NAMESPACE

useDynLib(SparseArray)

import(methods)
importFrom(utils, packageVersion)
importFrom(stats, setNames, rnorm, rpois)
importClassFrom(Matrix, dgCMatrix, lgCMatrix, ngCMatrix,
                        dgRMatrix, lgRMatrix, ngRMatrix)
importFrom(Matrix, sparseMatrix, crossprod, tcrossprod)

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


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

exportClasses(
    ## SparseArray-class.R:
    SparseArray, SparseMatrix,

    ## COO_SparseArray-class.R:
    COO_SparseArray, COO_SparseMatrix,

    ## SVT_SparseArray-class.R:
    NULL_OR_list, SVT_SparseArray, SVT_SparseMatrix,

    ## NaArray-class.R:
    NaArray, NaMatrix
)


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

S3method(aperm, COO_SparseArray)
S3method(aperm, SVT_SparseArray)
S3method(aperm, NaArray)

S3method(as.array, COO_SparseArray)
S3method(as.array, SVT_SparseArray)
S3method(as.array, NaArray)

S3method(mean, SparseArray)
S3method(mean, NaArray)

S3method(range, COO_SparseArray)
S3method(range, SVT_SparseArray)
S3method(range, NaArray)

S3method(rowsum, dgCMatrix)
S3method(rowsum, SparseMatrix)

S3method(t, SVT_SparseMatrix)
S3method(t, NaMatrix)

### 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.COO_SparseArray,
    aperm.SVT_SparseArray,
    aperm.NaArray,

    as.array.COO_SparseArray,
    as.array.SVT_SparseArray,
    as.array.NaArray,

    mean.SparseArray,
    mean.NaArray,

    range.COO_SparseArray,
    range.SVT_SparseArray,
    range.NaArray,

    rowsum.dgCMatrix,
    rowsum.SparseMatrix,

    t.SVT_SparseMatrix,
    t.NaMatrix
)


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

exportMethods(
    ## Methods for generics defined in the base package:
    dim, dimnames, "dimnames<-",
    "[[",
    as.array,
    t,
    which,
    is.na, is.nan, is.infinite, anyNA,
    any, all, min, max, range, sum, prod,  # "Summary" group generic
    mean,
    var, sd,
    nchar,
    crossprod, tcrossprod, "%*%",
    "+", "-", Arith, "!", Logic, Math, round, signif, Complex,

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

    ## Methods for generics defined in the BiocGenerics package:
    cbind, rbind,
    pmin, pmax,
    type, "type<-",

    ## Methods for generics defined in the MatrixGenerics package:
    colAnyNAs, rowAnyNAs,
    colAnys, rowAnys, colAlls, rowAlls,
    colMins, rowMins, colMaxs, rowMaxs, colRanges, rowRanges,
    colSums, rowSums, colProds, rowProds, colMeans, rowMeans,
    colSums2, rowSums2, colMeans2, rowMeans2,
    colVars, rowVars, colSds, rowSds,
    colMedians, rowMedians,

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

    ## Methods for generics defined in the S4Arrays package:
    rowsum, colsum, aperm, abind, tune_Array_dims, extract_array, is_sparse
)


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

export(
    ## thread-control.R:
    get_SparseArray_nthread, set_SparseArray_nthread,

    ## SparseArray-class.R:
    sparsity,

    ## COO_SparseArray-class.R:
    COO_SparseArray,

    ## SVT_SparseArray-class.R:
    SVT_SparseArray, SparseArray,

    ## randomSparseArray.R:
    randomSparseArray, randomSparseMatrix,
    poissonSparseArray, poissonSparseMatrix,

    ## readSparseCSV.R:
    writeSparseCSV, readSparseCSV, readSparseTable,

    ## NaArray-class.R:
    NaArray
)


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

export(
    ## is_nonzero.R:
    is_nonzero, nzcount, nzwhich, nzvals, "nzvals<-",

    ## COO_SparseArray-class.R:
    nzcoo, nzdata,

    ## extract_sparse_array.R:
    extract_sparse_array,

    ## read_block_as_sparse.R:
    read_block_as_sparse,

    ## is_nonna.R:
    is_nonna, nnacount, nnawhich, nnavals, "nnavals<-",

    ## NaArray-subsetting.R:
    extract_na_array
)

### Same list as above.
exportMethods(
    is_nonzero, nzcount, nzwhich, nzvals, "nzvals<-",
    nzcoo, nzdata,
    extract_sparse_array,
    read_block_as_sparse,
    is_nonna, nnacount, nnawhich, nnavals, "nnavals<-",
    extract_na_array
)