int key_press(int keycode, data_t *data)
{
//printf("key event %d\n", keycode);
if (keycode == 53 || keycode == 12)
exitProg("Key \"escape\" or \"Q\" detected, end of the process.\n");
return (0);
}
void *monrealloc(void *in, long size) {
void *point;
if(size<0 || !(point = realloc(in, size))) {
char tmp[200];
sprintf(tmp, "Try to reallocate %ld bytes\n", size);
exitProg(ErrorMemory, tmp);
}
return point;
}
int main(int ac, char **av)
{
t_d d;
if (ac != 2)
exitProg("Please, add one file after fdf.\n");
if (analyzeFile(ac, av, &d))
exitProg("Map specify may have incorrect values or error when reading file.\n");
/* if ((d.mlx = mlx_init()) == NULL)
exitProg("Fail to init the minilibx library.\n");
if ((d.win = mlx_new_window(d.mlx, 500, 500, av[1])) == NULL)
exitProg("Fail to open a new window.\n");
mlx_mouse_hook(d.win, mouse_click, &d);
mlx_key_hook(d.win, key_press, &d);
//mlx_expose_hook(d.win, expose_hook, &d);
mlx_loop(d.mlx);
*/ return (EXIT_SUCCESS);
}
int key_press(int keycode, t_d *d)
{
//printf("key event %d\n", keycode);
if (keycode == 53 || keycode == 12)
{
free(d->map);
exitProg("Key \"escape\" or \"Q\" detected, end of the process.\n");
}
return (0);
}
TypeTimeInterval toFossilInt(char *s) {
int i, ind;
TypeTimeInterval fossilInt;
char tmp[MAX_NAME_SIZE];
for(i=0; s[i] != '\0'; i++)
if(s[i] == ',')
s[i] = '.';
for(i=0; s[i] != '\0' && isspace(s[i]); i++);
if(s[i] == '(' || s[i] == '[') {
i++;
for(; s[i] != '\0' && isspace(s[i]); i++);
ind = 0;
for(; s[i] != '\0' && s[i] != ':' && s[i] != ';' && !isspace(s[i]); i++)
tmp[ind++] = s[i];
tmp[ind] = '\0';
fossilInt.inf = atof(tmp);
for(; s[i] != '\0' && isspace(s[i]); i++);
if(s[i] != ':' && s[i] != ';')
exitProg(ErrorReading, "Missing ':' or ';' while reading a fossilInt time interval.");
i++;
for(; s[i] != '\0' && isspace(s[i]); i++);
ind = 0;
for(; s[i] != '\0' && s[i] != ')' && s[i] != ']' && !isspace(s[i]); i++)
tmp[ind++] = s[i];
tmp[ind] = '\0';
fossilInt.sup = atof(tmp);
for(; s[i] != '\0' && isspace(s[i]); i++);
if(s[i] != ')' && s[i] != ']')
exitProg(ErrorReading, "Missing ')' or ']' while reading a fossilInt time interval.");
if(fossilInt.sup<fossilInt.inf) {
double tmp = fossilInt.sup;
fossilInt.sup = fossilInt.inf;
fossilInt.inf = tmp;
}
} else {
fossilInt.inf = atof(s);
fossilInt.sup = fossilInt.inf;
}
return fossilInt;
}
int expose_hook(t_d *d)
{
int x = 0;
int y = 0;
int pos;
printf("Enter in expose\n");
if ((d->img = mlx_new_image(d->mlx, 500, 500)) == NULL)
exitProg("Fail to init a new image in minilibx.\n");
d->strimg = mlx_get_data_addr(d->img, &(d->bpp), &(d->size_line), &(d->endian));
d->color = mlx_get_color_value(d->mlx, 0xFFFAFA);
while (x < 250)
{
put_pixel_in_img(d, x, y);
x++;
if (x == 250 && y < 250)
{
x = 0;
y++;
}
/* == CA MARCHE
y = 0;
while (y < 250)
{
pos = y * d->size_line + 4 * x;
d->strimg[pos] = 255;
y++;
}
x++;*/
}
mlx_put_image_to_window(d->mlx, d->win, d->img, 0, 0);
//mlx_destroy_image(d->mlx, d->img);
printf("End of expose\n");
return (0);
}
int main(int argc, char **argv) {
TypePosition orderstart=1, orderend=10;
char option[256], inputFileName[SIZE_BUFFER_CHAR], outputFileName[SIZE_BUFFER_CHAR], bufferOutput[SIZE_BUFFER_CHAR], *table,
outputFormat = 'r', typeDec = 'l', typeAlphabet = '?', typeCalc = 'g';
TypeSetOfSequences *set;
TypeAlignment aln, atmp;
int fixed = 0;
double threshold = 0.001, tmin = 0.00000000001, tmax=0.1, tstep = 0.00001;
double thre;
TypeNumber n;
TypeDistance distA, distB, distC;
TypePosition l, tot;
double corrAB, corrAC;
TypeSetOfSequences *dec;
TypeMarkovModel *model;
FILE *fi, *fo;
int i = 1, typeDist = 0;
for(i=0; i<256; i++)
option[i] = 0;
for(i=1; i<argc && *(argv[i]) == '-'; i++) {
int j;
for(j=1; argv[i][j] != '\0'; j++)
option[argv[i][j]] = 1;
if(option['f']) {
option['f'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &outputFormat) == 1)
i++;
}
if(option['s']) {
option['s'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeAlphabet) == 1)
i++;
}
if(option['c']) {
option['c'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeCalc) == 1)
i++;
}
if(option['m']) {
option['m'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%d", &typeDist) == 1)
i++;
if(typeDist >= MAX_FUNC)
typeDist = 0;
}
if(option['t']) {
option['t'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &threshold) == 1)
i++;
}
if(option['h']) {
printf("%s\n", HELPMESSAGE);
exitProg(ExitOk, NULL);
}
}
if (i>=argc || sscanf(argv[i++], "%s", inputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
if (i>=argc || sscanf(argv[i++], "%s", outputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
switch(typeAlphabet) {
case 'd':
table = (char*) monmalloc((strlen(DNA)+1)*sizeof(char));
strcpy(table, DNA);
break;
case 'r':
table = (char*) monmalloc((strlen(RNA)+1)*sizeof(char));
strcpy(table, RNA);
break;
case 'p':
table = (char*) monmalloc((strlen(PRO)+1)*sizeof(char));
