NAMESPACE

import(methods)
importFrom(stats, setNames)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(Biobase)


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### Export S4 classes
###

exportClasses(
    ## TODO: Uncomment the line below once these helper classes are defined in
    ## the SummarizedExperiment package. Otherwise, RangedSummarizedExperiment
    ## objects that have been serialized *before* these helper classes were
    ## moved are going to look broken (i.e. validObjet() will fail on them).
    #Assays, ShallowData, ShallowSimpleListAssays,

    SummarizedExperiment0,
    RangedSummarizedExperiment
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in SummarizedExperiment
###

exportMethods(
    length, names, "names<-",
    dim, dimnames, "dimnames<-",
    "[", "[<-", "[[", "[[<-", "$", "$<-",
    as.data.frame,
    coerce,
    show,
    c,
    merge,
    Compare,

    ## Generics defined in BiocGenerics:
    cbind, rbind,
    duplicated, match,
    order, rank, sort,
    updateObject,
    start, "start<-", end, "end<-", width, "width<-",
    strand, "strand<-",

    ## Generics defined in S4Vectors:
    "metadata<-",
    mcols, "mcols<-",
    elementMetadata, "elementMetadata<-",
    values, "values<-",
    extractROWS, replaceROWS,
    subset,
    compare,

    ## Generics defined in IRanges:
    ranges, "ranges<-",
    shift, narrow, resize, flank, promoters, restrict, trim,
    isDisjoint, disjointBins,
    coverage,
    findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps,
    precede, follow, nearest, distance, distanceToNearest,

    ## Generics defined in GenomeInfoDb:
    seqinfo, "seqinfo<-",
    seqnames, "seqnames<-",

    ## Generics defined in GenomicRanges (at some point, these generics will
    ## be defined in SummarizedExperiment):
    SummarizedExperiment,
    rowRanges, "rowRanges<-",
    colData, "colData<-",
    assayNames, "assayNames<-",
    assays, "assays<-",
    assay, "assay<-"
)


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### Export non-generic functions
###

export(
    Assays,
    .DollarNames.SummarizedExperiment0,
    makeSummarizedExperimentFromExpressionSet,
    naiveRangeMapper, probeRangeMapper, geneRangeMapper
)


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

export(
)

### Exactly the same list as above.
exportMethods(
)