Utilities class. This class contains shared methods to be used in multiple parts of the code. More...

Namespaces
	TerminalColors

Functions
void	initlVect (int *vector, int tam, int valor)
	Vector initialization. More...

void	initlVect (float *vector, int tam, float valor)
	Vector initialization. More...

void	copyVect (int vect1, int vect2, int tam)
	Integer vector copying. More...

void	copyVect (float vect1, float vect2, int tam)
	Float vector copying. More...

int	roundToInf (double number)
	Round double to inferior integer method. More...

int	roundInt (double number)
	Round double to integer method. More...

int	roundToSup (double number)
	Round double to greater integer method. More...

int	max (int x, int y)
	Maximum of two numbers method. More...

float	max (float x, float y)
	Maximum of two numbers method. More...

double	max (double x, double y)
	Maximum of two numbers method. More...

int	min (int x, int y)
	Minimum of two numbers method. More...

float	min (float x, float y)
	Minimum of two numbers method. More...

double	min (double x, double y)
	Minimum of two numbers method. More...

bool	isNumber (char *num)
	String-is-number checking. More...

bool	compare (char a, char b)
	String comparing method. More...

void	removeSpaces (char in, char out)
	Removing spaces method. More...

void	quicksort (float *list, int ini, int fin)
	Quicksort sorting method. More...

void	swap (float a, float b)
	Swapping elements method. More...

void	quicksort (int *list, int ini, int fin)
	Quicksort sorting method. More...

void	swap (int a, int b)
	Swapping elements method. More...

bool	checkFile (std::ifstream &file)
	Check if a given file exists and its size is greater than 0. More...

char *	readLine (std::ifstream &file)
	Read a new line from current input stream. This function is better than standard one since cares of operative system compatibility. It is useful as well because removes tabs and blank spaces at lines at beginning/ending. . More...

char *	readLine (std::istream &file)
	Read a new line from current input stream. This function is better than standard one since cares of operative system compatibility. It is useful as well because removes tabs and blank spaces at lines at beginning/ending. . More...

char *	trimLine (std::string nline)
	Remove all content surrounded by ("") or ([]). It warns as well when a mismatch for these flags is found. . More...

std::string	getReverse (const std::string &toReverse)
	Reverses a string. More...

std::string	removeCharacter (char c, std::string line)
	Removes a determined char from the string. More...

int	checkAlignmentType (int seqNumber, int residNumber, std::string *sequences)
	Checks an alignment type. More...

int *	readNumbers (const std::string &line)
	Reads a line and converts it to an array of number. More...

void	quicksort (int **vect, int ini, int fin)
	Quicksort sorting method. More...

void	swap (int a, int b)
	Swaps double pointers. More...

char	determineColor (char res, const std::string &column)
	Checks the color that has to be used on the output report. More...

bool	lookForPattern (const std::string &data, const std::string &pattern, const float threshold)
	Method to check for a pattern in a string. The method will check, character by character of the first string if there is some equality for each character in the pattern. When done, it will calculate the fraction of characters present in the pattern and compare to the threshold argument. More...

void	ReplaceStringInPlace (std::string &subject, const std::string &search, const std::string &replace)
	Function that replaces a substring with another substring in a string. It does not make a copy of the original string, but modifies it. More...

std::string	ReplaceString (std::string subject, const std::string &search, const std::string &replace)
	Function that replaces a substring with another substring in a string. It makes a copy of the original string. More...

int	GetGapStep (int *gapValue, int sequenNumber)
	Function that gives the gap classification of a column of values. More...

int	GetGapStep (int *gapValue, float inverseSequenNumber)
	Function that gives the gap classification of a column of values. This function should work faster than it's sister utils::GetGapStep(int * gapValue, int sequenNumber), as it uses a precomputed (by the user) inverseSequenNumber (1F / Alignment::sequenNumber), instead of calculating it over again each time the function is called (which is equal to number of residues). This comes with a precision cost that shouldn't be a problem. More...

int	GetSimStep (float *simValue)
	Function that gives the similarity classification of a column of values. More...

int	GetConsStep (float *consValue)
	Function that gives the consistency classification of a column of values. More...

bool	fileExists (std::string &path)
	Method to check the existance of a file. More...

bool	fileExists (std::string &&path)
	Method to check the existance of a file. Works exactly as fileExists(std::string & path), but accepts r-value reference. More...

char	toUpper (char c)

Detailed Description

Utilities class. This class contains shared methods to be used in multiple parts of the code.

