Matrix of custom dense chunks. More...

#include <CustomDenseChunkedMatrix.hpp>

Inheritance diagram for tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >:

Collaboration diagram for tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >:

Public Member Functions
	CustomDenseChunkedMatrix (Index_ mat_nrow, Index_ mat_ncol, Index_ chunk_nrow, Index_ chunk_ncol, std::vector< Chunk_ > chunks, bool row_major, const CustomDenseChunkedMatrixOptions &opt)

Index_	nrow () const

Index_	ncol () const

bool	prefer_rows () const

bool	uses_oracle (bool) const

double	prefer_rows_proportion () const

bool	is_sparse () const

double	is_sparse_proportion () 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::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::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::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 Chunk_>
class tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >

Matrix of custom dense chunks.

Template Parameters

Value_	Numeric type for the matrix value.
Index_	Integer type for the row/column indices.
Chunk_	Class of the chunk, implementing either the `MockSimpleDenseChunk` or `MockSubsetDenseChunk` interfaces.

Implements a Matrix subclass where data is contained in dense rectangular chunks. These chunks are typically compressed in some manner to reduce memory usage compared to, e.g., a tatami::DenseMatrix. On access, the relevant chunks are decompressed and the desired values are extracted. Each dimension should be divided into chunk boundaries at regular intervals starting from zero; this partitions the matrix according to a regular grid where each grid entry is a single chunk of the same size. The exception is for chunks at the non-zero boundaries of the matrix dimensions, which may be truncated.

Constructor & Destructor Documentation

◆ CustomDenseChunkedMatrix()

template<typename Value_ , typename Index_ , typename Chunk_ >

tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::CustomDenseChunkedMatrix	(	Index_	mat_nrow,
		Index_	mat_ncol,
		Index_	chunk_nrow,
		Index_	chunk_ncol,
		std::vector< Chunk_ >	chunks,
		bool	row_major,
		const CustomDenseChunkedMatrixOptions &	opt
	)

inline

Parameters

mat_nrow	Number of rows in the matrix.
mat_ncol	Number of columns in the matrix.
chunk_nrow	Number of rows in each chunk.
chunk_ncol	Number of columns in each chunk.
chunks	Vector containing a two-dimensional array of chunks that cover the entire matrix. This should have length equal to the product of the number of chunks along the rows and columns of the matrix, i.e., `ceil(mat_nrow / chunk_nrow) * ceil(mat_ncol / chunk_ncol)`.
row_major	Whether `chunks` is in row-major format.
opt	Further options for chunked extraction.

Member Function Documentation

◆ nrow()

template<typename Value_ , typename Index_ , typename Chunk_ >

Index_ tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::nrow ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ ncol()

template<typename Value_ , typename Index_ , typename Chunk_ >

Index_ tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::ncol ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ prefer_rows()

template<typename Value_ , typename Index_ , typename Chunk_ >

bool tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::prefer_rows ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ uses_oracle()

template<typename Value_ , typename Index_ , typename Chunk_ >

bool tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::uses_oracle ( bool ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ prefer_rows_proportion()

template<typename Value_ , typename Index_ , typename Chunk_ >

double tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::prefer_rows_proportion ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ is_sparse()

template<typename Value_ , typename Index_ , typename Chunk_ >

bool tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::is_sparse ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ is_sparse_proportion()

template<typename Value_ , typename Index_ , typename Chunk_ >

double tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::is_sparse_proportion ( ) const

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [1/6]

template<typename Value_ , typename Index_ , typename Chunk_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ dense() [2/6]

template<typename Value_ , typename Index_ , typename Chunk_ >

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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 Chunk_ >

std::unique_ptr< tatami::MyopicDenseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::dense	(	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 Chunk_ >

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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 Chunk_ >

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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 Chunk_ >

std::unique_ptr< tatami::OracularDenseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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() [1/6]

template<typename Value_ , typename Index_ , typename Chunk_ >

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

inlinevirtual

Implements tatami::Matrix< Value_, Index_ >.

◆ sparse() [2/6]

template<typename Value_ , typename Index_ , typename Chunk_ >

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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 Chunk_ >

std::unique_ptr< tatami::MyopicSparseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::sparse	(	bool	row,
		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 Chunk_ >

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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 Chunk_ >

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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 Chunk_ >

std::unique_ptr< tatami::OracularSparseExtractor< Value_, Index_ > > tatami_chunked::CustomDenseChunkedMatrix< Value_, Index_, Chunk_ >::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_chunked/CustomDenseChunkedMatrix.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CustomDenseChunkedMatrix()

Member Function Documentation

◆ nrow()

◆ ncol()

◆ prefer_rows()

◆ uses_oracle()

◆ prefer_rows_proportion()

◆ is_sparse()

◆ is_sparse_proportion()

◆ dense() [1/6]

◆ dense() [2/6]

◆ dense() [3/6]

◆ dense() [4/6]

◆ dense() [5/6]

◆ dense() [6/6]

◆ sparse() [1/6]

◆ sparse() [2/6]

◆ sparse() [3/6]

◆ sparse() [4/6]

◆ sparse() [5/6]

◆ sparse() [6/6]