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useDynLib(HDF5Array)
import(methods)
importFrom(utils, read.table)
importFrom(stats, setNames)
importFrom(tools, file_path_as_absolute)
importFrom(Matrix, sparseMatrix)
### We import rhdf5filters only for the side effect of setting system
### environment variable HDF5_PLUGIN_PATH to rhdf5filters::hdf5_plugin_path().
### This is done by rhdf5filters:::.onLoad(). The only filter we actually
### care about at the moment is LZF.
import(rhdf5filters)
import(rhdf5)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(S4Arrays)
import(SparseArray)
import(DelayedArray)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
H5FileID, H5File, character_OR_H5File,
H5DSetDescriptor,
HDF5ArraySeed,
HDF5Array, HDF5Matrix,
ReshapedHDF5ArraySeed,
ReshapedHDF5Array, ReshapedHDF5Matrix,
HDF5RealizationSink,
H5SparseMatrixSeed, CSC_H5SparseMatrixSeed, CSR_H5SparseMatrixSeed,
H5SparseMatrix,
H5ADMatrixSeed,
Dense_H5ADMatrixSeed, CSC_H5ADMatrixSeed, CSR_H5ADMatrixSeed,
H5ADMatrix,
TENxMatrixSeed,
TENxMatrix,
TENxRealizationSink
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(close, H5FileID)
S3method(close, H5File)
S3method(open, H5FileID)
S3method(open, H5File)
S3method(t, CSC_H5SparseMatrixSeed)
S3method(t, CSR_H5SparseMatrixSeed)
S3method(t, CSC_H5ADMatrixSeed)
S3method(t, CSR_H5ADMatrixSeed)
### 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(
close.H5FileID,
close.H5File,
open.H5FileID,
open.H5File,
t.CSC_H5SparseMatrixSeed,
t.CSR_H5SparseMatrixSeed,
t.CSC_H5ADMatrixSeed,
t.CSR_H5ADMatrixSeed
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in HDF5Array
###
exportMethods(
## Methods for generics defined in the base package:
dim, dimnames, t,
## Methods for generics defined in the methods package:
coerce, show,
## Methods for generics defined in the BiocGenerics package:
path, "path<-", type, updateObject,
## Methods for generics defined in the S4Arrays package:
extract_array, is_sparse, "is_sparse<-",
## Methods for generics defined in the SparseArray package:
nzcount, extract_sparse_array,
## Methods for generics defined in the DelayedArray package:
chunkdim, write_block,
OLD_extract_sparse_array, read_sparse_block,
matrixClass, DelayedArray,
close
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
H5FileID, H5File,
h5ls,
H5DSetDescriptor, destroy_H5DSetDescriptor,
get_h5mread_returned_type, h5mread,
h5mread_from_reshaped,
set_h5dimnames, get_h5dimnames, h5writeDimnames, h5readDimnames,
HDF5ArraySeed,
HDF5Array,
ReshapedHDF5ArraySeed,
ReshapedHDF5Array,
setHDF5DumpDir, getHDF5DumpDir,
setHDF5DumpFile, getHDF5DumpFile, lsHDF5DumpFile,
setHDF5DumpName, getHDF5DumpName,
setHDF5DumpChunkLength, getHDF5DumpChunkLength,
setHDF5DumpChunkShape, getHDF5DumpChunkShape,
getHDF5DumpChunkDim,
setHDF5DumpCompressionLevel, getHDF5DumpCompressionLevel,
appendDatasetCreationToHDF5DumpLog, showHDF5DumpLog,
HDF5RealizationSink, writeHDF5Array,
saveHDF5SummarizedExperiment, loadHDF5SummarizedExperiment,
quickResaveHDF5SummarizedExperiment,
H5SparseMatrixSeed,
H5SparseMatrix,
H5ADMatrixSeed,
H5ADMatrix,
TENxMatrixSeed,
TENxMatrix,
TENxRealizationSink, writeTENxMatrix
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in HDF5Array, and corresponding methods
###
export(
## H5SparseMatrixSeed-class.R:
extractNonzeroDataByCol, extractNonzeroDataByRow
)
### Exactly the same list as above.
exportMethods(
extractNonzeroDataByCol, extractNonzeroDataByRow
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export internal utility functions for developers
###
export(
shorten_assay2h5_links,
restore_absolute_assay2h5_links,
validate_HDF5ArraySeed_dataset_geometry,
write_h5_assays,
create_dir,
replace_dir,
check_and_delete_files,
stop_if_bad_dir
)
|
