Internal Alignment Class that represents a sequences matrix. More...

#include <sequencesMatrix.h>

Public Member Functions
	sequencesMatrix ()
	Null constructor. More...

	sequencesMatrix (string alignmentMatrix, string alignmentSeqsName, int sequences, int residues)
	Manual constructor. More...

	sequencesMatrix (Alignment *parent)
	Automatic constructor. More...

sequencesMatrix &	operator= (const sequencesMatrix &)

	~sequencesMatrix ()
	Destructor. More...

void	printMatrix ()
	Sequences Matrix printing method. More...

void	getColumn (int column, int *numResidueseqMatrix)
	Method to get a column out of the matrix. More...

void	getColumn (int value, int row, int *columnSeqMatrix)
	Method that looks to value in a row and stores a column's, corresponding to row, sequences matrix in a vector. More...

void	setOrder (int *order)
	Method that reorders the stored sequences with a given order list. More...

bool	getSequence (string seqName, int *sequence)
	Method to obtain a sequence based on its name. More...

int	getSeqNumber ()
	Number of sequences getter. More...

int	getResidNumber ()
	Number of residues getter. More...

Private Attributes
int	resNumber
	Number of residues per sequence. More...

int	seqsNumber
	Number of sequences in the matrix. More...

int **	matrix
	Matrix container. It contains the sequences and residues of each sequence. More...

string *	seqsName
	Sequences names container. More...

Alignment *	alig
	Pointer to the alignment this object is related to. More...

Detailed Description

Internal Alignment Class that represents a sequences matrix.

A Sequence matrix is a 2D matrix that represents MSA without any gaps included.
This class stores the alignment sequences matrix.
It provides methods to build the sequences matrix and print the matrix.
It also provides methods for look to a column in the matrix and for look to value at the position (row, column) in the matrix.
See:

Statistics::Consistency::compareAndChoose
Statistics::Consistency::forceComparison

Definition at line 55 of file sequencesMatrix.h.

Constructor & Destructor Documentation

◆ sequencesMatrix() [1/3]

Alignment::sequencesMatrix::sequencesMatrix ( void )

Null constructor.

This construction method initializes all attributes of the new object with 0 or nullptr value.

Definition at line 35 of file sequencesMatrix.cpp.

References matrix, resNumber, seqsName, and seqsNumber.

◆ sequencesMatrix() [2/3]

Alignment::sequencesMatrix::sequencesMatrix	(	string *	alignmentMatrix,
		string *	alignmentSeqsName,
		int	sequences,
		int	residues
	)

Manual constructor.

This construction method initializes all attributes using the information passed as arguments.

Parameters

alignmentMatrix	Sequences of the alignment to convert to sequenceMatrix
alignmentSeqsName	Sequences names
sequences	Number of sequences
residues	Number of residues

Definition at line 79 of file sequencesMatrix.cpp.

References utils::initlVect(), matrix, resNumber, seqsName, and seqsNumber.

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◆ sequencesMatrix() [3/3]

Alignment::sequencesMatrix::sequencesMatrix ( Alignment * parent )

explicit

Automatic constructor.

This construction method initializes all attributes using the information present in the alignment pointer passed.

Parameters

parent Alignment to associate the sequences matrix to.

Definition at line 48 of file sequencesMatrix.cpp.

References alig, utils::initlVect(), matrix, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, resNumber, seqsName, Alignment::seqsName, seqsNumber, and Alignment::sequences.

Referenced by statistics::Consistency::forceComparison(), and statistics::Consistency::perform().

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◆ ~sequencesMatrix()

Alignment::sequencesMatrix::~sequencesMatrix ( )

Destructor.

Destruction method that frees, if exists, previously allocated memory.

Definition at line 133 of file sequencesMatrix.cpp.

References matrix, resNumber, seqsName, and seqsNumber.

Member Function Documentation

◆ getColumn() [1/2]

void Alignment::sequencesMatrix::getColumn	(	int	column,
		int *	numResidueseqMatrix
	)

Method to get a column out of the matrix.

Parameters

	column	Column number at sequences matrix.
[out]	numResidueseqMatrix	Vector where storage a column's sequences matrix.

Method that storages a column's sequences matrix in a vector.

Definition at line 169 of file sequencesMatrix.cpp.

References matrix, resNumber, and seqsNumber.

Referenced by statistics::Consistency::compareAndChoose(), and statistics::Consistency::forceComparison().

