bool arlCore::PlaneSystem::getOrigin( unsigned int plane1, unsigned int plane2, Point::sptr pt)
{ // Set pt with the origin of Plane1 in the Plane2
arlCore::vnl_rigid_matrix T;
if(!getTrf( plane1, plane2, T)) return false;
arlCore::Point::sptr origin = arlCore::Point::New(0.0, 0.0, 0.0);
return T.trf(origin, pt);
}
bool arlCore::PlaneSystem::getTrf( unsigned int plane1, unsigned int plane2, vnl_rigid_matrix &T, long int date, long int time, double ageTolerance, bool verbose )
{
if(!getTrf(plane1, plane2, T, verbose)) return false;
long int d,t;
T.getTime(d,t);
if(date!=d) return false;
return fabs((double)(time-t))<=ageTolerance*10;
}
bool arlCore::PlaneSystem::distance( unsigned int plane1, unsigned int plane2, double &dist/*, long int &date, long int &time*/ )
{
dist=0;
vnl_rigid_matrix T;
if(!getTrf ( plane1, plane2, T/*, date, time*/ )) return false; // FIXME
dist=sqrt(T(0,3)*T(0,3)+T(1,3)*T(1,3)+T(2,3)*T(2,3));
// date = T.getDate();
// time = T.getTime();
return true;
}
bool arlCore::PlaneSystem::getTrf( unsigned int plane1, unsigned int plane2, vnl_rigid_matrix &T, double ageTolerance, bool verbose )
{
if(!getTrf(plane1, plane2, T, verbose)) return false;
if(ageTolerance<0.0) return true;
long int d,t;
T.getTime(d,t);
if(d==0 && t==0) return true;
if(getDate()!=d) return false;
return fabs((double)(getTime()-t))<=ageTolerance*10;
}
void netClass(char *inName, char *tDb, char *qDb, char *outName)
/* netClass - Add classification info to net. */
{
struct chainNet *net;
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct chrom *qChromList, *chrom;
struct hash *qChromHash;
struct hash *arHash = NULL;
struct sqlConnection *tConn = sqlConnect(tDb);
struct sqlConnection *qConn = sqlConnect(qDb);
qLm = lmInit(0);
if (!noAr)
arHash = getAncientRepeats(tConn, qConn);
getChroms(qConn, &qChromHash, &qChromList);
verbose(1, "Reading gaps in %s\n", qDb);
if (sqlTableExists(qConn, "gap"))
{
getSeqGapsUnsplit(qConn, qChromHash);
}
else
{
for (chrom = qChromList; chrom != NULL; chrom = chrom->next)
chrom->nGaps = getSeqGaps(qConn, chrom->name);
}
if (qNewR)
{
verbose(1, "Reading new repeats from %s\n", qNewR);
for (chrom = qChromList; chrom != NULL; chrom = chrom->next)
chrom->newRepeats = getNewRepeats(qNewR, chrom->name);
}
verbose(1, "Reading simpleRepeats in %s\n", qDb);
getTrfUnsplit(qConn, qChromHash);
if (qRepeatTable)
{
verbose(1, "Reading repeats in %s from table %s\n", qDb, qRepeatTable);
getRepeatsUnsplitTable(qConn, qChromHash, qRepeatTable);
}
else
{
verbose(1, "Reading repeats in %s\n", qDb);
if (sqlTableExists(qConn, "rmsk"))
getRepeatsUnsplit(qConn, qChromHash, arHash);
else
{
for (chrom = qChromList; chrom != NULL; chrom = chrom->next)
getRepeats(qConn, arHash, chrom->name, &chrom->repeats,
&chrom->oldRepeats);
}
}
while ((net = chainNetRead(lf)) != NULL)
{
struct rbTree *tN, *tRepeats, *tOldRepeats, *tTrf;
char *tName = net->name;
if (liftHashT != NULL)
{
struct liftSpec *lft = hashMustFindVal(liftHashT, net->name);
tName = lft->newName;
}
verbose(1, "Processing %s.%s\n", tDb, net->name);
tN = getSeqGaps(tConn, tName);
tAddN(net, net->fillList, tN);
rbTreeFree(&tN);
qAddN(net, net->fillList, qChromHash);
if (tRepeatTable)
getRepeatsTable(tConn, tRepeatTable, tName, &tRepeats, &tOldRepeats);
else
getRepeats(tConn, arHash, tName, &tRepeats, &tOldRepeats);
tAddR(net, net->fillList, tRepeats);
if (!noAr)
tAddOldR(net, net->fillList, tOldRepeats);
rbTreeFree(&tRepeats);
rbTreeFree(&tOldRepeats);
qAddR(net, net->fillList, qChromHash);
if (!noAr)
qAddOldR(net, net->fillList, qChromHash);
tTrf = getTrf(tConn, tName);
tAddTrf(net, net->fillList, tTrf);
rbTreeFree(&tTrf);
qAddTrf(net, net->fillList, qChromHash);
if (tNewR)
{
struct rbTree *tree = getNewRepeats(tNewR, tName);
tAddNewR(net, net->fillList, tree);
rbTreeFree(&tree);
}
if (qNewR)
qAddNewR(net, net->fillList, qChromHash);
chainNetWrite(net, f);
chainNetFree(&net);
}
sqlDisconnect(&tConn);
sqlDisconnect(&qConn);
}
bool arlCore::PlaneSystem::chgPlane( unsigned int plane1, Point::csptr pt1, unsigned int plane2, Point::sptr pt2)
{ // Set pt2 with the coordinates in Plane2 of pt1 set in Plane1
arlCore::vnl_rigid_matrix T;
if(!getTrf( plane1, plane2, T)) return false;
return T.trf(pt1,pt2);
}
