NAMESPACE

useDynLib(DelayedArray)

import(methods)
importFrom(utils, object.size)
importFrom(stats, setNames,
                  dnorm, pnorm, qnorm,
                  dbinom, pbinom, qbinom,
                  dpois, ppois, qpois,
                  dlogis, plogis, qlogis)
importFrom(stats4, summary)
importClassFrom(Matrix, dgCMatrix, dgRMatrix, lgCMatrix, lgRMatrix)
importFrom(Matrix, sparseMatrix, crossprod, tcrossprod)

import(BiocGenerics)
import(MatrixGenerics)
import(S4Vectors)
import(IRanges)
import(S4Arrays)
import(SparseArray)


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### Export S4 classes
###

exportClasses(
    ## SparseArraySeed-class.R:
    SparseArraySeed,

    ## DelayedOp-class.R:
    DelayedOp,
    DelayedUnaryOp,
    DelayedUnaryIsoOp,
    DelayedNaryOp,

    ## DelayedSubset-class.R:
    DelayedSubset,

    ## DelayedAperm-class.R:
    DelayedAperm,

    ## DelayedUnaryIsoOpStack-class.R:
    DelayedUnaryIsoOpStack,

    ## DelayedUnaryIsoOpWithArgs-class.R:
    DelayedUnaryIsoOpWithArgs,

    ## DelayedSubassign-class.R:
    DelayedSubassign,

    ## DelayedSetDimnames-class.R:
    DelayedSetDimnames,

    ## DelayedNaryIsoOp-class.R:
    DelayedNaryIsoOp,

    ## DelayedAbind-class.R:
    DelayedAbind,

    ## DelayedArray-class.R:
    DelayedArray, DelayedMatrix,
    DelayedArray1,

    ## chunkGrid.R:
    integer_OR_NULL,

    ## RealizationSink-class.R:
    RealizationSink, arrayRealizationSink,

    ## ConstantArray-class.R:
    ConstantArraySeed,
    ConstantArray, ConstantMatrix,

    ## RleArraySeed-class.R:
    RleArraySeed, SolidRleArraySeed, RleRealizationSink, ChunkedRleArraySeed,

    ## RleArray-class.R:
    RleArray, RleMatrix
)


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### Export S3 methods
###

S3method(aperm, SparseArraySeed)
S3method(aperm, DelayedArray)

S3method(as.array, SparseArraySeed)

S3method(as.matrix, SparseArraySeed)

S3method(mean, SparseArraySeed)
S3method(mean, DelayedArray)

S3method(range, SparseArraySeed)
S3method(range, DelayedArray)

S3method(rowsum, DelayedMatrix)

S3method(scale, DelayedMatrix)

S3method(split, DelayedArray)

S3method(summary, DelayedOp)
S3method(summary, DelayedSubset)
S3method(summary, DelayedAperm)
S3method(summary, DelayedUnaryIsoOpStack)
S3method(summary, DelayedUnaryIsoOpWithArgs)
S3method(summary, DelayedSetDimnames)
S3method(summary, DelayedNaryIsoOp)
S3method(summary, DelayedAbind)

S3method(unique, DelayedArray)

### 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(
    aperm.SparseArraySeed,
    aperm.DelayedArray,

    as.array.SparseArraySeed,

    as.matrix.SparseArraySeed,

    mean.SparseArraySeed,
    mean.DelayedArray,

    range.SparseArraySeed,
    range.DelayedArray,

    rowsum.DelayedMatrix,

    scale.DelayedMatrix,

    split.DelayedArray,

    summary.DelayedOp,
    summary.DelayedSubset,
    summary.DelayedAperm,
    summary.DelayedUnaryIsoOpStack,
    summary.DelayedUnaryIsoOpWithArgs,
    summary.DelayedSetDimnames,
    summary.DelayedNaryIsoOp,
    summary.DelayedAbind,

    unique.DelayedArray
)


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

exportMethods(
    ## Methods for generics defined in the base package:
    length, names, "names<-",
    dim, "dim<-", dimnames, "dimnames<-",
    "[", "[[", "[<-",
    lengths,
    as.array, as.matrix, as.data.frame, as.vector,
    as.logical, as.integer, as.numeric, as.complex, as.character, as.raw,
    c, split,
    drop,
    is.na, is.finite, is.infinite, is.nan,
    "!",
    #"+", "-", "*", "/", "^", "%%", "%/%",  # "Arith" group generic
    "==", "!=", "<=", ">=", "<", ">",       # "Compare" group generic
    anyNA, which,
    unique,
    max, min, range, sum, prod, any, all,   # "Summary" group generic
    mean,
    log, round, signif,
    nchar, tolower, toupper,
    sub, gsub,
    "%*%",

