TileDB-backed dense matrix. More...

#include <DenseMatrix.hpp>

Inheritance diagram for tatami_tiledb::DenseMatrix< Value_, Index_ >:

Collaboration diagram for tatami_tiledb::DenseMatrix< Value_, Index_ >:

Public Member Functions
	DenseMatrix (const std::string &uri, std::string attribute, tiledb::Context ctx, const DenseMatrixOptions &options)

	DenseMatrix (const std::string &uri, std::string attribute, const DenseMatrixOptions &options)

	DenseMatrix (const std::string &uri, std::string attribute)

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 &) const

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

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

TileDB-backed dense matrix.

Template Parameters

Value_	Numeric type of the matrix value.
Index_	Integer type for the row/column indices.

Numeric dense matrix stored in a 2-dimensional TileDB array. Chunks of data are loaded from file as needed by tatami::Extractor objects, with additional caching to avoid repeated reads from disk. The size of cached chunks is determined by the extent of the tiles in the TileDB array.

The TileDB library is thread-safe so no additional work is required to use this class in parallel code. Nonetheless, users can force all calls to TileDB to occur in serial by defining the TATAMI_TILEDB_PARALLEL_LOCK macro. This should be a function-like macro that accepts a function and executes it inside a user-defined serial section.

Constructor & Destructor Documentation

◆ DenseMatrix() [1/3]

template<typename Value_ , typename Index_ >

tatami_tiledb::DenseMatrix< Value_, Index_ >::DenseMatrix	(	const std::string &	uri,
		std::string	attribute,
		tiledb::Context	ctx,
		const DenseMatrixOptions &	options
	)

inline

Parameters

uri	File path (or some other appropriate location) of the TileDB array.
attribute	Name of the attribute containing the data of interest.
context	A TileDB `Context` object, typically with some custom configuration.
options	Further options.

◆ DenseMatrix() [2/3]

template<typename Value_ , typename Index_ >

tatami_tiledb::DenseMatrix< Value_, Index_ >::DenseMatrix	(	const std::string &	uri,
		std::string	attribute,
		const DenseMatrixOptions &	options
	)

inline

Parameters

uri	File path (or some other appropriate location) of the TileDB array.
attribute	Name of the attribute containing the data of interest.
options	Further options.

◆ DenseMatrix() [3/3]

template<typename Value_ , typename Index_ >

tatami_tiledb::DenseMatrix< Value_, Index_ >::DenseMatrix	(	const std::string &	uri,
		std::string	attribute
	)

inline

Parameters

uri	File path (or some other appropriate location) of the TileDB array.
attribute	Name of the attribute containing the data of interest.

Member Function Documentation

◆ nrow()

template<typename Value_ , typename Index_ >

Index_ tatami_tiledb::DenseMatrix< Value_, Index_ >::nrow ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ ncol()

template<typename Value_ , typename Index_ >

Index_ tatami_tiledb::DenseMatrix< Value_, Index_ >::ncol ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ is_sparse()

template<typename Value_ , typename Index_ >

bool tatami_tiledb::DenseMatrix< Value_, Index_ >::is_sparse ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ is_sparse_proportion()

template<typename Value_ , typename Index_ >

double tatami_tiledb::DenseMatrix< Value_, Index_ >::is_sparse_proportion ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ prefer_rows()

template<typename Value_ , typename Index_ >

bool tatami_tiledb::DenseMatrix< Value_, Index_ >::prefer_rows ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ prefer_rows_proportion()

template<typename Value_ , typename Index_ >

double tatami_tiledb::DenseMatrix< Value_, Index_ >::prefer_rows_proportion ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ uses_oracle()

template<typename Value_ , typename Index_ >

bool tatami_tiledb::DenseMatrix< Value_, Index_ >::uses_oracle ( bool ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [1/6]

template<typename Value_ , typename Index_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [2/6]

template<typename Value_ , typename Index_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [3/6]

template<typename Value_ , typename Index_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [1/6]

template<typename Value_ , typename Index_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [2/6]

template<typename Value_ , typename Index_ >

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_tiledb::DenseMatrix< Value_, Index_ >::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_ >

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_tiledb::DenseMatrix< Value_, Index_ >::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_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [5/6]

template<typename Value_ , typename Index_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [6/6]

template<typename Value_ , typename Index_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [4/6]

template<typename Value_ , typename Index_ >

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_tiledb::DenseMatrix< Value_, Index_ >::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_ >

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_tiledb::DenseMatrix< Value_, Index_ >::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_ >

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_tiledb::DenseMatrix< Value_, Index_ >::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_tiledb/DenseMatrix.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DenseMatrix() [1/3]

◆ DenseMatrix() [2/3]

◆ DenseMatrix() [3/3]

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]