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useDynLib(S4Arrays)
import(methods)
importFrom(stats, setNames)
importClassFrom(Matrix, CsparseMatrix, dgCMatrix, lgCMatrix, ngCMatrix,
RsparseMatrix, dgRMatrix, lgRMatrix, ngRMatrix,
TsparseMatrix, dgTMatrix, lgTMatrix, ngTMatrix)
importFrom(crayon, make_style)
importFrom(abind, abind)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
## Array-class.R:
Array,
## ArrayGrid-class.R:
ArrayViewport, DummyArrayViewport, SafeArrayViewport,
ArrayGrid, DummyArrayGrid, ArbitraryArrayGrid, RegularArrayGrid
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(aperm, DummyArrayGrid)
S3method(aperm, ArbitraryArrayGrid)
S3method(aperm, RegularArrayGrid)
S3method(as.array, Array)
S3method(as.character, Array)
S3method(as.character, ArrayGrid)
S3method(as.complex, Array)
S3method(as.data.frame, Array)
S3method(as.integer, Array)
S3method(as.logical, Array)
S3method(as.matrix, Array)
S3method(as.numeric, Array)
S3method(as.raw, Array)
S3method(as.vector, Array)
S3method(t, Array)
### 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.DummyArrayGrid,
aperm.ArbitraryArrayGrid,
aperm.RegularArrayGrid,
as.array.Array,
as.character.Array,
as.character.ArrayGrid,
as.complex.Array,
as.data.frame.Array,
as.integer.Array,
as.logical.Array,
as.matrix.Array,
as.numeric.Array,
as.raw.Array,
as.vector.Array,
t.Array
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in S4Arrays
###
exportMethods(
## Methods for generics defined in the base package:
length,
dim, "dim<-", dimnames,
drop,
"[", "[<-",
"[[",
lengths,
as.array, as.matrix, as.data.frame, as.vector,
as.logical, as.integer, as.numeric, as.complex, as.character, as.raw,
which,
min, max, range, sum, prod, any, all, # "Summary" group generic
mean,
anyNA,
var,
nchar,
## Methods for generics defined in the methods package:
coerce, show,
## Methods for generics defined in the BiocGenerics package:
cbind, rbind,
t, aperm,
dims,
type,
## Methods for generics defined in the S4Vectors package:
bindROWS,
showAsCell, isEmpty,
## Methods for generics defined in the IRanges package:
ranges, start, end, width
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
## aperm2.R:
aperm2,
## array_selection.R:
Lindex2Mindex, Mindex2Lindex,
## ArrayGrid-class.R:
DummyArrayViewport, ArrayViewport, makeNindexFromArrayViewport,
DummyArrayGrid, ArbitraryArrayGrid, RegularArrayGrid,
## read_block.R:
read_block
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in S4Arrays, and corresponding methods
###
export(
## rowsum.R:
rowsum, # no rowsum() method defined in S4Arrays!
colsum,
## abind.R:
abind, arbind, acbind,
## dim-tuning-utils.R:
tune_Array_dims, # no tune_Array_dims() method defined in S4Arrays!
## Array-subsetting.R:
subset_Array_by_logical_array,
subset_Array_by_Lindex,
subset_Array_by_Mindex,
subset_Array_by_Nindex,
## Array-subassignment.R:
subassign_Array_by_logical_array,
subassign_Array_by_Lindex,
subassign_Array_by_Mindex,
subassign_Array_by_Nindex,
## ArrayGrid-class.R:
refdim, maxlength, downsample,
## mapToGrid.R:
mapToGrid, mapToRef,
## extract_array.R:
extract_array,
## is_sparse.R:
is_sparse,
"is_sparse<-", # no "is_sparse<-" method defined in S4Arrays!
## read_block.R:
read_block_as_dense,
## write_block.R:
write_block
)
### Same list as above.
exportMethods(
colsum,
abind, arbind, acbind,
subset_Array_by_logical_array,
subset_Array_by_Lindex,
subset_Array_by_Mindex,
subset_Array_by_Nindex,
subassign_Array_by_logical_array,
subassign_Array_by_Lindex,
subassign_Array_by_Mindex,
subassign_Array_by_Nindex,
refdim, maxlength, downsample,
mapToGrid, mapToRef,
extract_array,
is_sparse,
read_block_as_dense,
write_block
)
|
