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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "sequence_4bits.h"
#include <math.h>
#define MASK_0_1 15
#define MASK_1_0 240
#define MASK_1_1 255
enum {NUCLEO_0, NUCLEO_A, NUCLEO_C, NUCLEO_M, NUCLEO_R, NUCLEO_V, NUCLEO_H, NUCLEO_W, NUCLEO_S, NUCLEO_D, NUCLEO_B, NUCLEO_Y, NUCLEO_K, NUCLEO_G, NUCLEO_T_U, NUCLEO_N, NUCLEO_IGN};
//--------------------------------------------------------------
unsigned char* createSequence(char *str)
{
int lg, i, dec;
int nucleo;
unsigned char * seq;
unsigned char * pseq;
//Initialisation du tableau de caractère
lg = strlen(str);
dec = lg%2;
if (dec == 0) lg = lg/2;
else lg = lg/2+1;
seq = calloc(lg+1, sizeof(unsigned char));
if (seq != NULL)
{
//lire la séquence
for(i = 0, dec = 0 ;*str != '\0'; str++)
{
switch(*str)
{
case 'a' :
case 'A' : nucleo = NUCLEO_A; break;
case 'c' :
case 'C' : nucleo = NUCLEO_C; break;
case 'g' :
case 'G' : nucleo = NUCLEO_G; break;
case 'u' :
case 'U' :
case 't' :
case 'T' : nucleo = NUCLEO_T_U; break;
case 'm' :
case 'M' : nucleo = NUCLEO_M; break;
case 'r' :
case 'R' : nucleo = NUCLEO_R; break;
case 'w' :
case 'W' : nucleo = NUCLEO_W; break;
case 's' :
case 'S' : nucleo = NUCLEO_S; break;
case 'y' :
case 'Y' : nucleo = NUCLEO_Y; break;
case 'k' :
case 'K' : nucleo = NUCLEO_K; break;
case 'v' :
case 'V' : nucleo = NUCLEO_V; break;
case 'h' :
case 'H' : nucleo = NUCLEO_H; break;
case 'd' :
case 'D' : nucleo = NUCLEO_D; break;
case 'b' :
case 'B' : nucleo = NUCLEO_B; break;
case 'n' :
case 'N' : nucleo = NUCLEO_N; break;
case ' ' :
case '\n': nucleo = NUCLEO_IGN; break;
default : printf("Invalid character encountered : - Operation aborted");
free(seq);
exit(0);
}
if(nucleo != NUCLEO_IGN) // ne traiter que si c'est un caractère valide
{
if (dec==0){
seq[i] = nucleo << 4;
dec++;
}
else {
seq[i] |= nucleo;
dec=0;
i++;
}
}
} // fin de lecture
if (dec==1) i++;
pseq = realloc(seq,i+1); // redimensionner le tableau
if(pseq != NULL) seq = pseq;
seq[i] = '\0'; // et le terminer
}
return seq;
}
//
int seqlen(unsigned char* seq){
int lg = strlen(seq);
int dec = seq[lg-1] & MASK_0_1;
if (dec == 0) return (lg-1)*2+1;
return 2*lg;
}
int seqcmp(unsigned char* seq1, int position1, unsigned char* seq2, int position2, int costMismatch){
int nb1, nb2;
switch (position1%2){
case 0: nb1 = seq1[position1/2] & MASK_0_1;
case 1: nb1 = (seq1[position1/2] & MASK_1_0) >> 4;
default: return -1;
}
switch (position2%2){
case 0: nb2 = seq2[position2/2] & MASK_0_1;
case 1: nb2 = (seq2[position2/2] & MASK_1_0) >> 4;
default: return -1;
}
if (nb1 == nb2) return 1;
return costMismatch;
}
unsigned char* reverseSequence(unsigned char* seq, int complement){
int i, lg, seq_lg = seqlen(seq);
//Calcul de la longueur du tableau de caractère
lg = strlen(seq);
char *newSeq = calloc(lg+1, sizeof(unsigned char));
if (newSeq != NULL){
if (complement==0){
for (i=0; i<lg; i++){
newSeq[i] = reverseCompChar(seq[i]);
}
