BayesicSpace::SimilarityMatrix Class Reference

Similarity matrix. More...

#include <similarityMatrix.hpp>

Public Member Functions
	SimilarityMatrix () noexcept=default
	Default constructor.
	SimilarityMatrix (const SimilarityMatrix &toCopy)=default
	Copy constructor.
SimilarityMatrix &	operator= (const SimilarityMatrix &toCopy)=default
	Copy assignment operator.
	SimilarityMatrix (SimilarityMatrix &&toMove) noexcept=default
	Move constructor.
SimilarityMatrix &	operator= (SimilarityMatrix &&toMove) noexcept=default
	Move assignment operator.
	~SimilarityMatrix ()=default
	Destructor.
size_t	objectSize () const noexcept
	Object size in bytes.
size_t	nElements () const noexcept
	Number of elements in the matrix.
void	insert (const RowColIdx &rowColPair, const JaccardPair &jaccardCounts)
	Insert a value (updating the index)
void	merge (SimilarityMatrix &toMerge)
	Merge two matrices.
void	save (const std::string &outFileName, const size_t &nThreads, const std::string &locusNameFile="") const
	Save to file.

Static Public Member Functions
static size_t	elementSize () noexcept
	Matrix element size.

Detailed Description

Similarity matrix.

A representation of a square symmetric similarity matrix, excluding the diagonal. Stores only the values present in the lower triangle by row. The representation is memory efficient if the matrix is sparse and attempts to strike a compromise between memory use and matrix manipulation speed.

Constructor & Destructor Documentation

SimilarityMatrix() [1/2]

BayesicSpace::SimilarityMatrix::SimilarityMatrix ( const SimilarityMatrix & toCopy )

default

Copy constructor.

Parameters

[in]

toCopy

object to copy

SimilarityMatrix() [2/2]

BayesicSpace::SimilarityMatrix::SimilarityMatrix ( SimilarityMatrix && toMove )

defaultnoexcept

Move constructor.

Parameters

[in]

toMove

object to move

Member Function Documentation

elementSize()

static size_t BayesicSpace::SimilarityMatrix::elementSize ( )

inlinestaticnoexcept

Matrix element size.

Returns

matrix element size in bytes

insert()

void BayesicSpace::SimilarityMatrix::insert	(	const RowColIdx &	rowColPair,
		const JaccardPair &	jaccardCounts )

Insert a value (updating the index)

Inserts a new value into the matrix. Addresses the lower triangle of the similarity matrix, therefore the row index must be larger than the column index. If not, the values are swapped. If the indexes are equal or the row index is 0, throws an exception. Inserts a quantized value of the Jaccard similarity calculated from the intersection and union counts provided.

Parameters

[in]	rowColPair	row and index pair
[in]	jaccardCounts	intersection and union counts for Jaccard similarity

merge()

void BayesicSpace::SimilarityMatrix::merge

(

SimilarityMatrix &

toMerge

)

Merge two matrices.

Merge a matrix with the current object, destroying the donor object. Duplicated indexes are discarded even if they differ in similarity values.

Parameters

[in]

toMerge

object to merge

nElements()

size_t BayesicSpace::SimilarityMatrix::nElements ( ) const

inlinenoexcept

Number of elements in the matrix.

Returns

number of elements

objectSize()

size_t BayesicSpace::SimilarityMatrix::objectSize ( ) const

inlinenoexcept

Object size in bytes.

Returns

object size in bytes

operator=() [1/2]

SimilarityMatrix & BayesicSpace::SimilarityMatrix::operator= ( const SimilarityMatrix & toCopy )

default

Copy assignment operator.

Parameters

[in]

toCopy

object to copy

Returns

SimilarityMatrix object

operator=() [2/2]

SimilarityMatrix & BayesicSpace::SimilarityMatrix::operator= ( SimilarityMatrix && toMove )

defaultnoexcept

Move assignment operator.

Parameters

[in]

toMove

object to move

Returns

SimilarityMatrix object

save()

void BayesicSpace::SimilarityMatrix::save	(	const std::string &	outFileName,
		const size_t &	nThreads,
		const std::string &	locusNameFile = "" ) const

Save to file.

Uses multi-threaded data prep to speed up saving. If the output file already exists, appends to it.

Parameters

[in]	outFileName	output file name
[in]	nThreads	number of threads
[in]	locusNameFile	name of the file with locus names (empty by default)

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

• similarityMatrix.hpp