strcpy(table, PRO);
break;
case '?':
default:
table = (char*) monmalloc(sizeof(char));
table[0] = '\0';
}
if(fi = fopen(inputFileName, "r")) {
aln = readAlignement(fi, table, typeAlphabet == '?');
switch(typeAlphabet) {
case 'd':
case 'r':
aln.ambiguity = getXNAAmbiguity();
break;
case 'p':
aln.ambiguity = getProteinAmbiguity();
break;
case '?':
default:
aln.ambiguity.number = 0;
}
aln.cardinal -= aln.ambiguity.number;
fclose(fi);
} else {
exitProg(ErrorReading, inputFileName);
}
if(!(fo = fopen(outputFileName, "w")))
exitProg(ErrorWriting, outputFileName);
fixAlignmentAmbiguity(&aln);
set=toSequences(&aln);
model = estimateMarkovModel(set);
distA = computeWholeDistancePairAln(aln, computeNorm1Aln);
dec = getDecodedFromThreshold(set, threshold, model);
distB = computeWholeDistanceDec(dec);
corrAB = computeCorrelation(distA, distB);
//printf("%lE\n", corrAB);
monfree((void*)distB.table);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
distC = computeMSMDistance(set);
corrAC = computeCorrelation(distA, distC);
monfree((void*)distC.table);
monfree((void*)distA.table);
fprintf(fo, "%lE\t%lE\n", corrAB, corrAC);
fprintf(stdout, "%lE\t%lE\n", corrAB, corrAC);
monfree((void*)set->size);
for(n=0; n<set->number; n++)
monfree((void*)set->sequence[n]);
monfree((void*)set->sequence);
monfree((void*)set);
fclose(fo);
/* sprintf(bufferOutput, "%s_Ali.nex", outputFileName);
if(!(fo = fopen(bufferOutput, "w")))
exitProg(ErrorWriting, bufferOutput);
printDistanceNexus(fo, distA);
fclose(fo);
sprintf(bufferOutput, "%s_New.nex", outputFileName);
if(!(fo = fopen(bufferOutput, "w")))
exitProg(ErrorWriting, bufferOutput);
printDistanceNexus(fo, distB);
fclose(fo);
*/
exitProg(ExitOk,NULL);
return 0;
}
int main(int argc, char **argv) {
TypePosition orderstart=1, orderend=10;
char option[256], inputFileName[SIZE_BUFFER_CHAR], outputFileName[SIZE_BUFFER_CHAR], bufferOutput[SIZE_BUFFER_CHAR], *table,
outputFormat = 'r', typeDec = 'l', typeAlphabet = '?', typeCalc = 'g';
TypeSetOfSequences set;
int fixed = 0;
double threshold = 0.001;
/* TypeDistFunction *distfunc[MAX_FUNC]=
{computeProba, computeKullbackLeiber1, computePham, computeCommon, computeCommonBis, computeGillesPham, computeMatchesBis, computeMatches, computeAlex, computeAlexBis};
*/
FILE *fi, *fo;
int i = 1, typeDist = 0;
for(i=0; i<256; i++)
option[i] = 0;
for(i=1; i<argc && *(argv[i]) == '-'; i++) {
int j;
for(j=1; argv[i][j] != '\0'; j++)
option[argv[i][j]] = 1;
if(option['f']) {
option['f'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &outputFormat) == 1)
i++;
}
if(option['s']) {
option['s'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeAlphabet) == 1)
i++;
}
if(option['c']) {
option['c'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeCalc) == 1)
i++;
}
if(option['m']) {
option['m'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%d", &typeDist) == 1)
i++;
if(typeDist >= MAX_FUNC)
typeDist = 0;
}
if(option['t']) {
option['t'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &threshold) == 1)
i++;
}
if(option['h']) {
printf("%s\n", HELPMESSAGE);
exitProg(ExitOk, NULL);
}
}
if (i>=argc || sscanf(argv[i++], "%s", inputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
if (i>=argc || sscanf(argv[i++], "%s", outputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
switch(typeAlphabet) {
case 'd':
table = (char*) monmalloc((strlen(DNA)+1)*sizeof(char));
strcpy(table, DNA);
break;
case 'r':
table = (char*) monmalloc((strlen(RNA)+1)*sizeof(char));
strcpy(table, RNA);
break;
case 'p':
table = (char*) monmalloc((strlen(PRO)+1)*sizeof(char));
strcpy(table, PRO);
break;
case '?':
default:
table = (char*) monmalloc(sizeof(char));
table[0] = '\0';
}
if(fi = fopen(inputFileName, "r")) {
set = readSequencesFasta(fi, table, typeAlphabet == '?');
switch(typeAlphabet) {
case 'd':
case 'r':
set.ambiguity = getXNAAmbiguity();
break;
case 'p':
set.ambiguity = getProteinAmbiguity();
break;
case '?':
default:
set.ambiguity.number = 0;
}
set.cardinal -= set.ambiguity.number;
fclose(fi);
} else {
exitProg(ErrorReading, inputFileName);
}
if(fo = fopen(outputFileName, "w")) {
TypeDistance dist;
fixSequencesAmbiguity(&set);
dist = computeMSMDistance(&set);
switch(outputFormat) {
case 't':
printDistanceTable(fo, dist);
break;
case 'r':
printDistanceRaw(fo, dist);
break;
case 'p':
printDistancePhylip(fo, dist);
break;
case 'n':
printDistanceNexus(fo, dist);
}
fclose(fo);
} else {
exitProg(ErrorWriting, outputFileName);
}
exitProg(ExitOk,NULL);
return 0;
}
/*read partition in Clustnsee format*/
TypePartition readPartition(FILE *f, char***name) {
char c;
TypePartition part;
int sizeBufItem = INC_SIZE_ITEM_BUF, index;
TypeLexiTree *dict;
dict = newLexiTree();
part.sizeAtom = -1;
part.sizeItem = 0;
part.atom = (int*) malloc(sizeBufItem*sizeof(int));
for(c = fgetc(f); c != EOF && issepline(c); c = fgetc(f));
while(c != EOF) {
char tmp[MAX_NAME_SIZE+1];
int i;