if (seq_lg%2==1) newSeq[i-1] = newSeq[i-1] & MASK_1_0;
newSeq[lg] = '\0';
return newSeq;
}
if (lg > 1){
for (i=0; i<lg/2; i++){
newSeq[i] = reverseCompChar(seq[lg-i-1]);
newSeq[lg-i-1] = reverseCompChar(seq[i]);
}
if (lg%2 == 1) newSeq[i] = reverseCompChar(seq[i]);
newSeq[lg] = '\0';
if (seq_lg%2 == 1){
char* res = subSequence(newSeq, 1, (lg*2)-1);
free(newSeq);
return res;
}
}
else{
newSeq[i] = reverseCompChar(seq[i]);
if (seq_lg%2==1) newSeq[i] = newSeq[i] << 4;
newSeq[lg] = '\0';
}
return newSeq;
}
else {
fprintf (stderr, "Insufficient memory\n");
exit (EXIT_FAILURE);
}
}
unsigned char* subSequence(unsigned char* seq, int posDeb, int posFin){
int i, k=0, lg, newSeq_lg, seq_lg, dec;
unsigned char tmp1;
unsigned char* newSeq;
//Calcul de la longueur du tableau de caractère
newSeq_lg = posFin-posDeb+1;
seq_lg = seqlen(seq);
dec = newSeq_lg%2;
if (dec == 0) lg = newSeq_lg/2;
else lg = newSeq_lg/2+1;
newSeq = calloc(lg+1,sizeof(unsigned char));
if (newSeq != NULL){
if (posDeb%2 == 0){
for (i = posDeb/2; i<posFin/2; i++){
newSeq[k] = seq[i];
k++;
}
if (dec == 1) newSeq[k] = seq[i] & MASK_1_0;
else newSeq[k] = seq[i];
}
else {
for (i = posDeb/2; i<posFin/2; i++){
tmp1 = seq[i] << 4;
if (seq_lg > 2) tmp1 = tmp1 | (seq[i+1] >> 4);
newSeq[k] = tmp1;
k++;
}
if (dec == 1) newSeq[k] = seq[i] << 4;
//else newSeq[k] = seq[i];
}
newSeq[lg] = '\0';
return newSeq;
}
else {
fprintf (stderr, "Insufficient memory\n");
exit (EXIT_FAILURE);
}
}
unsigned char* concatSequence(unsigned char* seq1, unsigned char* seq2){
int lgTab1, lgTab2, i, k, lgTmp, decTmp = 0;
int seq_lg;
unsigned char* seq;
seq_lg = seqlen(seq1) + seqlen(seq2);
if (seq_lg%2 == 0) lgTmp = seq_lg/2;
else lgTmp = (seq_lg/2)+1;
// Calcul de la longueur du tableau de la séquence 1
lgTab1 = strlen(seq1);
lgTab2 = strlen(seq2);
seq = calloc(lgTmp+1, sizeof(unsigned char));
// Recopie du tableau de la séquence 1 dans la nouvelle séquence
for (i=0; i<lgTab1; i++){
seq[i] = seq1[i];
}
if ((seq1[i-1] & MASK_0_1) == 0) decTmp = 1;
// Si aucun décalage dans la séquence 1, je recopie le tableau de la séquence 2 à la suite du 1 dans la nouvelle séquence
if (decTmp == 0){
for (k=0; k<lgTab2; k++){
seq[i] = seq2[k];
i++;
}
}
else {
// Gestion du décalage entre la dernière ligne du premier tableau et la première ligne du dernier tableau
seq[i-1] = seq[i-1] | (seq2[0] >> 4);
if (i < lgTmp) seq[i] = seq2[0] << 4;
// Recopie du deuxième tableau avec gestion du décalage
for (k=0; k<lgTab2-1; k++){
seq[i] = seq[i] | (seq2[k+1] >> 4);
seq[i+1] = seq2[k+1] << 4;
i++;
}
}
seq[lgTmp]= '\0';
return seq;
}
unsigned char reverseCompChar(unsigned char c){
int k;
unsigned char tmp = 0;
for (k=0; k<2; k++){
switch(k){
case 0: tmp = reverseNucl(c) << 4; break;
case 1: tmp = reverseNucl(c >> 4) | tmp; break;
}
}
return tmp;
}
unsigned char reverseNucl(unsigned char c){
switch (c){
case 7:
case 8:
case 15: return c;
default: return ~c & MASK_0_1;
}
} |
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