Function Documentation

◆ checkAlignmentType()

int utils::checkAlignmentType	(	int	seqNumber,
		int	residNumber,
		std::string *	sequences
	)

Checks an alignment type.

Parameters

seqNumber	Number of sequences to check it's type.
residNumber	Number of residues of the alignment.
sequences	Sequences pointer

Returns: Integer that represents the alignment type.

Definition at line 499 of file utils.cpp.

References AA, DEG, DNA, NotDefined, RNA, and toUpper().

Referenced by Alignment::getAlignmentType().

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◆ checkFile()

bool utils::checkFile ( std::ifstream & file )

Check if a given file exists and its size is greater than 0.

Parameters

file	ifstream to check

Definition at line 284 of file utils.cpp.

◆ compare()

bool utils::compare	(	char *	a,
		char *	b
	)

String comparing method.

Parameters

a	The first string that will be compared.
b	The second string that will be compared.

Returns: true if the two strings are the same, false if not.

This method compares the two strings given, and returns true if the two strings are equal.

Definition at line 139 of file utils.cpp.

◆ copyVect() [1/2]

void utils::copyVect	(	int *	vect1,
		int *	vect2,
		int	tam
	)

Integer vector copying.

Parameters

	vect1	Vector that we want to copy.
[out]	vect2	Destination vector of the copy.
	tam	Vectors size.

This method copies integer vector 1 to integer vector 2.

Definition at line 51 of file utils.cpp.

Referenced by statistics::Gaps::printGapsColumns().

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◆ copyVect() [2/2]

void utils::copyVect	(	float *	vect1,
		float *	vect2,
		int	tam
	)

Float vector copying.

Parameters

	vect1	Vector that we want to copy.
[out]	vect2	Destination vector of the copy.
	tam	Vectors size.

This method copies float vector 1 to float vector 2.

Definition at line 57 of file utils.cpp.

Referenced by statistics::Similarity::calcCutPoint(), Cleaner::cleanCompareFile(), statistics::Mold::printAccumulative(), statistics::Similarity::printConservationAcl(), and statistics::Consistency::printStatisticsFileAcl().

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◆ determineColor()

char utils::determineColor	(	char	res,
		const std::string &	column
	)

Checks the color that has to be used on the output report.

Parameters

res	Resiude to check its color
column	Column to which this residue belongs.

Returns: Char that represents the color to be used.

Definition at line 675 of file utils.cpp.

References lookForPattern().

Referenced by Alignment::alignmentSummaryHTML(), and Alignment::alignmentSummarySVG().

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◆ fileExists() [1/2]

bool utils::fileExists ( std::string & path )

Method to check the existance of a file.

Parameters

path	Path to the file to check

Returns: Wheter the file exists or not.

Definition at line 948 of file utils.cpp.

◆ fileExists() [2/2]

bool utils::fileExists ( std::string && path )

Method to check the existance of a file. Works exactly as fileExists(std::string & path), but accepts r-value reference.

Parameters

path	Path to the file to check

Returns: Wheter the file exists or not.

Definition at line 953 of file utils.cpp.

Referenced by FormatHandling::FormatManager::saveAlignments().

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◆ GetConsStep()

int utils::GetConsStep ( float * consValue )

Function that gives the consistency classification of a column of values.

Parameters

consValue Consistency value.

Returns: Int representing the classification of this gap value.

Definition at line 920 of file utils.cpp.

◆ GetGapStep() [1/2]

int utils::GetGapStep	(	int *	gapValue,
		int	sequenNumber
	)

Function that gives the gap classification of a column of values.

Parameters

gapValue	Number of gaps present in the column.
sequenNumber	Number of sequences.

Returns: Int representing the classification of this gap value.

Definition at line 832 of file utils.cpp.

◆ GetGapStep() [2/2]

int utils::GetGapStep	(	int *	gapValue,
		float	inverseSequenNumber
	)

Function that gives the gap classification of a column of values.
This function should work faster than it's sister utils::GetGapStep(int * gapValue, int sequenNumber), as it uses a precomputed (by the user) inverseSequenNumber (1F / Alignment::sequenNumber), instead of calculating it over again each time the function is called (which is equal to number of residues).
This comes with a precision cost that shouldn't be a problem.

Parameters

gapValue	Number of gaps present in the column.
inverseSequenNumber	Inverse of number of sequences. (1F / sequenNumber)

Returns: Int representing the classification of this gap value.