if(c == '\'' || c == '"') {
c = fgetc(f);
for(i=0; i<MAX_NAME_SIZE && c != EOF && c != '\'' && c != '"'; i++) {
tmp[i] = c;
c = fgetc(f);
}
if(c == '\'' || c == '"')
c = fgetc(f);
else
exitProg(ErrorReading, "Missing closing \" or '...");
} else {
for(i=0; i<MAX_NAME_SIZE && c !=EOF && !issepline(c); i++) {
tmp[i] = c;
c = fgetc(f);
}
}
/* if(i == 0)
exitProg(ErrorExec, "Empty name...");
*/ if(i == MAX_NAME_SIZE)
exitProg(ErrorExec, "Name too much long...");
if(i>0) {
tmp[i++] = '\0';
//printf("%s\n", tmp);
if(tmp[0] == '#') {
for(; c != EOF && !isline(c); c = fgetc(f));
} else {
if(strncmp(tmp, CLUSTERID, strlen(CLUSTERID)) == 0) {
// printf("Class\n");
part.sizeAtom++;
for(; c != EOF && !isline(c); c = fgetc(f));
} else {
// printf("Ident\n");
if(findWordLexi(tmp, dict) >= 0) {
printf("Duplicate identifier %s(%d)\n", tmp, findWordLexi(tmp, dict));
fprintLexiTree(stdout, dict);
exit(1);
}
index = addWordLexiTree(tmp, dict);
if(index>part.sizeItem)
part.sizeItem = index;
if(index>=sizeBufItem) {
sizeBufItem += INC_SIZE_ITEM_BUF;
part.atom = (int*) realloc((void*)part.atom, sizeBufItem*sizeof(int));
}
part.atom[index] = part.sizeAtom;
}
}
}
for(; c != EOF && issepline(c); c = fgetc(f));
}
part.sizeItem++;
part.sizeAtom++;
part.atom = (int*) realloc((void*)part.atom, part.sizeItem*sizeof(int));
*name = (char**) malloc(part.sizeItem*sizeof(char*));
fillLexiTree(*name, dict);
freeLexiTree(dict);
return part;
}
/*read partition in Line Number format*/
TypePartition readPartitionNumber(FILE *f) {
char c;
TypePartition part;
int sizeBufItem = INC_SIZE_ITEM_BUF, index;
TypeLexiTree *dict;
dict = newLexiTree();
part.sizeAtom = 0;
part.sizeItem = 0;
part.atom = (int*) malloc(sizeBufItem*sizeof(int));
for(c = fgetc(f); c != EOF && issepline(c); c = fgetc(f));
while(c != EOF) {
char tmp[MAX_NAME_SIZE+1];
int i;
while(c != EOF && !isline(c)) {
if(c == '\'' || c == '"') {
c = fgetc(f);
for(i=0; i<MAX_NAME_SIZE && c != EOF && c != '\'' && c != '"'; i++) {
tmp[i] = c;
c = fgetc(f);
}
if(c == '\'' || c == '"')
c = fgetc(f);
else
exitProg(ErrorReading, "Missing closing \" or '...");
} else {
for(i=0; i<MAX_NAME_SIZE && c !=EOF && !issep(c); i++) {
tmp[i] = c;
c = fgetc(f);
}
}
if(i == MAX_NAME_SIZE)
exitProg(ErrorExec, "Name too much long...");
if(i>0) {
tmp[i++] = '\0';
index = atoi(tmp);
if(index>part.sizeItem)
part.sizeItem = index;
if(index>=sizeBufItem) {
sizeBufItem += INC_SIZE_ITEM_BUF;
part.atom = (int*) realloc((void*)part.atom, sizeBufItem*sizeof(int));
}
for(; c != EOF && issep(c); c = fgetc(f));
if(c == '\'' || c == '"') {
c = fgetc(f);
for(i=0; i<MAX_NAME_SIZE && c != EOF && c != '\'' && c != '"'; i++) {
tmp[i] = c;
c = fgetc(f);
}
if(c == '\'' || c == '"')
c = fgetc(f);
else
exitProg(ErrorReading, "Missing closing \" or '...");
} else {
for(i=0; i<MAX_NAME_SIZE && c !=EOF && !issepline(c); i++) {
tmp[i] = c;
c = fgetc(f);
}
}
if(i == MAX_NAME_SIZE)
exitProg(ErrorExec, "Name too much long...");
if(i>0) {
tmp[i++] = '\0';
part.atom[index] = atoi(tmp);
if(part.atom[index]>=part.sizeAtom)
part.sizeAtom = part.atom[index]+1;
}
}
for(; c != EOF && issep(c); c = fgetc(f));
}
for(; c != EOF && issepline(c); c = fgetc(f));
}
part.sizeItem++;
part.atom = (int*) realloc((void*)part.atom, part.sizeItem*sizeof(int));
return part;
}
/*compare part1 vs part2*/
double comparePart(TypePartitionCompareIndex type, TypePartition *part1, TypePartition *part2) {
int i,ii, j,jj, k, ci, cj, common, appar1, appar2, clasmax=0, NbR, NbS, cas, kas, *card1, *card2, **inter;
double Max, Exp;
if(part1->sizeItem != part2->sizeItem)
exitProg(ErrorExec, "Trying to compare two partitions not on the same set");
switch(type) {
case correctedRandIndex:
// Indice de inter corrigé
default:
clasmax = UTILS_MAX(part1->sizeAtom, part2->sizeAtom); // Nb. max de atomes dans le fichier des partitions
card1 = (int*) malloc(clasmax*sizeof(int)); // Somme Ligne de inter
card2 = (int*) malloc(clasmax*sizeof(int)); // Somme colonne
inter = (int**) malloc(clasmax*sizeof(int *));
assert(card1 != NULL && card2 != NULL && inter != NULL);
for(i=0; i<clasmax; i++) {
inter[i] = (int*) malloc(clasmax*sizeof(int));
assert(inter[i] != NULL);
}
// Initialisation du tableau de contingence des atomes
for(i=0; i<clasmax; i++) {
card1[i]=0; card2[i]=0; //cardinal de la atome i dans la partition 1, cardinal de la atome j dans la partition 2
for(j=0; j<clasmax; j++)
inter[i][j]=0; //intersection de la atome i de la partition 1 et de la atome j de la partition 2
}
// Table des cardinaux des intersections des atomes
for(k=0; k<part1->sizeItem; k++) {
inter[part1->atom[k]][part2->atom[k]]++;
card1[part1->atom[k]]++;
card2[part2->atom[k]]++;
}
common=0; //nombre de paires communes entre les deux partitions
for(i=0; i<part1->sizeAtom; i++)
for(j=0; j<part2->sizeAtom; j++)
common += (inter[i][j]*(inter[i][j]-1))/2;
appar1=0; //nombre de paires appariées dans la partition 1