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

    ## Methods for generics defined in the stats package:
    dnorm, pnorm, qnorm,
    dbinom, pbinom, qbinom,
    dpois, ppois, qpois,
    dlogis, plogis, qlogis,

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

    ## Methods for generics defined in the Matrix package:
    crossprod, tcrossprod,

    ## Methods for generics defined in the BiocGenerics package:
    cbind, rbind,
    aperm,
    dims,
    grepl,
    path, "path<-",
    table,
    type, "type<-",
    updateObject,
    rowSums, colSums, rowMeans, colMeans,

    ## Methods for generics defined in the MatrixGenerics package:
    rowMins, colMins,
    rowMaxs, colMaxs,
    rowRanges, colRanges,
    rowVars, colVars,

    ## Methods for generics defined in the S4Vectors package:
    bindROWS,
    showAsCell, isEmpty,
    splitAsList,

    ## Methods for generics defined in the IRanges package:
    ranges, start, end, width,

    ## Methods for generics defined in the S4Arrays package:
    rowsum, arbind, acbind, extract_array, is_sparse, write_block,

    ## Methods for generics defined in the SparseArray package:
    nzwhich, nzdata, extract_sparse_array
)


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

export(
    ## SparseArraySeed-class.R:
    SparseArraySeed, dense2sparse, sparse2dense,

    ## makeCappedVolumeBox.R:
    makeCappedVolumeBox, makeRegularArrayGridOfCappedLengthViewports,

    ## AutoBlock-global-settings.R:
    setAutoBlockSize, getAutoBlockSize,
    get_type_size, getAutoBlockLength,
    setAutoBlockShape, getAutoBlockShape,

    ## AutoGrid.R:
    defaultAutoGrid, blockGrid,
    rowAutoGrid, rowGrid,
    colAutoGrid, colGrid,
    setAutoGridMaker, getAutoGridMaker,
    defaultSinkAutoGrid,
    defaultMultAutoGrids, multGrids,

    ## blockApply.R:
    setAutoBPPARAM, getAutoBPPARAM,
    set_grid_context, effectiveGrid, currentBlockId, currentViewport,
    gridApply, viewportApply, blockApply,
    gridReduce, viewportReduce, blockReduce,

    ## showtree.R:
    showtree, seedApply, modify_seeds,

    ## simplify.R:
    isPristine, contentIsPristine,

    ## DelayedArray-class.R:
    new_DelayedArray,

    ## RealizationSink-class.R:
    registeredRealizationBackends, supportedRealizationBackends,
    getAutoRealizationBackend, setAutoRealizationBackend,
    getRealizationBackend, setRealizationBackend,
    AutoRealizationSink,
    sinkApply,

    ## realize.R:
    BLOCK_write_to_sink,

    ## RleArray-class.R:
    RleArray,

    ## ConstantArray-class.R:
    ConstantArray,
    ConstantArraySeed
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in DelayedArray, and corresponding methods
###

export(
    ## SparseArraySeed-class.R:
    nzindex, OLD_extract_sparse_array,

    ## read_sparse_block.R:
    read_sparse_block,

    ## makeCappedVolumeBox.R:
    isLinear,

    ## DelayedOp-class.R:
    is_noop,

    ## showtree.R:
    nseed, seed, "seed<-",

    ## simplify.R:
    simplify, netSubsetAndAperm,

    ## DelayedArray-class.R:
    matrixClass, DelayedArray,

    ## chunkGrid.R:
    chunkdim, chunkGrid,

    ## RealizationSink-class.R:
    close,

    ## realize.R:
    realize,

    ## DelayedArray-utils.R:
    pmax2, pmin2, apply, sweep, scale,

    ## matrixStats-methods.R:
    rowMaxs, colMaxs, rowMins, colMins, rowRanges, colRanges
)

### Same list as above.
exportMethods(
    nzindex, OLD_extract_sparse_array,
    read_sparse_block,
    isLinear,
    is_noop,
    nseed, seed, "seed<-",
    simplify, netSubsetAndAperm,
    matrixClass, DelayedArray,
    chunkdim, chunkGrid,
    close,
    realize,
    pmax2, pmin2, apply, sweep, scale,
    rowMaxs, colMaxs, rowMins, colMins, rowRanges, colRanges
)


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### TEMPORARY HACK: Re-export stuff that used to be defined in DelayedArray
### but that has been moved to and is now imported from S4Arrays. This is
### for compatibility with package code written before this move.
### TODO: Fix affected packages and get rid of this.

export(
    ## Used in DelayedMatrixStats package (DelayedArray::t() also used
    ## in beachmat):
    t, makeNindexFromArrayViewport,

    ## Used in beachmat:
    DummyArrayGrid, RegularArrayGrid, extract_array, is_sparse, write_block,

    ## Used in bsseq:
    colsum, ArbitraryArrayGrid, read_block
)

exportMethods(
    t
)