinfo,

    update.Seqinfo
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics NOT defined in this package
###

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

    ## Generics defined in the stats package:
    update,

    ## Generics defined in the stats4 package:
    summary,

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


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### Export non-generic functions
###

export(
    ## utils.R:
    DEFAULT_CIRC_SEQS,

    ## list_ftp_dir.R:
    list_ftp_dir,

    ## rankSeqlevels.R:
    orderSeqlevels,
    rankSeqlevels,

    ## NCBI-utils.R:
    find_NCBI_assembly_ftp_dir,
    fetch_assembly_report,

    ## getChromInfoFromNCBI.R:
    registered_NCBI_assemblies,
    getChromInfoFromNCBI,

    ## getChromInfoFromUCSC.R:
    registered_UCSC_genomes,
    getChromInfoFromUCSC,
    get_and_fix_chrom_info_from_UCSC,
    saveAssembledMoleculesInfoFromUCSC,

    ## getChromInfoFromEnsembl.R:
    getChromInfoFromEnsembl,

    ## loadTaxonomyDb.R:
    loadTaxonomyDb,

    ## mapGenomeBuilds.R
    mapGenomeBuilds,
    genomeBuilds,
    listOrganisms,

    ## Seqinfo-class.R:
    Seqinfo, checkCompatibleSeqinfo,

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

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

    ## GenomeDescription-classR:
    GenomeDescription
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 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, bsgenomeName
)

### Exactly the same list as above.
exportMethods(
    seqinfo,
    seqnames, "seqnames<-",
    seqlevels, "seqlevels<-",
    sortSeqlevels,
    seqlevelsInUse,
    seqlengths, "seqlengths<-",
    isCircular, "isCircular<-",
    genome, "genome<-",
    seqlevelsStyle, "seqlevelsStyle<-",
    commonName, provider, providerVersion,
    releaseDate, bsgenomeName
)