Class that contains information of similarity matrices.
These are used to calculate the similarity between residues on the same column.
Default matrices for AA, NT and DEG NT are provided, along with method for loading custom matrices. More...

#include <similarityMatrix.h>

Public Member Functions
	similarityMatrix ()
	Constructor. More...

	~similarityMatrix ()
	Destructor. More...

bool	loadSimMatrix (char *filename)
	Method to load a custom matrix. More...

void	defaultAASimMatrix ()
	Method to load the default AA similarity matrix. More...

void	defaultNTSimMatrix ()
	Method to load the default NT similarity matrix. More...

void	defaultNTDegeneratedSimMatrix ()
	Method to load the default DEG NT similarity matrix. More...

void	alternativeSimilarityMatrices (int matrix_code, int datatype)
	Method to load alternative similarity matrices also included on the suite. Currently, only one type of alternative matrix is available: matrix_code: 1 datatype SequenceTypes::AA. More...

float	getDistance (char a, char b)
	Method to get the similarity distance between two residues, A and B Characters provided must be both uppercase, please, refer to utils::toUpper. More...

void	printMatrix ()
	Method to print the loaded matrix. More...

Private Member Functions
void	memoryAllocation (int nPos)
	Method to allocate memory for the similiarity matrix. More...

void	memoryDeletion ()
	Method to deallocate memory allocated on the similarityMatrix::memoryAllocation method. It makes use of the numPositions to effectively remove the memory. More...

Private Attributes
int *	vhash

float **	simMat

float **	distMat

int	numPositions

Detailed Description

Class that contains information of similarity matrices.
These are used to calculate the similarity between residues on the same column.
Default matrices for AA, NT and DEG NT are provided, along with method for loading custom matrices.

Definition at line 50 of file similarityMatrix.h.

Constructor & Destructor Documentation

◆ similarityMatrix()

statistics::similarityMatrix::similarityMatrix ( )

Constructor.

Definition at line 50 of file similarityMatrix.cpp.

References distMat, numPositions, simMat, and vhash.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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◆ ~similarityMatrix()

statistics::similarityMatrix::~similarityMatrix ( )

Destructor.

Definition at line 88 of file similarityMatrix.cpp.

References memoryDeletion(), and numPositions.

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Member Function Documentation

◆ alternativeSimilarityMatrices()

void statistics::similarityMatrix::alternativeSimilarityMatrices	(	int	matrix_code,
		int	datatype
	)

Method to load alternative similarity matrices also included on the suite. Currently, only one type of alternative matrix is available:
matrix_code: 1 datatype SequenceTypes::AA.

Parameters

matrix_code	ID of the matrix
datatype	Numberical representation of the data type. See SequenceTypes

Definition at line 353 of file similarityMatrix.cpp.

References AA, DEG, distMat, DNA, memoryAllocation(), numPositions, RNA, simMat, and vhash.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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◆ defaultAASimMatrix()

void statistics::similarityMatrix::defaultAASimMatrix ( void )

Method to load the default AA similarity matrix.

Definition at line 251 of file similarityMatrix.cpp.

References distMat, memoryAllocation(), numPositions, simMat, and vhash.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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◆ defaultNTDegeneratedSimMatrix()

void statistics::similarityMatrix::defaultNTDegeneratedSimMatrix ( void )

Method to load the default DEG NT similarity matrix.

Definition at line 320 of file similarityMatrix.cpp.

References distMat, memoryAllocation(), numPositions, simMat, and vhash.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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◆ defaultNTSimMatrix()

void statistics::similarityMatrix::defaultNTSimMatrix ( void )

Method to load the default NT similarity matrix.

Definition at line 286 of file similarityMatrix.cpp.

References distMat, memoryAllocation(), numPositions, simMat, and vhash.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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◆ getDistance()

float statistics::similarityMatrix::getDistance	(	char	a,
		char	b
	)

Method to get the similarity distance between two residues, A and B
Characters provided must be both uppercase, please, refer to utils::toUpper.

Parameters

a	First residue to compare
b	Second residue to compare

Returns: Distance between A and B based on the similarity matrix loaded.

Definition at line 430 of file similarityMatrix.cpp.

