Compressed sparse matrix in a HDF5 file. More...

#include <CompressedSparseMatrix.hpp>

Inheritance diagram for tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >:

Collaboration diagram for tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >:

Public Member Functions
	CompressedSparseMatrix (Index_ nrow, Index_ ncol, std::string file_name, std::string value_name, std::string index_name, std::string pointer_name, bool csr, const CompressedSparseMatrixOptions &options)

	CompressedSparseMatrix (Index_ ncsr, Index_ ncol, std::string file_name, std::string value_name, std::string index_name, std::string pointer_name, bool csr)

Index_	nrow () const

Index_	ncol () const

bool	is_sparse () const

double	is_sparse_proportion () const

bool	prefer_rows () const

double	prefer_rows_proportion () const

bool	uses_oracle (bool) const

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > >	dense (bool row, const tatami::Options &opt) const

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > >	dense (bool row, Index_ block_start, Index_ block_length, const tatami::Options &opt) const

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > >	dense (bool row, tatami::VectorPtr< Index_ > indices_ptr, const tatami::Options &opt) const

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > >	sparse (bool row, const tatami::Options &opt) const

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > >	sparse (bool row, Index_ block_start, Index_ block_length, const tatami::Options &opt) const

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > >	sparse (bool row, tatami::VectorPtr< Index_ > indices_ptr, const tatami::Options &opt) const

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > >	dense (bool row, std::shared_ptr< const tatami::Oracle< Index_ > > oracle, const tatami::Options &opt) const

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > >	dense (bool row, std::shared_ptr< const tatami::Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length, const tatami::Options &opt) const

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > >	dense (bool row, std::shared_ptr< const tatami::Oracle< Index_ > > oracle, tatami::VectorPtr< Index_ > indices_ptr, const tatami::Options &opt) const

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > >	sparse (bool row, std::shared_ptr< const tatami::Oracle< Index_ > > oracle, const tatami::Options &opt) const

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > >	sparse (bool row, std::shared_ptr< const tatami::Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length, const tatami::Options &opt) const

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > >	sparse (bool row, std::shared_ptr< const tatami::Oracle< Index_ > > oracle, tatami::VectorPtr< Index_ > indices_ptr, const tatami::Options &opt) const

Public Member Functions inherited from tatami::Matrix< Value_, Index_ >
std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row () const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (Index_ block_start, Index_ block_length) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_row (std::vector< Index_ > indices) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_row (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column () const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (Index_ block_start, Index_ block_length) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< MyopicDenseExtractor< Value_, Index_ > >	dense_column (std::vector< Index_ > indices) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< OracularDenseExtractor< Value_, Index_ > >	dense_column (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row () const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (Index_ block_start, Index_ block_length) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_row (std::vector< Index_ > indices) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_row (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column () const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (Index_ block_start, Index_ block_length) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< MyopicSparseExtractor< Value_, Index_ > >	sparse_column (std::vector< Index_ > indices) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices, const Options &opt) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, Index_ block_start, Index_ block_length) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, VectorPtr< Index_ > indices_ptr) const

std::unique_ptr< OracularSparseExtractor< Value_, Index_ > >	sparse_column (std::shared_ptr< const Oracle< Index_ > > oracle, std::vector< Index_ > indices) const

Additional Inherited Members
Public Types inherited from tatami::Matrix< Value_, Index_ >
typedef Value_	value_type

typedef Index_	index_type

Detailed Description

template<typename Value_, typename Index_, typename CachedValue_ = Value_, typename CachedIndex_ = Index_>
class tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >

Compressed sparse matrix in a HDF5 file.

This class retrieves sparse data from the HDF5 file on demand rather than loading it all in at the start. This allows us to handle very large datasets in limited memory at the cost of speed.

We manually handle the chunk caching to speed up access for consecutive rows or columns (for compressed sparse row and column matrices, respectively). The policy is to minimize the number of calls to the HDF5 library - and thus expensive file reads - by requesting large contiguous slices where possible, i.e., multiple columns or rows for CSC and CSR matrices, respectively. These are held in memory in the Extractor while the relevant column/row is returned to the user by row() or column(). The size of the slice is determined by the options in the constructor.

Callers should follow the prefer_rows() suggestion when extracting data, as this tries to minimize the number of chunks that need to be read per access request. This recommendation is even stronger than for the DenseMatrix, as the access pattern on disk for the non-preferred dimension is very suboptimal.

As the HDF5 library is not generally thread-safe, the HDF5-related operations should only be run in a single thread. This is normally handled automatically but developers can check out serialize() to customize the locking scheme.

Template Parameters

Value_	Type of the matrix values.
Index_	Type of the row/column indices.
CachedValue_	Type of the matrix value to store in the cache. This can be set to a narrower type than `Value_` to save memory and improve cache performance, if a smaller type is known to be able to store all values (based on their HDF5 type or other knowledge).
CachedIndex_	Type of the index value to store in the cache. This can be set to a narrower type than `Index_` to save memory and improve cache performance, if a smaller type is known to be able to store all indices (based on their HDF5 type or other knowledge).

