import(methods)
import(utils)
import(graphics)
import(stats)
import(parallel)

exportClasses(
    ## from R/S3-classes-as-S4-classes.R:
    connection,
    file, url, gzfile, bzfile, unz, pipe,
    fifo, sockconn, terminal, textConnection,
    gzcon,
    characterORconnection,
    AsIs,
    #table, xtabs,
    dist
)


### ==========================================================================
### Export functions defined in base R and explicitly promoted to generics in
### the BiocGenerics package
### --------------------------------------------------------------------------

### Generics for functions defined in package base:
export(
    ## from R/append.R:
    append,

    ## from R/as.data.frame.R:
    as.data.frame,

    ## from R/as.list.R:
    as.list,

    ## from R/as.vector.R:
    as.vector,

    ## from R/cbind.R:
    cbind, rbind,

    ## from R/do.call.R:
    do.call,

    ## from R/duplicated.R:
    duplicated, anyDuplicated,

    ## from R/eval.R:
    eval, evalq,

    ## from R/Extremes.R:
    pmax, pmin, pmax.int, pmin.int,

    ## from R/funprog.R:
    Reduce, Filter, Find, Map, Position,

    ## from R/get.R:
    get, mget,

    ## from R/grepl.R:
    grep, grepl,

    ## from R/is.unsorted.R:
    is.unsorted,
 
    ## from R/lapply.R:
    lapply, sapply,

    ## from R/lengths.R:
    lengths,

    ## from R/mapply.R:
    mapply,

    ## from R/match.R:
    match,

    ## from R/matrix-summary.R:
    rowSums, rowMeans,
    colSums, colMeans,

    ## from R/mean.R:
    mean,

    ## from R/nrow.R:
    nrow, ncol, NROW, NCOL,

    ## from R/order.R:
    order,

    ## from R/paste.R:
    paste,

    ## from R/rank.R:
    rank,

    ## from R/rep.R:
    rep.int,

    ## from R/row_colnames.R:
    rownames, "rownames<-", colnames, "colnames<-",

    ## from R/sets.R:
    union, intersect, setdiff,

    ## from R/sort.R:
    sort,

    ## from R/start.R:
    start, "start<-",
    end, "end<-",
    width, "width<-",

    ## from R/subset.R:
    subset,

    ## from R/t.R:
    t,

    ## from R/table.R:
    table,

    ## from R/tapply.R:
    tapply,

    ## from R/unique.R:
    unique,

    ## from R/unlist.R:
    unlist,

    ## from R/unsplit.R:
    unsplit,

    ## from R/which.R:
    which, which.max, which.min
)

### Generics for functions defined in package utils:
export(
    ## from R/relist.R:
    relist
)

### Generics for functions defined in package graphics:
export(
    ## from R/boxplot.R:
    boxplot,

    ## from R/image.R:
    image
)

### Generics for functions defined in package stats:
export(
    ## from R/density.R:
    density,

    ## from R/IQR.R:
    IQR,

    ## from R/mad.R:
    mad,

    ## from R/residuals.R:
    residuals,

    ## from R/var.R:
    var, sd,

    ## from R/weights.R:
    weights,

    ## from R/xtabs.R:
    xtabs
)

### Generics for functions defined in package parallel:
export(
    ## from R/clusterApply.R:
    clusterCall, clusterApply, clusterApplyLB,
    clusterEvalQ, clusterExport,
    clusterMap, clusterSplit,
    parLapply, parSapply, parApply, parRapply, parCapply,
    parLapplyLB, parSapplyLB
)


### ==========================================================================
### Export Bioconductor specific generics and their methods
### --------------------------------------------------------------------------

export(
    ## from R/annotation.R:
    annotation, "annotation<-",

    ## from R/combine.R:
    combine,

    ## from R/dbconn.R:
    dbconn, dbfile,

    ## from R/fileName.R:
    fileName,

    ## from R/normalize.R:
    normalize,

    ## from R/Ontology.R:
    Ontology,

    ## from R/organism_species.R:
    organism, "organism<-",
    species, "species<-",

    ## from R/plotMA.R:
    plotMA,

    ## from R/plotPCA.R:
    plotPCA,

    ## from R/score.R:
    score, "score<-",

    ## from R/strand.R:
    strand, "strand<-", invertStrand,

    ## from R/updateObject.R:
    updateObject,
    updateObjectFromSlots,
    getObjectSlots
)

exportMethods(
    ## from R/combine.R:
    combine,

    ## from R/updateObject.R:
    updateObject,

    ## from R/dge.R:
    counts, "counts<-",
    design, "design<-",
    dispTable, "dispTable<-",
    sizeFactors, "sizeFactors<-",
    conditions, "conditions<-",
    estimateSizeFactors, 
    estimateDispersions,
    plotDispEsts,
    plotMA,
    plotPCA,

    ## from R/strand.R:
    invertStrand
)


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

export(
    ## from R/strand.R:
    unstrand
)