Definition at line 863 of file utils.cpp.

◆ getReverse()

std::string utils::getReverse ( const std::string & toReverse )

Reverses a string.

Parameters

toReverse String to get a reversed copy.

Returns: Reversed string of toReverse.

Definition at line 475 of file utils.cpp.

◆ GetSimStep()

int utils::GetSimStep ( float * simValue )

Function that gives the similarity classification of a column of values.

Parameters

simValue Similarity value.

Returns: Int representing the classification of this gap value.

Definition at line 893 of file utils.cpp.

◆ initlVect() [1/2]

void utils::initlVect	(	int *	vector,
		int	tam,
		int	valor
	)

Vector initialization.

Parameters

[out]	vector	The vector that will be initialized.
	tam	The size of the vector.
	valor	The initialization value that will of all positions of the vector.

This method is used to initialize all positions of a vector with a given value.

Definition at line 40 of file utils.cpp.

Referenced by statistics::Gaps::applyWindow(), Cleaner::cleanCombMethods(), statistics::Consistency::forceComparison(), statistics::Gaps::Gaps(), statistics::similarityMatrix::loadSimMatrix(), and Alignment::sequencesMatrix::sequencesMatrix().

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◆ initlVect() [2/2]

void utils::initlVect	(	float *	vector,
		int	tam,
		float	valor
	)

Vector initialization.

Parameters

[out]	vector	The vector that will be initialized.
	tam	The size of the vector.
	valor	The initialization value of all positions of the vector.

This method is used to initialize all positions of a vector with a given value.

Definition at line 46 of file utils.cpp.

Referenced by statistics::Gaps::calcCutPoint2ndSlope(), statistics::Gaps::calcCutPointMixSlope(), statistics::Consistency::compareAndChoose(), statistics::Consistency::forceComparison(), and statistics::Similarity::Similarity().

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◆ isNumber()

bool utils::isNumber ( char * num )

String-is-number checking.

Parameters

num	The string we want to check.

Returns: true if the string is a number, false if not.

This method checks if the given string is a number (taking in mind the possibility of floating numbers and scientific notation)

Definition at line 116 of file utils.cpp.

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◆ lookForPattern()

bool utils::lookForPattern	(	const std::string &	data,
		const std::string &	pattern,
		const float	threshold
	)

Method to check for a pattern in a string.
The method will check, character by character of the first string if there is some equality for each character in the pattern.
When done, it will calculate the fraction of characters present in the pattern and compare to the threshold argument.

Parameters

data	string that will be compared against a pattern
pattern	string that contains the pattern.
threshold	minimum ratio of hits to consider the pattern valid

Definition at line 793 of file utils.cpp.

References toUpper().

Referenced by determineColor().

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◆ max() [1/3]

int utils::max	(	int	x,
		int	y
	)

Maximum of two numbers method.

Parameters

x	The first number.
y	The second number.

Returns: The maximum between the two given numbers.

This method returns the maximum between the two numbers given as parameters.

Definition at line 80 of file utils.cpp.

Referenced by Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), Alignment::printSeqIdentity(), and Alignment::printSeqOverlap().

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◆ max() [2/3]

float utils::max	(	float	x,
		float	y
	)

Maximum of two numbers method.

Parameters

x	The first number.
y	The second number.

Returns: The maximum between the two given numbers.

This method returns the maximum between the two numbers given as parameters.

Definition at line 86 of file utils.cpp.

◆ max() [3/3]

double utils::max	(	double	x,
		double	y
	)

Maximum of two numbers method.

Parameters

x	The first number.
y	The second number.

Returns: The maximum between the two given numbers.

This method returns the maximum between the two numbers given as parameters.

Definition at line 92 of file utils.cpp.

Referenced by statistics::Gaps::calcCutPoint().

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◆ min() [1/3]

int utils::min	(	int	x,
		int	y
	)

Minimum of two numbers method.

Parameters

x	The first number.
y	The second number.

Returns: The minumum between the two given numbers.

This method returns the minimum between the two numbers given as parameters.

Definition at line 98 of file utils.cpp.

Referenced by Alignment::checkCorrespondence().

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◆ min() [2/3]

float utils::min	(	float	x,
		float	y
	)

Minimum of two numbers method.

Parameters

x	The first number.
y	The second number.

Returns: The minumum between the two given numbers.

This method returns the minimum between the two numbers given as parameters.

Definition at line 104 of file utils.cpp.

