void freeSchemePack(SchemePack* pack) {
if(pack != NULL) {
freeScheme(pack->def);
free(pack->id2ind);
freeNames(pack->names, pack->namesLen);
free(pack);
}
}
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;
}
