utils.h

/*--------------------------------
           Master BIBS
     Universite Paris-Saclay
   Projet MiniInfo 1 2023-2024

Sujet propose par George Marchment
      george.marchment@lisn.fr
----------------------------------*/

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include <ctype.h>

// Escape codes for colors
#define COLOR_RED     "\x1b[31m"
#define COLOR_GREEN   "\x1b[32m"
#define COLOR_BLUE    "\x1b[34m"
#define COLOR_YELLOW  "\x1b[33m"
#define COLOR_RESET   "\x1b[0m"
#define BOLD_TEXT     "\x1b[1m"
#define UNDERLINE_TEXT "\x1b[4m"
#define COLOR_PURPLE  "\x1b[35m"

// Sequence
#define ID_MAX_LENGTH 50
#define seq_MAX_LENGTH 400

typedef struct Sequence
{
    char ID[ID_MAX_LENGTH];
    char seq[seq_MAX_LENGTH];
} Sequence;

void show_sequences_file(char* file);
void set_empty_string(char* str);
void parse_file(char* address, Sequence tab_sequences[]);
void appendString(char* str, char c);
void affiche_sequence(Sequence* sequence);

// Alignment
#define NB_BASE 5

typedef enum Base_Azotee
{
    A = 0,
    C = 1,
    G = 2,
    T = 3,
    E = 4
} Base_Azotee;

int score_alignement(char* alignement1, char* alignement2);
int get_number_entries(char* address);
void print_quality_alignement(char* ali1, char* ali2, int score);
void set_sequence(Sequence* sequence, char* ID, char* seq);
void needleman_wunsch(Sequence seq1, Sequence seq2, char* alignement1, char* alignement2);
char symbole(int entier);

// Distance Matrix
void show_distance_matrix(char* file_aligne);
void initialise_matrice(int entries, float matrice_distance[][entries]);
void fill_distance_matrix(int entries, float matrice_distance[][entries], Sequence sequences[]);
void print_matrix_float(int row, int col, float matrice_distance[][col]);

// Tree
typedef struct Noeud {
    char* valeur;
    struct Noeud* suivant_left;
    struct Noeud* suivant_right;
    int nb_noeud;
} Noeud;

typedef struct Element
{
    struct Element *next;
    Noeud *data;
} Element;

typedef struct List_Noeuds
{
    Element *head;
    int nb_elements;
} List_Noeuds;

typedef struct Arbre
{
    Noeud *tete;
} Arbre;

void show_tree(char *file_aligne, char Algorithme);