appar2=0; //nombre de paires appariées dans la partition 2
for(i=0; i<part1->sizeAtom; i++)
appar1 += (card1[i]*(card1[i]-1))/2;
for(j=0; j<part2->sizeAtom; j++)
appar2 += (card2[j]*(card2[j]-1))/2;
free((void*)card1);
free((void*)card2);
for(i=0; i<clasmax; i++)
free((void*)inter[i]);
free((void*)inter);
//if((1.-((double)((part1->sizeItem*(part1->sizeItem-1))*common-2.*appar1*appar2))/((double)(((part1->sizeItem*(part1->sizeItem-1))*(appar1+appar2))/2.-2.*appar1*appar2)))>1.) {
//printf("size %d, common %d, appar1 %d, appar2 %d\n", part1->sizeItem, common, appar1, appar2);
//printf("%.3lf/%.3lf\n", ((double)(((double)part1->sizeItem*((double)part1->sizeItem-1.))*((double)common)-2.*((double)appar1)*((double)appar2))), ((double)(((((double)part1->sizeItem)*((double)part1->sizeItem-1.))*(((double)appar1)+((double)appar2)))/2.-2.*((double)appar1)*((double)appar2))));
//}
return ((double)(((double)part1->sizeItem*((double)part1->sizeItem-1.))*((double)common)-2.*((double)appar1)*((double)appar2)))/((double)(((((double)part1->sizeItem)*((double)part1->sizeItem-1.))*(((double)appar1)+((double)appar2)))/2.-2.*((double)appar1)*((double)appar2)));
//((double)((part1->sizeItem*(part1->sizeItem-1))*common-2.*appar1*appar2))/((double)(((part1->sizeItem*(part1->sizeItem-1))*(appar1+appar2))/2.-2.*appar1*appar2));
case standardJacquardIndex: // indice de Jaccard
NbR=0; NbS=0;
for(i=1; i<part1->sizeItem; i++)
for(j=0; j<i; j++) {
if(part1->atom[i]==part1->atom[j])
cas=1;
else
cas=0;
if(part2->atom[i]==part2->atom[j])
kas=1;
else
kas=0;
if(cas==1 && kas==1)
NbR++;
else
if(cas==1 || kas==1)
NbS++; // Reunies au moins une fois
}
return 1.*NbR/(NbS+NbR);
case standardRandIndex: // Taux de paires simultanement reunies ou separees - Indice de inter
NbR=0;
for(i=1; i<part1->sizeItem; i++)
for(j=0; j<i; j++) {
cas = (part1->atom[i]==part1->atom[j])?1:0;
kas = (part2->atom[i]==part2->atom[j])?1:0;
if(cas==kas)
NbR++;
}
return 2.*NbR/part1->sizeItem/(part1->sizeItem-1);
}
}
TypeAnnotation *readAnnotation(FILE *f) {
char c, tmpS[MAX_NAME_SIZE+1];
int sizeBufferG, sizeBufferL, indexG, indexA, indexL, i;
TypeAnnotation *an;
TypeAnnotationList *list;
int *start;
TypeLexiTree *dictG, *dictA;
dictG = newLexiTree();
dictA = newLexiTree();
an = (TypeAnnotation*) malloc(sizeof(TypeAnnotation));
indexG = 0;
indexL = 0;
sizeBufferG = BASIC_INC_BUFFER_G;
sizeBufferL = BASIC_INC_BUFFER_L;
start = (int*) malloc(sizeBufferG*sizeof(int));
list = (TypeAnnotationList*) malloc(sizeBufferL*sizeof(TypeAnnotationList));
for(i=0; i<sizeBufferG; i++)
start[i] = -1;
for(c=getc(f); c!=EOF && issepline(c); c = fgetc(f));
while(c != EOF) { //read first line
int i, indexG;
if(c == '\'' || c == '"') {
c = fgetc(f);
for(i=0; i<MAX_NAME_SIZE && c != EOF && c != '\'' && c != '"'; i++) {
tmpS[i] = c;
c = fgetc(f);
}
if(c == '\'' || c == '"')
c = fgetc(f);
else
exitProg(ErrorReading, "Missing closing \" or '...");
} else {
for(i=0; i<MAX_NAME_SIZE && c !=EOF && !issepline(c); i++) {
tmpS[i] = c;
c = fgetc(f);
}
}
if(i == 0)
exitProg(ErrorExec, "Empty name ...");
if(i == MAX_NAME_SIZE)
exitProg(ErrorExec, "Name too much long...");
tmpS[i++] = '\0';
indexG = addWordLexiTree(tmpS, dictG);
if(indexG >= sizeBufferG) {
int i;
sizeBufferG += BASIC_INC_BUFFER_G;
start = (int*) realloc((void *) start, sizeBufferG*sizeof(int));
for(i=sizeBufferG-BASIC_INC_BUFFER_G; i<sizeBufferG; i++)
start[i] = -1;
}
for(; c != EOF && issepX(c); c = fgetc(f));
while(!issepline(c)) {
if(c == '\'' || c == '"') {
c = fgetc(f);
for(i=0; i<MAX_NAME_SIZE && c != EOF && c != '\'' && c != '"'; i++) {
tmpS[i] = c;
c = fgetc(f);
}
if(c == '\'' || c == '"')
c = fgetc(f);
else
exitProg(ErrorReading, "Missing closing \" or '...");
} else {
for(i=0; i<MAX_NAME_SIZE && c !=EOF && !issepline(c); i++) {
tmpS[i] = c;
c = fgetc(f);
}
}
if(i == 0)
exitProg(ErrorExec, "Empty name ...");
if(i == MAX_NAME_SIZE)
exitProg(ErrorExec, "Name too much long...");
tmpS[i++] = '\0';
if(!((i != 2) && (tmpS[0] == 'N') && (tmpS[1] == 'A'))) {
indexA = addWordLexiTree(tmpS, dictA);
if(indexL >= sizeBufferL) {
sizeBufferL += BASIC_INC_BUFFER_L;
list = (TypeAnnotationList*) realloc((void *) list, sizeBufferL*sizeof(double*));
}
list[indexL].annot = indexA;
list[indexL].next = start[indexG];
start[indexG] = indexL;
indexL++;
}
for(; c != EOF && issepX(c); c = fgetc(f));
}
for(; c!=EOF && issepline(c); c = fgetc(f));
}
an->sizeG = dictG->sizeWord;
an->sizeA = dictA->sizeWord;
start = (int*) realloc((void *) start, an->sizeG*sizeof(int));
an->mat = (int**) malloc( an->sizeG*sizeof(int*));
for(i=0; i<an->sizeG; i++) {
int j;
an->mat[i] = (int*) malloc(an->sizeA*sizeof(int));
for(j=0; j<an->sizeA; j++)
an->mat[i][j] = 0;
for(j=start[i]; j>=0; j=list[j].next)
an->mat[i][list[j].annot] = 1;
}
free((void*) start);
free((void*) list);
an->nameG = (char**) malloc(an->sizeG*sizeof(char*));
