void spring::divideDeformationsAndReset( spring &in )
{
// find current spring lengths
pReal aLen( ( secondary().position() - primary().position() ).length() );
pReal bLen( ( in.secondary().position() - in.primary().position() ).length() );
// find the total length
pReal totalLength( aLen + bLen );
//Initial Rest Length
{
// find the length we are aiming at
pReal aimLength( _initialRestLength );
pReal totalLength( aLen + bLen );
// divide the length between them
_initialRestLength = ( aimLength / totalLength ) * aLen;
in._initialRestLength = ( aimLength / totalLength ) * bLen;
}
//Rest Length
{
pReal aimLength( restLength() );
// divide the length between them
restLength( ( aimLength / totalLength ) * aLen );
in.restLength( ( aimLength / totalLength ) * bLen );
}
}
string Printlines::info() const
{
ostringstream ostr;
ostr << "Printlines "<<name<<": " <<size()<<" lines"
<< ", total "<<totalLength()<< "mm" ;
return ostr.str();
}
String StyledMarkupAccumulator::takeResults()
{
StringBuilder result;
result.reserveCapacity(totalLength(m_reversedPrecedingMarkup) + length());
for (size_t i = m_reversedPrecedingMarkup.size(); i > 0; --i)
result.append(m_reversedPrecedingMarkup[i - 1]);
concatenateMarkup(result);
// We remove '\0' characters because they are not visibly rendered to the user.
return result.toString().replace(0, "");
}
int TPCI::encode(unique_ptr<NetworkBuffer>& nsdu) {
if (nsdu.get() != nullptr)
throw InvalidArgumentException();
int total = totalLength();
int userlen = 0;
if (tp_buffer != nullptr) {
total += tp_buffer->remaining();
} else
if (tp_len > 0 && tp_data != nullptr) {
total += tp_len;
}
unique_ptr<NetworkBuffer> newBuffer(new NetworkBuffer(total));
nsdu = std::move(newBuffer);
nsdu->putByte(tp_li = headerLength());
nsdu->putByte(tp_code);
return OK;
}
int
main(int argc, char **argv) {
uint64 genomeSize = 0;
char *atacFileName = 0L;
char *prefix = 0L;
char *trFile1 = 0L;
char *trFile2 = 0L;
char prefixFull[1024];
bool error = false;
int arg=1;
while (arg < argc) {
if (strcmp(argv[arg], "-g") == 0) {
++arg;
if (argv[arg][0] == 'A') {
genomeSize = 0;
} else if (argv[arg][0] == 'B') {
genomeSize = 1;
} else {
genomeSize = strtouint64(argv[arg], 0L);
}
} else if (strcmp(argv[arg], "-a") == 0) {
atacFileName = argv[++arg];
} else if (strcmp(argv[arg], "-p") == 0) {
prefix = argv[++arg];
} else if (strcmp(argv[arg], "-ta") == 0) {
trFile1 = argv[++arg];
} else if (strcmp(argv[arg], "-tb") == 0) {
trFile2 = argv[++arg];
} else {
error = true;
}
arg++;
}
if (!atacFileName || !prefix || error) {
fprintf(stderr, "usage: %s -a <file.atac> -p <outprefix> [-ta trfile] [-tb trfile] [-g {A | B | g}]\n", argv[0]);
fprintf(stderr, " -a read input from 'file.atac'\n");
fprintf(stderr, " -p write stats to files prefixed with 'outprefix'\n");
fprintf(stderr, " -g use a genome size of g for the Nx computation, defaults to\n");
fprintf(stderr, " the length of the A sequence. Or use the actual length\n");
fprintf(stderr, " of sequence A or B.\n");
fprintf(stderr, " -ta read tandem repeats for A from trfile\n");
fprintf(stderr, " -tb read tandem repeats for B from trfile\n");
exit(1);
}
atacFile AF(atacFileName);
atacMatchList &matches = *AF.matches();
atacMatchList &runs = *AF.runs();
atacMatchList &clumps = *AF.clumps();
// We end up using sequences a lot here, so just bite it and load them in a cache.
//
seqCache *A = new seqCache(AF.assemblyFileA(), 0, true);
seqCache *B = new seqCache(AF.assemblyFileB(), 0, true);
A->loadAllSequences();
B->loadAllSequences();
fprintf(stdout, "\nSEQUENCE\n");
totalLength(AF, A, B);
if (trFile1 && trFile2) {
atacFileStream tr1(trFile1);
atacFileStream tr2(trFile2);
tandemRepeatStats(tr1, tr2, AF, A, B);
}
// XXX unmappedInRuns only works on runs, and if we have clumps in
// the input it fails.
//
if ((runs.numberOfMatches() > 0) && (clumps.numberOfMatches() == 0)) {
fprintf(stdout, "\nMATCHES IN RUNS\n");
unmappedInRuns(AF, A, B, prefix);
}
if (matches.numberOfMatches() > 0) {
fprintf(stdout, "\nMATCHES\n");
sprintf(prefixFull, "%s-matches", prefix);
mappedLengths(AF, matches, A, B, prefixFull);
NxOfMapped(AF, matches, genomeSize, prefixFull);
MappedByChromosome(AF, matches, A, B, prefixFull);
}
if (runs.numberOfMatches() > 0) {
fprintf(stdout, "\nRUNS\n");
sprintf(prefixFull, "%s-runs", prefix);
mappedLengths(AF, runs, A, B, prefixFull);
NxOfMapped(AF, runs, genomeSize, prefixFull);
MappedByChromosome(AF, runs, A, B, prefixFull);
}
if (clumps.numberOfMatches() > 0) {
fprintf(stdout, "\nCLUMPS\n");
sprintf(prefixFull, "%s-clumps", prefix);
mappedLengths(AF, clumps, A, B, prefixFull);
NxOfMapped(AF, clumps, genomeSize, prefixFull);
MappedByChromosome(AF, clumps, A, B, prefixFull);
}
delete A;
delete B;
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;
}