Referenced by Cleaner::cleanCompareFile().

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◆ min() [3/3]

double utils::min	(	double	x,
		double	y
	)

Minimum of two numbers method.

Parameters

x	The first number.
y	The second number.

Returns: The minumum between the two given numbers.

This method returns the minimum between the two numbers given as parameters.

Definition at line 110 of file utils.cpp.

◆ quicksort() [1/3]

void utils::quicksort	(	float *	list,
		int	ini,
		int	fin
	)

Quicksort sorting method.

Parameters

list	The vector that we want to sort.
ini	The first element of the vector.
fin	The last element of the vector.

This method sorts the vector using the quicksort method.

Definition at line 159 of file utils.cpp.

References quicksort(), and swap().

Referenced by statistics::Similarity::calcCutPoint(), Cleaner::cleanByCutValueOverpassOrEquals(), Cleaner::cleanCombMethods(), Cleaner::cleanCompareFile(), statistics::Mold::printAccumulative(), statistics::Similarity::printConservationAcl(), statistics::Consistency::printStatisticsFileAcl(), quicksort(), and Alignment::statSVG().

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◆ quicksort() [2/3]

void utils::quicksort	(	int *	list,
		int	ini,
		int	fin
	)

Quicksort sorting method.

Parameters

list	The vector that we want to sort.
ini	The first element of the vector.
fin	The last element of the vector.

This method sorts the vector using the quicksort method.

Definition at line 204 of file utils.cpp.

References quicksort(), and swap().

Referenced by Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), and quicksort().

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◆ quicksort() [3/3]

void utils::quicksort	(	int **	vect,
		int	ini,
		int	fin
	)

Quicksort sorting method.

Parameters

vect	The vector that we want to sort.
ini	The first element of the vector.
fin	The last element of the vector.

Definition at line 246 of file utils.cpp.

References quicksort(), and swap().

Referenced by Cleaner::calculateRepresentativeSeq(), Cleaner::getCutPointClusters(), and quicksort().

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◆ readLine() [1/2]

char * utils::readLine ( std::ifstream & file )

Read a new line from current input stream.
This function is better than standard one since cares of operative system compatibility.
It is useful as well because removes tabs and blank spaces at lines at beginning/ending.
.

Parameters

file	ifstream to read line from.

Returns: Line that has been read or nullptr if there is nothing to read.

Definition at line 304 of file utils.cpp.

◆ readLine() [2/2]

char * utils::readLine ( std::istream & file )

Read a new line from current input stream.
This function is better than standard one since cares of operative system compatibility.
It is useful as well because removes tabs and blank spaces at lines at beginning/ending.
.

Parameters

file	ifstream to read line from.

Returns: nullptr if there is nothing to read.
Line that has been read.

Definition at line 348 of file utils.cpp.

◆ readNumbers()

int * utils::readNumbers ( const std::string & line )

Reads a line and converts it to an array of number.

Parameters

line	Line to convert to array of ints

Returns: Pointer to an array of numbers that contains line

Definition at line 624 of file utils.cpp.

Referenced by trimAlManager::select_cols_argument(), and trimAlManager::seqs_select_argument().

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◆ removeCharacter()

std::string utils::removeCharacter	(	char	c,
		std::string	line
	)

Removes a determined char from the string.

Parameters

c	Character to remove from line
line	String to remove c from.

Returns: New string without c character

Definition at line 485 of file utils.cpp.

Referenced by Cleaner::calculateRepresentativeSeq(), Alignment::checkCorrespondence(), Cleaner::getCutPointClusters(), and Alignment::getSequences().

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◆ removeSpaces()

void utils::removeSpaces	(	char *	in,
		char *	out
	)

Removing spaces method.

Parameters

	in	The string that we want to clean.
[out]	out	The destination of the clean string.

This method removes spaces in the input string and put the result in the output string.

Definition at line 144 of file utils.cpp.

Referenced by statistics::similarityMatrix::loadSimMatrix().

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◆ ReplaceString()

std::string utils::ReplaceString	(	std::string	subject,
		const std::string &	search,
		const std::string &	replace
	)

Function that replaces a substring with another substring in a string. It makes a copy of the original string.

Parameters

[in]	subject	String to be modified
	search	Substring to search and change
	replace	Substring to put in place of search

Definition at line 820 of file utils.cpp.

Referenced by trimAlManager::output_reports(), trimAlManager::perform(), FormatHandling::FormatManager::replaceINtag(), and FormatHandling::FormatManager::saveAlignments().