fillLexiTree(an->nameG, dictG);
an->nameA = (char**) malloc(an->sizeA*sizeof(char*));
fillLexiTree(an->nameA, dictA);
freeLexiTree(dictG);
freeLexiTree(dictA);
return an;
}
int main(int argc, char **argv) {
TypePosition orderstart=1, orderend=10, length = 10;
char option[256], inputFileName[SIZE_BUFFER_CHAR], outputFileName[SIZE_BUFFER_CHAR], bufferOutput[SIZE_BUFFER_CHAR], *table,
outputFormat = 'r', typeDec = 'l', typeAlphabet = 'd', typeCalc = 'g';
TypeSetOfSequences set;
int fixed = 0, flagThre = 1;
double threshold = 0.001, tmin = -25, tmax = -3, tprec = 0.5;
/* TypeDistFunction *distfunc[MAX_FUNC]=
{computeProba, computeKullbackLeiber1, computePham, computeCommon, computeCommonBis, computeGillesPham, computeMatchesBis, computeMatches, computeAlex, computeAlexBis};
*/
FILE *fi, *fo;
int i = 1, typeDist = 0;
for(i=0; i<256; i++)
option[i] = 0;
for(i=1; i<argc && *(argv[i]) == '-'; i++) {
int j;
for(j=1; argv[i][j] != '\0'; j++)
option[argv[i][j]] = 1;
if(option['f']) {
option['f'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &outputFormat) == 1)
i++;
}
if(option['s']) {
option['s'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeAlphabet) == 1)
i++;
}
if(option['c']) {
option['c'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeCalc) == 1)
i++;
}
if(option['m']) {
option['m'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%d", &typeDist) == 1)
i++;
if(typeDist >= MAX_FUNC)
typeDist = 0;
}
if(option['t']) {
option['t'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &threshold) == 1)
i++;
flagThre = 1;
}
if(option['l']) {
option['l'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%ld", &length) == 1)
i++;
flagThre = 0;
}
if(option['h']) {
printf("%s\n", HELPMESSAGE);
exitProg(ExitOk, NULL);
}
}
if (i>=argc || sscanf(argv[i++], "%s", inputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
if (i>=argc || sscanf(argv[i++], "%s", outputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
switch(typeAlphabet) {
case 'd':
table = (char*) monmalloc((strlen(DNA)+1)*sizeof(char));
strcpy(table, DNA);
break;
case 'r':
table = (char*) monmalloc((strlen(RNA)+1)*sizeof(char));
strcpy(table, RNA);
break;
case 'p':
table = (char*) monmalloc((strlen(PRO)+1)*sizeof(char));
strcpy(table, PRO);
break;
case '?':
default:
table = (char*) monmalloc(sizeof(char));
table[0] = '\0';
}
if(fi = fopen(inputFileName, "r")) {
set = readSequencesFasta(fi, table, typeAlphabet == '?');
switch(typeAlphabet) {
case 'd':
case 'r':
set.ambiguity = getXNAAmbiguity();
break;
case 'p':
set.ambiguity = getProteinAmbiguity();
break;
case '?':
default:
set.ambiguity.number = 0;
}
set.cardinal -= set.ambiguity.number;
fclose(fi);
} else {
exitProg(ErrorReading, inputFileName);
}
if(fo = fopen(outputFileName, "w")) {
TypeSetOfSequences *dec;
TypeDistance dist;
double tmid, t, smax, tres, sc, scl, scr;
TypeNumber n;
TypeCodeScheme *scheme;
TypeMarkovModel *model;
fixSequencesAmbiguity(&set);
scheme = (TypeCodeScheme*) monmalloc(sizeof(TypeCodeScheme));
scheme->suffixTree = getSuffixTree(&set);
scheme->code = (TypePosition*) monmalloc(scheme->suffixTree->size*sizeof(TypePosition));
scheme->buffSize = INC_SIZE_CODE;
scheme->lengthCode = (TypePosition*) monmalloc(scheme->buffSize*sizeof(TypePosition));
model = estimateMarkovModel(&set);
while((tmax-tmin)>4*tprec) {
tmid = (tmax+tmin)/2.;
scheme->cardCode = 0;
buildCodeThreshold(exp(tmid-3.*tprec/2.), scheme->suffixTree->root, 0, 1., model, scheme);
dec = getDecodedFromScheme(scheme);
scl = score(dec);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
scheme->cardCode = 0;
buildCodeThreshold(exp(tmid+3.*tprec/2.), scheme->suffixTree->root, 0, 1., model, scheme);
dec = getDecodedFromScheme(scheme);
scr = score(dec);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
if(scl>scr)
tmax = tmid+3.*tprec/2.;
else
tmin = tmid-3.*tprec/2.;
}
if(scl>scr) {
smax = scl;
tres = exp(tmid-3.*tprec/2.);
} else {
smax = scr;
tres = exp(tmid+3.*tprec/2.);
}
scheme->cardCode = 0;
buildCodeThreshold(exp(tmid), scheme->suffixTree->root, 0, 1., model, scheme);
dec = getDecodedFromScheme(scheme);
sc = score(dec);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
if(sc>smax) {
smax = scl;
tres = exp(tmid);
}
printf("%.4lE\t%lf\n", tres, smax);
scheme->cardCode = 0;
buildCodeThreshold(tres, scheme->suffixTree->root, 0, 1., model, scheme);
dec = getDecodedFromScheme(scheme);
freeModel(model);
freeScheme(scheme);
dist = computeWholeDistanceDec(dec);
switch(outputFormat) {
case 't':
printDistanceTable(fo, dist);
break;
case 'r':
printDistanceRaw(fo, dist);
break;
case 'p':
printDistancePhylip(fo, dist);
break;
case 'n':
printDistanceNexus(fo, dist);
}
fclose(fo);
} else {
exitProg(ErrorWriting, outputFileName);
}
exitProg(ExitOk,NULL);
return 0;
}
int main(int argc, char **argv) {
TypePosition orderstart=1, orderend=10;
char option[256], inputFileName[SIZE_BUFFER_CHAR], outputFileName[SIZE_BUFFER_CHAR], bufferOutput[SIZE_BUFFER_CHAR], *table,
