NAMESPACE

# Native routines that are to be used in R via .Call
useDynLib(SCArray,
    c_add, c_get_split,
    c_rowSums, c_colSums, c_rowProds, c_colProds,
    c_rowMeans, c_rowMeans_final, c_colMeans,
    c_rowWMeans, c_rowWMeans_final, c_colWMeans,
    c_rowVars, c_rowVars_final, c_colVars,
    c_rowWVars, c_rowWVars_final, c_colWVars,
    c_rowMeanVar_final, c_colMeanVar,
    c_rowMins, c_colMins, c_rowMaxs, c_colMaxs, c_rowRanges, c_colRanges,
    c_row_sum_grp, c_col_sum_grp, c_row_nnzero, c_col_nnzero,
    c_row_anyNA, c_col_anyNA,
    c_rowCollapse_init, c_rowCollapse_done, c_rowCollapse,
    c_colCollapse_init, c_colCollapse,
    c_sparse_blocksize)

# Export the following names
exportPattern("^sc*")
exportClasses(SCArrayFileClass, SC_GDSArray, SC_GDSMatrix)
exportMethods(
    rowSums, colSums, rowSums2, colSums2, rowProds, colProds,
    rowMeans, colMeans, rowMeans2, colMeans2,
    rowWeightedMeans, colWeightedMeans,
    rowVars, colVars, rowSds, colSds,
    rowWeightedVars, colWeightedVars, rowWeightedSds, colWeightedSds,
    rowMins, colMins, rowMaxs, colMaxs, rowRanges, colRanges,
    rowAnyNAs, colAnyNAs, rowCollapse, colCollapse,
    row_nnzero, col_nnzero,
    colsum, rowsum, scale, pmin2, pmax2
)


# Import all packages listed as Imports or Depends
import(methods)
import(gdsfmt)
import(DelayedArray)
import(DelayedMatrixStats)
importFrom(utils, head, object.size, packageVersion, read.delim, str,
    txtProgressBar, setTxtProgressBar)
importFrom(Matrix, crossprod, tcrossprod, nnzero, readMM)
importFrom(S4Vectors, DataFrame, metadata, new2)
importFrom(BiocSingular, bsparam, runPCA)
importFrom(BiocParallel,
    bplapply, bpnworkers, bpstart, bpstop, bpisup, SerialParam)
importFrom(SummarizedExperiment, SummarizedExperiment, colData, rowData,
    assays, "assays<-", assay, "assay<-")
importFrom(SingleCellExperiment, SingleCellExperiment, altExp,
    reducedDim, "reducedDim<-")