double arlCore::Mesh::getRMSDistance( void ) const
{
double distance = 0.0;
unsigned int i, j;
const unsigned int Size = (unsigned int)m_triangles.size();
for( i=0 ; i<Size ; ++i )
{
vnl_vector_fixed<double,3> lengths = getLengths(i);
for( j=0 ; j<3 ; ++j )
distance += lengths[j]*lengths[j];
}
return sqrt(distance/(double)(Size*3));
}
bool arlCore::Mesh::resampling( double step )
{
if(step<=0) return false;
unsigned int i, j;
const double Tol = 2.0*step;
std::vector<arlCore::Point::sptr > points(3);
for( i=0 ; i<(unsigned int)m_triangles.size() ; )
{
vnl_vector_fixed<double,3> lengths = getLengths(i);
if((lengths[0]+lengths[1])>=Tol)
{
std::vector<unsigned int> index(6);
for( j=0 ; j<3 ; ++j )
index[j] = m_triangles[i][j];
const arlCore::Point::sptr A = (*m_pointList)[index[0]];
const arlCore::Point::sptr B = (*m_pointList)[index[1]];
const arlCore::Point::sptr C = (*m_pointList)[index[2]];
m_freeTriangles.push_back(i);
--m_nbReferences[m_triangles[i][0]];
--m_nbReferences[m_triangles[i][1]];
--m_nbReferences[m_triangles[i][2]];
for( j=0 ; j<3 ; ++j )
{
points[0]->set(j, ( (*A)[j]+(*B)[j])/2.0);
points[1]->set(j, ( (*B)[j]+(*C)[j])/2.0);
points[2]->set(j, ( (*C)[j]+(*A)[j])/2.0);
}
for( j=0 ; j<3 ; ++j )
index[3+j] = addPoint(points[j]);
addTriangle( index[0], index[3], index[5] );
addTriangle( index[3], index[1], index[4] );
addTriangle( index[4], index[2], index[5] );
addTriangle( index[5], index[3], index[4] );
}else ++i;
}
assert(m_freePoints.size()==0);
assert(m_freeTriangles.size()==0);
return true;
}
/* void getParams()
* Parses the command line.
*/
void getParams(int argc, char** argv) {
char* outFile = NULL, *inFile = NULL, *primFile = NULL,
*bedFile = NULL, *fwdPos = NULL, *revPos = NULL,
*bedPos = NULL, *logFile = NULL, *wasteFile = NULL,
*corrFile = NULL;
int misAllow = 0, revLen = 0, revMis = 0, revLMis = 0,
revOpt = 0;
// parse argv
for (int i = 1; i < argc; i++) {
if (!strcmp(argv[i], HELP))
usage();
else if (!strcmp(argv[i], REVOPT))
revOpt = 1;
else if (i < argc - 1) {
if (!strcmp(argv[i], OUTFILE))
outFile = argv[++i];
else if (!strcmp(argv[i], INFILE))
inFile = argv[++i];
else if (!strcmp(argv[i], PRIMFILE))
primFile = argv[++i];
else if (!strcmp(argv[i], BEDFILE))
bedFile = argv[++i];
else if (!strcmp(argv[i], FWDPOS))
fwdPos = argv[++i];
else if (!strcmp(argv[i], REVPOS))
revPos = argv[++i];
else if (!strcmp(argv[i], BEDPOS))
bedPos = argv[++i];
else if (!strcmp(argv[i], LOGFILE))
logFile = argv[++i];
else if (!strcmp(argv[i], WASTEFILE))
wasteFile = argv[++i];
else if (!strcmp(argv[i], MISALLOW))
misAllow = getInt(argv[++i]);
else if (!strcmp(argv[i], REVMIS))
revMis = getInt(argv[++i]);
else if (!strcmp(argv[i], REVLENGTH))
revLen = getInt(argv[++i]);
else if (!strcmp(argv[i], REVLMIS))
revLMis = getInt(argv[++i]);
else if (!strcmp(argv[i], CORRFILE))
corrFile = argv[++i];
else
exit(error(argv[i], ERRINVAL));
} else
exit(error(argv[i], ERRINVAL));
}
if (outFile == NULL || inFile == NULL || primFile == NULL)
usage();
int gz = 0;
if (!strcmp(inFile + strlen(inFile) - strlen(GZEXT), GZEXT))
gz = 1;
// open files, load primer sequences
File out, in, waste, corr;
FILE* prim = NULL, *log = NULL, *bed = NULL;
openFiles(outFile, &out, primFile, &prim, inFile, &in,
logFile, &log, bedFile, &bed, wasteFile, &waste,
corrFile, &corr, gz);
int pr = loadSeqs(prim);
// get start and end locations
int fwdSt = 0, fwdEnd = 1, revSt = 0, revEnd = 1,
bedSt = 0, bedEnd = 1;
getPos(fwdPos, &fwdSt, &fwdEnd);
getPos(revPos, &revSt, &revEnd);
if (bed != NULL) {
getLengths(bed);
getPos(bedPos, &bedSt, &bedEnd);
}
// read file
int match = 0, rcmatch = 0; // counting variables
int count = readFile(in, out, misAllow, &match, &rcmatch,
fwdSt, fwdEnd, revSt, revEnd, bedSt, bedEnd,
waste, wasteFile != NULL, revMis, revLen, revLMis,
revOpt, corr, corrFile != NULL, gz);
// print log output
if (log != NULL) {
fprintf(log, "Primer pairs: %d\nRead count: %d\n", pr, count);
fprintf(log, "Primer matches: %d\nBoth primer matches: %d\n\n", match, rcmatch);
fprintf(log, "Matches:\nPrimer\tFwd\tFwd-Both\tRev\tRev-Both\n");
for (Primer* p = primo; p != NULL; p = p->next)
fprintf(log, "%s\t%d\t%d\t%d\t%d\n", p->name, p->fcount, p->fcountr,
p->rcount, p->rcountr);
}
// close files
if ( (gz && (gzclose(in.gzf) != Z_OK || gzclose(out.gzf) != Z_OK ||
(wasteFile != NULL && gzclose(waste.gzf) != Z_OK) ||
(corrFile != NULL && gzclose(corr.gzf) != Z_OK) ) ) ||
( ! gz && (fclose(in.f) || fclose(out.f) ||
(wasteFile != NULL && fclose(waste.f)) ||
(corrFile != NULL && fclose(corr.f)) ) ) ||
fclose(prim) || (log != NULL && fclose(log)) ||
(bed != NULL && fclose(bed)) )
exit(error("", ERRCLOSE));
}