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◆ getColumn() [2/2]

void Alignment::sequencesMatrix::getColumn	(	int	value,
		int	row,
		int *	columnSeqMatrix
	)

Method that looks to value in a row and stores a column's, corresponding to row, sequences matrix in a vector.

Parameters

value	to look in a row's sequences matrix.
row	where to look for a value.
columnSeqMatrix	Vector where storage a column's sequences matrix.

Definition at line 185 of file sequencesMatrix.cpp.

References matrix, resNumber, and seqsNumber.

Referenced by statistics::Consistency::compareAndChoose(), and statistics::Consistency::forceComparison().

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◆ getResidNumber()

int Alignment::sequencesMatrix::getResidNumber ( void )

Number of residues getter.

Returns: Number of residues.

Definition at line 251 of file sequencesMatrix.cpp.

References resNumber.

◆ getSeqNumber()

int Alignment::sequencesMatrix::getSeqNumber ( void )

Number of sequences getter.

Returns: Number of sequences.

Definition at line 244 of file sequencesMatrix.cpp.

References seqsNumber.

◆ getSequence()

bool Alignment::sequencesMatrix::getSequence	(	string	seqName,
		int *	sequence
	)

Method to obtain a sequence based on its name.

Parameters

	seqName	Name of the sequence to find.
[out]	sequence	Where to store the sequence.

Returns: True if found. False if not.

Definition at line 225 of file sequencesMatrix.cpp.

References matrix, resNumber, seqsName, and seqsNumber.

◆ operator=()

Alignment::sequencesMatrix & Alignment::sequencesMatrix::operator= ( const sequencesMatrix & old )

Definition at line 110 of file sequencesMatrix.cpp.

References matrix, resNumber, seqsName, and seqsNumber.

◆ printMatrix()

void Alignment::sequencesMatrix::printMatrix ( void )

Sequences Matrix printing method.

Method that prints the alignment sequences matrix.

Warning: Not In Use

Definition at line 152 of file sequencesMatrix.cpp.

References matrix, resNumber, and seqsNumber.

◆ setOrder()

void Alignment::sequencesMatrix::setOrder ( int * order )

Method that reorders the stored sequences with a given order list.

Parameters

order Pointer that contains the new order we want to give the matrix.

Definition at line 203 of file sequencesMatrix.cpp.

References matrix, resNumber, and seqsNumber.

Referenced by statistics::Consistency::compareAndChoose(), and statistics::Consistency::forceComparison().

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Member Data Documentation

◆ alig

Alignment* Alignment::sequencesMatrix::alig

private

Pointer to the alignment this object is related to.

Definition at line 178 of file sequencesMatrix.h.

Referenced by sequencesMatrix().

◆ matrix

int** Alignment::sequencesMatrix::matrix

private

Matrix container.
It contains the sequences and residues of each sequence.

Definition at line 69 of file sequencesMatrix.h.

Referenced by getColumn(), getSequence(), operator=(), printMatrix(), sequencesMatrix(), setOrder(), and ~sequencesMatrix().

◆ resNumber

int Alignment::sequencesMatrix::resNumber

private

Number of residues per sequence.

Definition at line 59 of file sequencesMatrix.h.

Referenced by getColumn(), getResidNumber(), getSequence(), operator=(), printMatrix(), sequencesMatrix(), setOrder(), and ~sequencesMatrix().

◆ seqsName

string* Alignment::sequencesMatrix::seqsName

private

Sequences names container.

Definition at line 74 of file sequencesMatrix.h.

Referenced by getSequence(), operator=(), sequencesMatrix(), and ~sequencesMatrix().

◆ seqsNumber

int Alignment::sequencesMatrix::seqsNumber

private

Number of sequences in the matrix.

Definition at line 63 of file sequencesMatrix.h.

Referenced by getColumn(), getSeqNumber(), getSequence(), operator=(), printMatrix(), sequencesMatrix(), setOrder(), and ~sequencesMatrix().

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

/home/vfernandez/git/MyFork/include/Alignment/sequencesMatrix.h
/home/vfernandez/git/MyFork/source/Alignment/sequencesMatrix.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ sequencesMatrix() [1/3]

◆ sequencesMatrix() [2/3]

◆ sequencesMatrix() [3/3]

◆ ~sequencesMatrix()

Member Function Documentation

◆ getColumn() [1/2]

◆ getColumn() [2/2]

◆ getResidNumber()

◆ getSeqNumber()

◆ getSequence()

◆ operator=()

◆ printMatrix()

◆ setOrder()

Member Data Documentation

◆ alig

◆ matrix

◆ resNumber

◆ seqsName

◆ seqsNumber