NAMESPACE

useDynLib(S4Vectors)

import(methods)
importFrom(utils, head, tail, head.matrix, tail.matrix, getS3method)
importFrom(stats, cov, cor, median, quantile,
           smoothEnds, runmed, window, "window<-", aggregate,
           na.omit, na.exclude, complete.cases, setNames, terms)
importFrom(stats4, summary, update)

import(BiocGenerics)


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

exportClasses(
    character_OR_NULL, vector_OR_factor,
    LLint, integer_OR_LLint,
    DataTable,
    NSBS,
    Annotated,
    DataTable_OR_NULL, Vector,
    Hits, SelfHits, SortedByQueryHits, SortedByQuerySelfHits,
    Rle,
    List, list_OR_List,
    SimpleList,
    HitsList, SortedByQueryHitsList,
    DataFrame,
    Pairs,
    expression_OR_function, FilterRules, FilterMatrix
)


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

S3method(aggregate, Vector)

S3method(anyDuplicated, NSBS)

S3method(as.character, LLint)

S3method(as.data.frame, Vector)
S3method(as.data.frame, DataTable)

S3method(as.integer, LLint)

S3method(as.list, Vector)

S3method(as.logical, LLint)

S3method(as.matrix, Vector)

S3method(as.numeric, LLint)

S3method(as.vector, Rle)

S3method(cbind, DataFrame)

S3method(diff, Rle)

S3method(droplevels, List)
S3method(droplevels, Rle)

S3method(duplicated, DataTable)
S3method(duplicated, Vector)

S3method(head, DataTable)
S3method(head, LLint)
S3method(head, Vector)

S3method(intersect, Vector)

S3method(levels, Rle)

S3method(mean, Rle)

S3method(median, Rle)

S3method(quantile, Rle)

S3method(rbind, DataFrame)

S3method(rev, Vector)
S3method(rev, Rle)

S3method(setdiff, Vector)

S3method(setequal, Vector)

S3method(sort, Vector)

S3method(subset, Vector)

S3method(summary, Rle)

S3method(t, Hits)
S3method(t, HitsList)

S3method(tail, DataTable)
S3method(tail, LLint)
S3method(tail, Vector)

S3method(union, Vector)

S3method(unique, DataTable)
S3method(unique, Vector)

S3method(window, LLint)
S3method(window, Vector)

### 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(
    aggregate.Vector,

    anyDuplicated.NSBS,

    as.character.LLint,

    as.data.frame.Vector,
    as.data.frame.DataTable,

    as.integer.LLint,

    as.list.Vector,

    as.logical.LLint,

    as.matrix.Vector,

    as.numeric.LLint,

    as.vector.Rle,

    cbind.DataFrame,

    diff.Rle,

    droplevels.Rle,
    droplevels.List,
    
    duplicated.DataTable,
    duplicated.Vector,

    head.DataTable,
    head.LLint,
    head.Vector,

    intersect.Vector,

    levels.Rle,

    mean.Rle,

    median.Rle,

    quantile.Rle,

    rbind.DataFrame,

    rev.Vector,
    rev.Rle,

    setdiff.Vector,

    setequal.Vector,

    sort.Vector,

    subset.Vector,

    summary.Rle,

    t.Hits,
    t.HitsList,

    tail.DataTable,
    tail.LLint,
    tail.Vector,

    union.Vector,

    unique.DataTable,
    unique.Vector,

    window.LLint,
    window.Vector
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in S4Vectors
###

exportMethods(
    ## Methods for generics defined in the base package:
    length, names, "names<-",
    nrow, ncol, dim,
    NROW, NCOL,
    rownames, "rownames<-",
    colnames, "colnames<-",
    dimnames, "dimnames<-",
    is.na, anyNA,
    as.logical, as.integer, as.numeric,
    as.complex, as.character, as.raw, as.factor,
    as.list, as.data.frame,
    as.matrix, as.table,
    "[", "[<-",
    subset, rev, rep, rep.int,
    c, append,
    "==", "!=", "<=", ">=", "<", ">",
    "Ops", "Summary",
    "!",
    match, duplicated, unique, anyDuplicated, "%in%",
    order, sort, is.unsorted, rank, xtfrm,
    merge,
    t,
    by,
    transform,
    nchar, substr, substring, levels, "levels<-", droplevels,
    "[[", "[[<-", "$", "$<-",
    lengths,
    split,
    eval, with, within,
    expand.grid,

    ## Methods for generics defined in the methods package:
    coerce, show,

    ## Methods for generics defined in the utils package:
    head, tail,

    ## Methods for generics defined in the stats package:
    var, cov, cor, sd, window, aggregate, na.omit, na.exclude, complete.cases,

    ## Methods for generics defined in the stats4 package:
    summary,

    ## Methods for generics defined in the BiocGenerics package:
    cbind, rbind,
    lapply, sapply,
    Reduce, Filter,
    unlist,
    do.call,
    union, intersect, setdiff, setequal,
    xtabs,
    start, end, width,
    grep, grepl,
    updateObject
)