outputFormat = 'r', typeDec = 'l', typeAlphabet = '?', typeCalc = 'g', type = 't';
TypeSetOfSequences *set, seq;
TypeAlignment aln, atmp;
int fixed = 0;
double threshold = 0.001, tmin = 1E-20, tmax=0.1, tstep = 0.00001, qmin = -25, qmax = -3, qprec = 0.5;
double thre;
TypeNumber n;
TypeDistance distA, distB;
TypePosition l, tot, lmax = 50;
TypeSuffixTree *suffixTree;
TypeMarkovModel *model;
TypeCodeScheme *scheme;
/* TypeDistFunction *distfunc[MAX_FUNC]=
{computeProba, computeKullbackLeiber1, computePham, computeCommon, computeCommonBis, computeGillesPham, computeMatchesBis, computeMatches, computeAlex, computeAlexBis};
*/
FILE *fi, *fo;
int i = 1, typeDist = 0;
for(i=0; i<256; i++)
option[i] = 0;
for(i=1; i<argc && *(argv[i]) == '-'; i++) {
int j;
for(j=1; argv[i][j] != '\0'; j++)
option[argv[i][j]] = 1;
if(option['f']) {
option['f'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &outputFormat) == 1)
i++;
}
if(option['s']) {
option['s'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeAlphabet) == 1)
i++;
}
if(option['c']) {
option['c'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &typeCalc) == 1)
i++;
}
if(option['m']) {
option['m'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &tmin) == 1)
i++;
if(typeDist >= MAX_FUNC)
typeDist = 0;
}
if(option['t']) {
option['t'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &threshold) == 1)
i++;
}
if(option['y']) {
option['y'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%c", &type) == 1)
i++;
}
if(option['h']) {
printf("%s\n", HELPMESSAGE);
exitProg(ExitOk, NULL);
}
}
if (i>=argc || sscanf(argv[i++], "%s", inputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
if (i>=argc || sscanf(argv[i++], "%s", outputFileName) != 1) exitProg(ErrorArgument, HELPMESSAGE);
switch(typeAlphabet) {
case 'd':
table = (char*) monmalloc((strlen(DNA)+1)*sizeof(char));
strcpy(table, DNA);
break;
case 'r':
table = (char*) monmalloc((strlen(RNA)+1)*sizeof(char));
strcpy(table, RNA);
break;
case 'p':
table = (char*) monmalloc((strlen(PRO)+1)*sizeof(char));
strcpy(table, PRO);
break;
case '?':
default:
table = (char*) monmalloc(sizeof(char));
table[0] = '\0';
}
if(fi = fopen(inputFileName, "r")) {
aln = readAlignement(fi, table, typeAlphabet == '?');
switch(typeAlphabet) {
case 'd':
case 'r':
aln.ambiguity = getXNAAmbiguity();
break;
case 'p':
aln.ambiguity = getProteinAmbiguity();
break;
case '?':
default:
aln.ambiguity.number = 0;
}
aln.cardinal -= aln.ambiguity.number;
fclose(fi);
} else {
exitProg(ErrorReading, inputFileName);
}
fixAlignmentAmbiguity(&aln);
set=toSequences(&aln);
if(!(fo = fopen(outputFileName, "w")))
exitProg(ErrorWriting, outputFileName);
distA = computeWholeDistancePairAln(aln, computeNorm1Aln);
scheme = (TypeCodeScheme*) monmalloc(sizeof(TypeCodeScheme));
scheme->suffixTree = getSuffixTree(set);
scheme->code = (TypePosition*) monmalloc(scheme->suffixTree->size*sizeof(TypePosition));
scheme->buffSize = INC_SIZE_CODE;
scheme->lengthCode = (TypePosition*) monmalloc(scheme->buffSize*sizeof(TypePosition));
if(type == 't') {
int l;
model = estimateMarkovModel(set);
// for(thre=tmin; thre<=tmax; thre *= 10.0) {
for(l=tmin; l<=-1; l++) {
double t;
int k;
thre = pow(10.0, (double) l);
for(k=0; k<10; k++) {
// for(t=thre; t<thre*10; t+=thre) {
double corr, sc;
TypeSetOfSequences *dec;
t = ((double)k+1.)*thre;
scheme->cardCode = 0;
buildCodeThreshold(t, scheme->suffixTree->root, 0, 1., model, scheme);
//printLengthDistribution(stdout, scheme->lengthCode,scheme->cardCode);
dec = getDecodedFromScheme(scheme);
//printf("cardinal dec = %ld\n", dec->cardinal);
distB = computeWholeDistanceDec(dec);
corr = computeCorrelation(distA, distB);
monfree((void*)distB.table);
sc = score(dec);
printf("%lE\t%lf\t%.2lf\n", t, corr, sc);
fprintf(fo, "%lE\t%lf\t%.2lf\n", t, corr, sc);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
}
}
fprintf(stdout, "\n\n%.4lE\n\n", findMode(set, qmin, qmax, qprec, scheme, model));
freeModel(model);
} else {
for(l = lmax; l>=1; l--) {
double corr;
TypeSetOfSequences *dec;
scheme->cardCode = 0;
buildCodeLength(l, scheme->suffixTree->root, 0, scheme);
//printLengthDistribution(stdout, scheme->lengthCode,scheme->cardCode);
dec = getDecodedFromScheme(scheme);
//printf("cardinal dec = %ld\n", dec->cardinal);
distB = computeWholeDistanceDec(dec);
corr = computeCorrelation(distA, distB);
monfree((void*)distB.table);
fprintf(fo, "%ld\t%lf\n", l, corr);
fprintf(stdout, "%ld\t%lf\n", l, corr);
for(n=0; n<dec->number; n++)
monfree((void*) dec->sequence[n]);
monfree((void*) dec->sequence);
monfree((void*) dec->size);
monfree((void*) dec);
}
}
freeScheme(scheme);
monfree((void*)distA.table);
fprintf(stdout, "\n\n%ld\n\n", totalLength(*set));
monfree((void*)set->size);
for(n=0; n<set->number; n++)
monfree((void*)set->sequence[n]);
monfree((void*)set->sequence);