Constructor & Destructor Documentation

◆ CompressedSparseMatrix() [1/2]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::CompressedSparseMatrix	(	Index_	nrow,
		Index_	ncol,
		std::string	file_name,
		std::string	value_name,
		std::string	index_name,
		std::string	pointer_name,
		bool	csr,
		const CompressedSparseMatrixOptions &	options
	)

inline

Parameters

nr	Number of rows in the matrix.
nc	Number of columns in the matrix.
file_name	Path to the file.
value_name	Name of the 1D dataset inside `file_name` containing the values of the structural non-zero elements.
index_name	Name of the 1D dataset inside `file_name` containing the indices of the structural non-zero elements. If `csr = true`, this should contain column indices sorted within each row, otherwise it should contain row indices sorted within each column.
pointer_name	Name of the 1D dataset inside `file_name` containing the index pointers for the start and end of each row (if `row = true`) or column (otherwise). This should have length equal to the number of rows (if `row = true`) or columns (otherwise).
csr	Whether the matrix is stored on disk in compressed sparse row format. If false, the matrix is assumed to be stored in compressed sparse column format.
options	Further options.

◆ CompressedSparseMatrix() [2/2]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::CompressedSparseMatrix	(	Index_	ncsr,
		Index_	ncol,
		std::string	file_name,
		std::string	value_name,
		std::string	index_name,
		std::string	pointer_name,
		bool	csr
	)

inline

Overload that uses the default CompressedSparseMatrixOptions.

Parameters

nrow	Number of rows in the matrix.
ncol	Number of columns in the matrix.
file_name	Path to the file.
value_name	Name of the 1D dataset inside `file_name` containing the values of the structural non-zero elements.
index_name	Name of the 1D dataset inside `file_name` containing the indices of the structural non-zero elements.
pointer_name	Name of the 1D dataset inside `file_name` containing the index pointers for the start and end of each csr (if `csr = true`) or column (otherwise).
csr	Whether the matrix is stored in compressed sparse csr format.

Member Function Documentation

◆ nrow()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

Index_ tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::nrow ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ ncol()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

Index_ tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::ncol ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ is_sparse()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

bool tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::is_sparse ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ is_sparse_proportion()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

double tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::is_sparse_proportion ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ prefer_rows()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

bool tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::prefer_rows ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ prefer_rows_proportion()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

double tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::prefer_rows_proportion ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ uses_oracle()

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

bool tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::uses_oracle ( bool ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [1/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::dense	(	bool	row,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [2/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::dense	(	bool	row,
		Index_	block_start,
		Index_	block_length,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [3/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::dense	(	bool	row,
		tatami::VectorPtr< Index_ >	indices_ptr,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [1/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::sparse	(	bool	row,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [2/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::sparse	(	bool	row,
		Index_	block_start,
		Index_	block_length,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [3/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::sparse	(	bool	row,
		tatami::VectorPtr< Index_ >	indices_ptr,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [4/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::dense	(	bool	row,
		std::shared_ptr< const tatami::Oracle< Index_ > >	oracle,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [5/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::dense	(	bool	row,
		std::shared_ptr< const tatami::Oracle< Index_ > >	oracle,
		Index_	block_start,
		Index_	block_length,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [6/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::dense	(	bool	row,
		std::shared_ptr< const tatami::Oracle< Index_ > >	oracle,
		tatami::VectorPtr< Index_ >	indices_ptr,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [4/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::sparse	(	bool	row,
		std::shared_ptr< const tatami::Oracle< Index_ > >	oracle,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [5/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::sparse	(	bool	row,
		std::shared_ptr< const tatami::Oracle< Index_ > >	oracle,
		Index_	block_start,
		Index_	block_length,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [6/6]

template<typename Value_ , typename Index_ , typename CachedValue_ = Value_, typename CachedIndex_ = Index_>

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_hdf5::CompressedSparseMatrix< Value_, Index_, CachedValue_, CachedIndex_ >::sparse	(	bool	row,
		std::shared_ptr< const tatami::Oracle< Index_ > >	oracle,
		tatami::VectorPtr< Index_ >	indices_ptr,
		const tatami::Options &	opt
	)		const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

The documentation for this class was generated from the following file:

tatami_hdf5/CompressedSparseMatrix.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CompressedSparseMatrix() [1/2]

◆ CompressedSparseMatrix() [2/2]

Member Function Documentation

◆ nrow()

◆ ncol()

◆ is_sparse()

◆ is_sparse_proportion()

◆ prefer_rows()

◆ prefer_rows_proportion()

◆ uses_oracle()

◆ dense() [1/6]

◆ dense() [2/6]

◆ dense() [3/6]

◆ sparse() [1/6]

◆ sparse() [2/6]

◆ sparse() [3/6]

◆ dense() [4/6]

◆ dense() [5/6]

◆ dense() [6/6]

◆ sparse() [4/6]

◆ sparse() [5/6]

◆ sparse() [6/6]