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◆ ReplaceStringInPlace()

void utils::ReplaceStringInPlace	(	std::string &	subject,
		const std::string &	search,
		const std::string &	replace
	)

Function that replaces a substring with another substring in a string. It does not make a copy of the original string, but modifies it.

Parameters

[in,out]	subject	String to be modified
	search	Substring to search and change
	replace	Substring to put in place of search

Definition at line 810 of file utils.cpp.

Referenced by trimAlManager::examples(), trimAlManager::menu(), trimAlManager::output_reports(), trimAlManager::perform(), and FormatHandling::FormatManager::saveAlignments().

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◆ roundInt()

int utils::roundInt ( double number )

Round double to integer method.

Parameters

number The number that will be rounded.

Returns: the rounded number.

This method rounds a double number to a integer.

Definition at line 68 of file utils.cpp.

Referenced by statistics::Gaps::applyWindow(), statistics::Gaps::calcCutPoint(), Cleaner::cleanByCutValueFallBehind(), Cleaner::cleanByCutValueOverpass(), Cleaner::cleanByCutValueOverpassOrEquals(), and Cleaner::cleanStrict().

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◆ roundToInf()

int utils::roundToInf ( double number )

Round double to inferior integer method.

Parameters

number The number that will be rounded.

Returns: the rounded number.

This method rounds a double number to the inferior integer.

Definition at line 62 of file utils.cpp.

◆ roundToSup()

int utils::roundToSup ( double number )

Round double to greater integer method.

Parameters

number The number that will be rounded.

Returns: the rounded number.

This method rounds a double number to the greater integer.

Definition at line 74 of file utils.cpp.

◆ swap() [1/3]

void utils::swap	(	float *	a,
		float *	b
	)

Swapping elements method.

Parameters

a	One element to swap.
b	Other element to swap.

This method swaps the values in a and b.

Definition at line 193 of file utils.cpp.

Referenced by quicksort().

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◆ swap() [2/3]

void utils::swap	(	int *	a,
		int *	b
	)

Swapping elements method.

Parameters

a	One element to swap.
b	Other element to swap.

This method swaps the values in a and b.

Definition at line 237 of file utils.cpp.

Referenced by quicksort().

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◆ swap() [3/3]

void utils::swap	(	int **	a,
		int **	b
	)

Swaps double pointers.

Parameters

a	Double pointer A
b	Double pointer B

Definition at line 275 of file utils.cpp.

Referenced by quicksort().

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◆ toUpper()

char utils::toUpper ( char c )

Definition at line 958 of file utils.cpp.

Referenced by statistics::Similarity::calculateVectors(), checkAlignmentType(), and lookForPattern().

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◆ trimLine()

char * utils::trimLine ( std::string nline )

Remove all content surrounded by ("") or ([]).
It warns as well when a mismatch for these flags is found.
.

Parameters

nline Line to be trimmed.

Returns: Line trimmed of comments or nullptr if there has been a mismatch

Definition at line 392 of file utils.cpp.

References BracketsMissmatchFound, debug, PossibleMissmatch, and reporting::reportManager::report().

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Namespaces

Functions

Detailed Description

Function Documentation

◆ checkAlignmentType()

◆ checkFile()

◆ compare()

◆ copyVect() [1/2]

◆ copyVect() [2/2]

◆ determineColor()

◆ fileExists() [1/2]

◆ fileExists() [2/2]

◆ GetConsStep()

◆ GetGapStep() [1/2]

◆ GetGapStep() [2/2]

◆ getReverse()

◆ GetSimStep()

◆ initlVect() [1/2]

◆ initlVect() [2/2]

◆ isNumber()

◆ lookForPattern()

◆ max() [1/3]

◆ max() [2/3]

◆ max() [3/3]

◆ min() [1/3]

◆ min() [2/3]

◆ min() [3/3]

◆ quicksort() [1/3]

◆ quicksort() [2/3]

◆ quicksort() [3/3]

◆ readLine() [1/2]

◆ readLine() [2/2]

◆ readNumbers()

◆ removeCharacter()

◆ removeSpaces()

◆ ReplaceString()

◆ ReplaceStringInPlace()

◆ roundInt()

◆ roundToInf()

◆ roundToSup()

◆ swap() [1/3]

◆ swap() [2/3]

◆ swap() [3/3]

◆ toUpper()

◆ trimLine()