import(methods)
importFrom(utils, read.delim, .DollarNames)
importFrom(stats, setNames)
importFrom(tools, file_path_as_absolute)
importClassFrom(Matrix, Matrix)  # for the "acbind" and "arbind" methods
import(BiocGenerics)
importFrom(MatrixGenerics, rowRanges)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(Biobase)
import(DelayedArray)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###

exportClasses(
    Assays, SimpleAssays, ShallowData, ShallowSimpleListAssays,
    Assays_OR_NULL,
    SummarizedExperiment,
    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,
    is.unsorted, order, rank, sort,
    start, "start<-", end, "end<-", width, "width<-",
    strand, "strand<-",
    updateObject,

    ## Generics defined in S4Vectors:
    showAsCell,
    "metadata<-",
    parallel_slot_names, vertical_slot_names, horizontal_slot_names,
    mcols, "mcols<-",
    elementMetadata, "elementMetadata<-",
    values, "values<-",
    subset,
    pcompare,

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

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

    ## Generics defined in DelayedArray:
    acbind, arbind,
    rowRanges, realize
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###

export(
    Assays,
    SummarizedExperiment,
    .DollarNames.SummarizedExperiment,
    .DollarNames.RangedSummarizedExperiment,
    makeSummarizedExperimentFromExpressionSet,
    makeSummarizedExperimentFromDataFrame,
    makeSummarizedExperimentFromLoom,
    naiveRangeMapper, probeRangeMapper, geneRangeMapper,
    readKallisto, readKallistoBootstrap, KALLISTO_ASSAYS
)


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

export(
    "rowRanges<-",
    rowData, "rowData<-",
    colData, "colData<-",
    assayNames, "assayNames<-",
    assays, "assays<-",
    assay, "assay<-"
)

### Exactly the same list as above.
exportMethods(
    "rowRanges<-",
    rowData, "rowData<-",
    colData, "colData<-",
    assayNames, "assayNames<-",
    assays, "assays<-",
    assay, "assay<-"
)

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Register S3 methods
###

S3method(.DollarNames, SummarizedExperiment)
S3method(.DollarNames, RangedSummarizedExperiment)