/*return the ordered table of index of base*/
size_t *qsortTable(void *base, size_t nitems, size_t size, int (*compar)(const void *, const void*)) {
size_t *index, i;
void **p, *data;
if(size == 0 || nitems == 0)
return NULL;
index = (size_t*) malloc(nitems*sizeof(size_t*));
p = (void**) malloc(nitems*sizeof(void*));
data = (void*) malloc(nitems*size);
memcpy(data, base, nitems*size);
for(i=0; i<nitems; i++)
p[i] = (((char*)data)+i*size);
comparisonFunction = compar;
qsort(p, nitems, sizeof(void*), compareIndirect);
for(i=0; i<nitems; i++)
index[i] = (size_t)((((char*)p[i])-((char*)data))/size);
monfree((void*)data);
monfree((void*)p);
return index;
}
double score(TypeSetOfSequences *dec) {
TypeNumber n, *present, *total;
TypePosition p;
double score;
int *out;
TypeSymbol c;
present =(TypeNumber*) monmalloc(dec->cardinal*sizeof(TypeNumber));
total =(TypeNumber*) monmalloc(dec->cardinal*sizeof(TypeNumber));
out =(int*) monmalloc(dec->cardinal*sizeof(int));
for(c=0; c<dec->cardinal; c++) {
present[c] = -1;
total[c] = 0;
out[c] = 0;
}
for(n=0; n<dec->number; n++) {
for(p=0; p<dec->size[n]; p++)
if(dec->sequence[n][p]<dec->cardinal && !out[dec->sequence[n][p]]) {
if(present[dec->sequence[n][p]] == n)
out[dec->sequence[n][p]] = 1;
else {
present[dec->sequence[n][p]] = n;
total[dec->sequence[n][p]]++;
}
}
}
score = 0;
for(c=0; c<dec->cardinal; c++)
if(!out[c])
// score += (total[c]*(total[c]-1))/2;
score += (pow(total[c], 1)*(total[c]-1));
monfree((void*)out);
monfree((void*)total);
monfree((void*)present);
return score;
}
double scorebis(TypeSetOfSequences *dec) {
TypeNumber n, *last, *present;
TypePosition p, *total;
double score;
TypeSymbol c;
last =(TypeNumber*) monmalloc(dec->cardinal*sizeof(TypeNumber));
present =(TypeNumber*) monmalloc(dec->cardinal*sizeof(TypeNumber));
total =(TypePosition*) monmalloc(dec->cardinal*sizeof(TypePosition));
for(c=0; c<dec->cardinal; c++) {
present[c] = 0;
total[c] = 0;
last[c] = -1;
}
for(n=0; n<dec->number; n++) {
for(p=0; p<dec->size[n]; p++)
if(dec->sequence[n][p]<dec->cardinal) {
if(last[dec->sequence[n][p]] != n) {
last[dec->sequence[n][p]] = n;
present[dec->sequence[n][p]]++;
}
total[dec->sequence[n][p]]++;
}
}
score = 0;
for(c=0; c<dec->cardinal; c++)
if(total[c]>1 && total[c] <3* present[c])
score += (pow(total[c], 0.5));
// score += pow(((double)present[c])/((double)total[c]), 20.);
// score /= dec->cardinal;
monfree((void*)last);
monfree((void*)total);
monfree((void*)present);
return score;
}
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;
}
/* weptyp: uwep->otyp or 0 */
void
cutworm(struct monst *mtmp, xchar x, xchar y, uchar weptyp)
{
struct wseg *wtmp, *wtmp2;
struct monst *mtmp2;
int tmp, tmp2;
if (mtmp->mx == x && mtmp->my == y) /* hit headon */
return;
/* cutting goes best with axe or sword */
tmp = rnd(20);
if (weptyp == LONG_SWORD || weptyp == TWO_HANDED_SWORD ||
weptyp == AXE)
tmp += 5;
if (tmp < 12)
return;
/* if tail then worm just loses a tail segment */
tmp = mtmp->wormno;
wtmp = wsegs[tmp];
if (wtmp->wx == x && wtmp->wy == y) {
wsegs[tmp] = wtmp->nseg;
remseg(wtmp);
return;
}
/* cut the worm in two halves */
mtmp2 = newmonst(0);
*mtmp2 = *mtmp;
mtmp2->mxlth = mtmp2->mnamelth = 0;
/* sometimes the tail end dies */
if (rn2(3) || !getwn(mtmp2)) {
monfree(mtmp2);
tmp2 = 0;
} else {
tmp2 = mtmp2->wormno;
wsegs[tmp2] = wsegs[tmp];
wgrowtime[tmp2] = 0;
}
do {
if (wtmp->nseg->wx == x && wtmp->nseg->wy == y) {
if (tmp2)
wheads[tmp2] = wtmp;
wsegs[tmp] = wtmp->nseg->nseg;
remseg(wtmp->nseg);
wtmp->nseg = 0;
if (tmp2) {
pline("You cut the worm in half.");
mtmp2->mhpmax = mtmp2->mhp =
d(mtmp2->data->mlevel, 8);
mtmp2->mx = wtmp->wx;
mtmp2->my = wtmp->wy;
mtmp2->nmon = fmon;
fmon = mtmp2;
pmon(mtmp2);
} else {
pline("You cut off part of the worm's tail.");
remseg(wtmp);
}
mtmp->mhp /= 2;
return;
}
wtmp2 = wtmp->nseg;
if (!tmp2)
remseg(wtmp);
wtmp = wtmp2;
} while (wtmp->nseg);
panic("Cannot find worm segment");
}
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;
}
double findMode(TypeSetOfSequences *set, double tmin, double tmax, double tprec, TypeCodeScheme *scheme, TypeMarkovModel *model) {
double tmid, t, smax, tres, sc, scl, scr;
TypeNumber n;
// TypeCodeScheme *scheme;
TypeSetOfSequences *dec;
/* 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));
*/ 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);
}
// freeScheme(scheme);
return tres;
}