monfree((void*)set);
fclose(fo);
/* sprintf(bufferOutput, "%s_Ali.nex", outputFileName);
if(!(fo = fopen(bufferOutput, "w")))
exitProg(ErrorWriting, bufferOutput);
printDistanceNexus(fo, distA);
fclose(fo);
sprintf(bufferOutput, "%s_New.nex", outputFileName);
if(!(fo = fopen(bufferOutput, "w")))
exitProg(ErrorWriting, bufferOutput);
printDistanceNexus(fo, distB);
fclose(fo);
*/
;
exitProg(ExitOk,NULL);
return 0;
}
TypeNameFossilIntTab *readFossilIntTab(FILE *f) {
int sizeBuf;
char c;
TypeNameFossilIntTab *res;
res = (TypeNameFossilIntTab *) malloc(sizeof(TypeNameFossilIntTab));
sizeBuf = INC_FOSSIL_ITEM;
res->name = (char**) malloc(sizeBuf*sizeof(char*));
res->fossilIntTab = (TypeFossilIntTab*) malloc(sizeBuf*sizeof(TypeFossilIntTab));
res->size = 0;
do {
char *tmp;
int i;
tmp = (char*) malloc((MAX_NAME_SIZE+1)*sizeof(char));
for(c = fgetc(f); c != EOF && issepline(c); c = fgetc(f));
if(c == '\'' || c == '"') {
c = fgetc(f);
for(i=0; i<MAX_NAME_SIZE && c != EOF && c != '\'' && c != '"'; i++) {
tmp[i] = c;
c = fgetc(f);
}
if(c == '\'' || c == '"')
c = fgetc(f);
} else {
for(i=0; i<MAX_NAME_SIZE && c !=EOF && !issep(c); i++) {
tmp[i] = c;
c = fgetc(f);
}
}
if(i == MAX_NAME_SIZE)
exitProg(ErrorExec, "Name too much long...");
tmp[i++] = '\0';
if(i>1) {
char bof[MAX_NAME_SIZE+1];
int sizeFossilIntBuf = INC_FOSSIL_ITEM;
if(res->size >= sizeBuf) {
sizeBuf += INC_FOSSIL_ITEM;
res->name = (char**) realloc((void*) res->name, sizeBuf*sizeof(char*));
res->fossilIntTab = (TypeFossilIntTab*) realloc((void*) res->fossilIntTab, sizeBuf*sizeof(TypeFossilIntTab));
}
res->name[res->size] = (char *) realloc((void*) tmp, i*sizeof(char));
fixSpace(res->name[res->size]);
res->fossilIntTab[res->size].size = 0;
res->fossilIntTab[res->size].fossilInt = (TypeTimeInterval*) malloc(sizeFossilIntBuf*sizeof(TypeTimeInterval));
for(; c != EOF && issep(c); c = fgetc(f));
while(c != EOF && !isline(c)) {
for(i=0; c != EOF && !issepline(c) && i<MAX_NAME_SIZE; i++) {
bof[i] = c;
c = fgetc(f);
}
bof[i++] = '\0';
if(res->fossilIntTab[res->size].size>=sizeFossilIntBuf) {
sizeFossilIntBuf += INC_FOSSIL_ITEM;
res->fossilIntTab[res->size].fossilInt = (TypeTimeInterval*) realloc((void*) res->fossilIntTab[res->size].fossilInt, sizeFossilIntBuf*sizeof(TypeTimeInterval));
}
res->fossilIntTab[res->size].fossilInt[res->fossilIntTab[res->size].size++] = toFossilInt(bof);
DEBUG(
printf("\"%s\"\t%s\t", tmp, bof);
fprintFossilInt(stdout, res->fossilIntTab[res->size].fossilInt[res->fossilIntTab[res->size].size-1]);
printf("\n");
)
for(; c != EOF && issep(c); c = fgetc(f));
}
res->size++;
} else
int main(int argc, char **argv) {
char **inputNameTable, **name, inputFileName[STRING_SIZE], outputFileName[STRING_SIZE], effectifFileName[STRING_SIZE], outputPrefix[STRING_SIZE], outputFileNameRand[STRING_SIZE], buffer[STRING_SIZE], inputFileNameModel[STRING_SIZE], *tmp, option[256];
FILE *fi, *fo, *fs;
int i, j, t, sizeTable, singleF = 0;
TypeMultiGraph *graph, *gtmp;
TypeGraph **tableGraph, *g;
TypePartition part, *tablePart;
double alpha = 1.;
for(i=0; i<256; i++)
option[i] = 0;
sprintf(outputFileName, "%s.%s", NAME_OUTPUT, EXT_OUTPUT);
tableGraph = (TypeGraph**) malloc((argc+3)*sizeof(TypeGraph*));
inputNameTable = (char**) malloc((argc+3)*sizeof(char*));
sizeTable = 0;
for(i=1; i<argc && *(argv[i]) == '-'; i++) {
for(j=1; argv[i][j] != '\0'; j++)
option[argv[i][j]] = 1;
if(option['o']) {
option['o'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%s", outputFileName) == 1)
i++;
else
exitProg(ErrorArgument, "a file name is required after option -f");
}
if(option['s']) {
option['s'] = 0;
singleF = 1;
}
if(option['p']) {
option['p'] = 0;
if((i+1)<argc && sscanf(argv[i+1], "%lf", &alpha) == 1)
i++;
else
exitProg(ErrorArgument, "a real number is required after option -p");
}
if(option['m']) {
option['m'] = 0;
if(!(sscanf(argv[i+1], "%s", inputFileName) == 1))
exitProg(ErrorArgument, "wrong file name");
i++;
inputNameTable[sizeTable] = (char*) malloc((strlen(inputFileName)+1)*sizeof(char));
strcpy(inputNameTable[sizeTable], inputFileName);
printf("Reading file %s\n", inputNameTable[sizeTable]);
if(fi = fopen(inputNameTable[sizeTable], "r")) {
tableGraph[sizeTable++] = readMatrixGraph(fi);
fclose(fi);
} else
exitProg(ErrorReading, inputNameTable[sizeTable]);
}
if(option['h']) {
option['h'] = 0;
printf("%s\n", HELPMESSAGE);
exit(0);
}
}
for(j=i; j<argc; j++) {
if(!(sscanf(argv[j], "%s", inputFileName) == 1))
exitProg(ErrorArgument, "wrong file name");
inputNameTable[sizeTable] = (char*) malloc((strlen(inputFileName)+1)*sizeof(char));
strcpy(inputNameTable[sizeTable], inputFileName);
printf("Reading file %s\n", inputNameTable[sizeTable]);
if(fi = fopen(inputNameTable[sizeTable], "r")) {
tableGraph[sizeTable] = readGraph(fi);
fclose(fi);
} else
exitProg(ErrorReading, inputNameTable[sizeTable]);
fixEdgeGraph(tableGraph[sizeTable]);