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

export(
    ## S4-utils.R:
    setValidity2, new2, setMethods,

    ## utils.R:
    wmsg,
    .Call2,
    get_showHeadLines, get_showTailLines,
    printAtomicVectorInAGrid,

    ## normarg-utils.R:
    isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString,
    isSingleNumberOrNA, isSingleStringOrNA,
    recycleIntegerArg, recycleNumericArg,
    recycleLogicalArg, recycleCharacterArg,
    recycleArg,
    fold,

    ## LLint-class.R:
    is.LLint, as.LLint, LLint,

    ## subsetting-utils.R:
    normalizeSingleBracketSubscript,
    normalizeDoubleBracketSubscript,

    ## integer-utils.R:
    isSequence,
    toListOfIntegerVectors, strsplitAsListOfIntegerVectors,
    orderIntegerPairs,
    matchIntegerPairs, selfmatchIntegerPairs, duplicatedIntegerPairs,
    orderIntegerQuads,
    matchIntegerQuads, selfmatchIntegerQuads, duplicatedIntegerQuads,

    ## character-utils.R:
    safeExplode,
    svn.time,

    ## Hits-class.R:
    queryHits, subjectHits,
    queryLength, subjectLength,
    countQueryHits, countSubjectHits,
    Hits, SelfHits,
    selectHits,
    breakTies,
    remapHits,
    isSelfHit,
    isRedundantHit,

    ## List-class.R:
    List, phead, ptail, pc,

    ## List-utils.R:
    endoapply, mendoapply,

    ## SimpleList-class.R:
    SimpleList,

    ## HitsList-class.R:
    HitsList,

    ## DataFrame-class.R:
    DataFrame,

    ## Pairs-class.R:
    Pairs,

    ## FilterRules-class.R:
    FilterRules, FilterMatrix
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics obtained by explicit promotion of functions not
### defined in S4Vectors to S4 generics
###

export(
    ## DataTable-class.R:
    rowSums, colSums, rowMeans, colMeans
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in S4Vectors + export corresponding methods
###

export(
    ## show-utils.R:
    classNameForDisplay, showAsCell,

    ## LLint-class.R:
    bindROWS,

    ## isSorted.R:
    isConstant, isSorted, isStrictlySorted,

    ## subsetting-utils.R:
    NSBS,
    normalizeSingleBracketReplacementValue,
    extractROWS, replaceROWS,
    getListElement, setListElement,

    ## character-utils.R:
    unstrsplit,

    ## DataTable-class.R:
    ROWNAMES,
    as.env,

    ## Annotated-class.R:
    metadata, "metadata<-",

    ## Vector-class.R:
    parallelSlotNames, parallelVectorNames,
    elementMetadata, mcols, values,
    "elementMetadata<-", "mcols<-", "values<-",
    rename,

    ## Vector-comparison.R:
    pcompare,
    selfmatch,
    findMatches, countMatches,

    ## Hits-class.R:
    from, to, nLnode, nRnode, nnode, countLnodeHits, countRnodeHits,

    ## Rle-class.R:
    runLength, "runLength<-", runValue, "runValue<-", nrun,
    Rle,
    findRun, decode,

    ## Rle-utils.R:
    runsum, runmean, runwtsum, runq,

    ## List-class.R:
    elementType, elementNROWS, isEmpty, relistToClass,

    ## List-comparison.R:
    pcompareRecursively,

    ## List-utils.R:
    revElements,

    ## HitsList-class.R:
    space,

    ## Pairs-class.R:
    first, "first<-", second, "second<-", zipup, zipdown,

    ## expand-methods.R
    expand,

    ## FilterRules-class.R:
    active, "active<-", evalSeparately, subsetByFilter, params, filterRules,

    ## shiftApply-methods.R:
    shiftApply
)

### Exactly the same list as above.
exportMethods(
    classNameForDisplay, showAsCell,
    bindROWS,
    isConstant, isSorted, isStrictlySorted,
    NSBS,
    normalizeSingleBracketReplacementValue,
    extractROWS, replaceROWS,
    getListElement, setListElement,
    unstrsplit,
    ROWNAMES,
    as.env,
    metadata, "metadata<-",
    parallelSlotNames, parallelVectorNames,
    elementMetadata, mcols, values,
    "elementMetadata<-", "mcols<-", "values<-",
    rename,
    pcompare, 
    selfmatch,
    findMatches, countMatches,
    from, to, nLnode, nRnode, nnode, countLnodeHits, countRnodeHits,
    runLength, "runLength<-", runValue, "runValue<-", nrun,
    Rle,
    findRun,
    runsum, runmean, runwtsum, runq,
    elementType, elementNROWS, isEmpty, relistToClass,
    pcompareRecursively,
    revElements,
    space,
    first, "first<-", second, "second<-", zipup, zipdown,
    expand,
    active, "active<-", evalSeparately, subsetByFilter, params, filterRules,
    shiftApply
)