#include <iostream>
#include <cstring>
#include <cstdlib>
#include <fstream>
#include <sstream>
#include <iomanip>
#include <vector>
#include <cstdio>
#include <string>
#include <cmath>
#include <map>
#include <sys/stat.h>

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

	utils::TerminalColors

Enumerations
enum	utils::TerminalColors::terminalColor { utils::TerminalColors::RESET, utils::TerminalColors::BLACK, utils::TerminalColors::RED, utils::TerminalColors::GREEN, utils::TerminalColors::YELLOW, utils::TerminalColors::BLUE, utils::TerminalColors::MAGENTA, utils::TerminalColors::CYAN, utils::TerminalColors::WHITE, utils::TerminalColors::BOLD, utils::TerminalColors::UNDERLINE }

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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. . More...

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. . More...

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

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

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

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

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

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

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

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. More...

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. More...

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. More...

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

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. More...

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

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

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

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. More...

char	utils::toUpper (char c)

Variables
std::map< terminalColor, const std::string >	utils::TerminalColors::colors

Namespaces

Enumerations

Functions

Variables