printf("%d nodes\n", tableGraph[sizeTable]->sizeGraph);
sizeTable++;
}
if(sizeTable <= 0)
exitProg(ErrorArgument, "at least one graph is required.");
strcpy(outputPrefix, outputFileName);
if((tmp = strrchr(outputPrefix, '.')) != NULL)
tmp[0] = '\0';
graph = toMultiGraph(tableGraph, sizeTable);
part = getPartition(graph, LouvainType, &alpha);
tableGraph[sizeTable] = sumMultiGraph(graph);
inputNameTable[sizeTable] = (char*) malloc((strlen("Sum")+1)*sizeof(char));
strcpy(inputNameTable[sizeTable], "Sum");
sizeTable++;
tableGraph[sizeTable] = unionMultiGraph(graph);
inputNameTable[sizeTable] = (char*) malloc((strlen("Union")+1)*sizeof(char));
strcpy(inputNameTable[sizeTable], "Union");
sizeTable++;
tableGraph[sizeTable] = interMultiGraph(graph);
inputNameTable[sizeTable] = (char*) malloc((strlen("Intersection")+1)*sizeof(char));
strcpy(inputNameTable[sizeTable], "Intersection");
sizeTable++;
name = (char**) malloc(sizeTable*sizeof(char*));
for(t=0; t<sizeTable; t++) {
char *tmp;
if((tmp = strrchr(inputNameTable[t], '.')) != NULL)
tmp[0] = '\0';
if((tmp=strrchr(inputNameTable[t], '/')) == NULL)
tmp = inputNameTable[t];
else
tmp++;
name[t] = (char*) malloc((strlen(tmp)+1)*sizeof(char));
strcpy(name[t], tmp);
// printf("name[%d]\t%s\n", t, name[t]);
}
tablePart = (TypePartition*) malloc(sizeTable*sizeof(TypePartition));
if(singleF) {
TypeMultiGraph *gtmp;
gtmp = (TypeMultiGraph*) malloc(sizeof(TypeMultiGraph));
gtmp->sizeTable = 1;
gtmp->edge = (TypeEdgeG***) malloc(sizeof(TypeEdgeG**));
gtmp->present = (int**) malloc(sizeof(int*));
gtmp->present[0] = (int*) malloc(graph->sizeGraph*sizeof(int));
for(i=0; i<graph->sizeGraph; i++)
gtmp->present[0][i] = 1;
for(t=0; t<sizeTable; t++) {
char output[STRING_SIZE], *tmp;
fillMultiOne(tableGraph[t], gtmp);
sprintf(output, "%s_%s.%s", outputPrefix, name[t], EXT_OUTPUT);
printf("Computing %s\n", output);
tablePart[t] = getPartition(gtmp, LouvainType, &alpha);
if(fo = fopen(output, "w")) {
fprintPartitionClustNSee(fo, &(tablePart[t]), gtmp->name);
fclose(fo);
} else
exitProg(ErrorWriting, output);
}
free((void*)gtmp->present[0]);
free((void*)gtmp->present);
free((void*)gtmp->edge);
free((void*)gtmp);
}
if(fo = fopen(outputFileName, "w")) {
fprintPartitionClustNSee(fo, &part, graph->name);
fclose(fo);
} else
exitProg(ErrorWriting, outputFileName);
sprintf(effectifFileName, "%s_effectif.csv", outputPrefix);
if(fo = fopen(effectifFileName, "w")) {
int **eff, c, t, *cs;
eff = getEdgesNumbers(&part, graph);
cs = getClassSize(&part);
fprintf(fo, "\tSize");
for(t=0; t<graph->sizeTable; t++)
fprintf(fo, "\t%s", name[t]);
fprintf(fo, "\n");
for(c=0; c<part.sizeAtom; c++) {
fprintf(fo, "ClusterID:%d", c+1);
fprintf(fo, "\t%d", cs[c]);
for(t=0; t<graph->sizeTable; t++) {
fprintf(fo, "\t%d", eff[c][t]);
}
fprintf(fo, "\n");
}
fclose(fo);
for(c=0; c<part.sizeAtom; c++)
free((void*)eff[c]);
free((void*)eff);
free((void*)cs);
} else
exitProg(ErrorWriting, effectifFileName);
if(singleF) {
for(t=sizeTable-3; t<sizeTable; t++) {
sprintf(effectifFileName, "%s_%s_effectif.csv", outputPrefix, name[t]);
if((fo = fopen(effectifFileName, "w"))) {
int **eff, c, t, *cs;
eff = getEdgesNumbers(&(tablePart[sizeTable-1]), graph);
cs = getClassSize(&(tablePart[sizeTable-1]));
fprintf(fo, "\tSize");
for(t=0; t<graph->sizeTable; t++)
fprintf(fo, "\t%s", name[t]);
fprintf(fo, "\n");
for(c=0; c<tablePart[sizeTable-1].sizeAtom; c++) {
fprintf(fo, "ClusterID:%d", c+1);
fprintf(fo, "\t%d", cs[c]);
for(t=0; t<graph->sizeTable; t++) {
fprintf(fo, "\t%d", eff[c][t]);
}
fprintf(fo, "\n");
}
fclose(fo);
for(c=0; c<tablePart[sizeTable-1].sizeAtom; c++)
free((void*)eff[c]);
free((void*)eff);
free((void*)cs);
} else
exitProg(ErrorWriting, effectifFileName);
sprintf(effectifFileName, "%s_%s_graph.csv", outputPrefix, name[t]);
if((fo = fopen(effectifFileName, "w"))) {
fprintGraph(fo, tableGraph[t]);
} else
exitProg(ErrorWriting, effectifFileName);
}
}
if(singleF) {
int tl, tc;
char *tmp;
sprintf(outputFileNameRand, "%s_Rand.csv", outputPrefix);
if(fo = fopen(outputFileNameRand, "w")) {
char *tmp;
fprintf(fo,"All\t%lf\n", comparePartDiff(correctedRandIndex, &(part), graph->name, &(part), graph->name));
for(tl=0; tl<sizeTable; tl++) {
fprintf(fo, "%s\t%lf", name[tl], comparePartDiff(correctedRandIndex, &(part), graph->name, &(tablePart[tl]), tableGraph[tl]->name));
for(tc=0; tc<=tl; tc++)
fprintf(fo, "\t%lf", comparePartDiff(correctedRandIndex, &(tablePart[tc]), tableGraph[tc]->name, &(tablePart[tl]), tableGraph[tl]->name));
fprintf(fo, "\n");
}
fprintf(fo, "\tAll");
for(tl=0; tl<sizeTable; tl++) {
fprintf(fo, "\t%s", name[tl]);
}
fprintf(fo, "\n");
fclose(fo);
} else
exitProg(ErrorWriting, outputFileNameRand);
}
for(t=0; t<sizeTable; t++) {
freeGraph(tableGraph[t]);
free((void*) name[t]);
free((void*) inputNameTable[t]);
}
free((void*) tableGraph);
free((void*) name);
free((void*) inputNameTable);
exit(0);
return 0;
}