References debug, distMat, IncorrectSymbol, reporting::reportManager::report(), UndefinedSymbol, and vhash.

Referenced by statistics::Similarity::calculateVectors().

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◆ loadSimMatrix()

bool statistics::similarityMatrix::loadSimMatrix ( char * filename )

Method to load a custom matrix.

Parameters

filename Path to file containing the matrix to load

Returns: True if loaded
False if an error ocurred

Definition at line 118 of file similarityMatrix.cpp.

References distMat, utils::initlVect(), memoryAllocation(), memoryDeletion(), numPositions, utils::removeSpaces(), simMat, and vhash.

Referenced by trimAlManager::create_or_use_similarity_matrix().

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◆ memoryAllocation()

void statistics::similarityMatrix::memoryAllocation ( int nPos )

private

Method to allocate memory for the similiarity matrix.

Parameters

nPos	Number of different possible residues in the alignment. This are, on the default matrices: AA: 20 residues NT: 5 residues DEG NT: 15 residues

Definition at line 60 of file similarityMatrix.cpp.

References distMat, memoryDeletion(), numPositions, simMat, and vhash.

Referenced by alternativeSimilarityMatrices(), defaultAASimMatrix(), defaultNTDegeneratedSimMatrix(), defaultNTSimMatrix(), and loadSimMatrix().

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◆ memoryDeletion()

void statistics::similarityMatrix::memoryDeletion ( )

private

Method to deallocate memory allocated on the similarityMatrix::memoryAllocation method.
It makes use of the numPositions to effectively remove the memory.

Definition at line 97 of file similarityMatrix.cpp.

References distMat, numPositions, simMat, and vhash.

Referenced by loadSimMatrix(), memoryAllocation(), and ~similarityMatrix().

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◆ printMatrix()

void statistics::similarityMatrix::printMatrix ( )

Method to print the loaded matrix.

Definition at line 418 of file similarityMatrix.cpp.

References numPositions, and simMat.

Member Data Documentation

◆ distMat

float** statistics::similarityMatrix::distMat

private

Definition at line 54 of file similarityMatrix.h.

Referenced by alternativeSimilarityMatrices(), defaultAASimMatrix(), defaultNTDegeneratedSimMatrix(), defaultNTSimMatrix(), getDistance(), loadSimMatrix(), memoryAllocation(), memoryDeletion(), and similarityMatrix().

◆ numPositions

int statistics::similarityMatrix::numPositions

private

Definition at line 55 of file similarityMatrix.h.

Referenced by alternativeSimilarityMatrices(), defaultAASimMatrix(), defaultNTDegeneratedSimMatrix(), defaultNTSimMatrix(), loadSimMatrix(), memoryAllocation(), memoryDeletion(), printMatrix(), similarityMatrix(), and ~similarityMatrix().

◆ simMat

float** statistics::similarityMatrix::simMat

private

Definition at line 53 of file similarityMatrix.h.

Referenced by alternativeSimilarityMatrices(), defaultAASimMatrix(), defaultNTDegeneratedSimMatrix(), defaultNTSimMatrix(), loadSimMatrix(), memoryAllocation(), memoryDeletion(), printMatrix(), and similarityMatrix().

◆ vhash

int* statistics::similarityMatrix::vhash

private

Definition at line 52 of file similarityMatrix.h.

Referenced by alternativeSimilarityMatrices(), defaultAASimMatrix(), defaultNTDegeneratedSimMatrix(), defaultNTSimMatrix(), getDistance(), loadSimMatrix(), memoryAllocation(), memoryDeletion(), and similarityMatrix().

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

/home/vfernandez/git/MyFork/include/Statistics/similarityMatrix.h
/home/vfernandez/git/MyFork/source/Statistics/similarityMatrix.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ similarityMatrix()

◆ ~similarityMatrix()

Member Function Documentation

◆ alternativeSimilarityMatrices()

◆ defaultAASimMatrix()

◆ defaultNTDegeneratedSimMatrix()

◆ defaultNTSimMatrix()

◆ getDistance()

◆ loadSimMatrix()

◆ memoryAllocation()

◆ memoryDeletion()

◆ printMatrix()

Member Data Documentation

◆ distMat

◆ numPositions

◆ simMat

◆ vhash