// AddLoci
// Add loci on target which has identified SNP when aligned to from probe sequences
int
CMarkers::AddLoci(char *pszTargSpecies, // reads were aligned to this cultivar or species
char *pszTargSeq, // alignments to this sequence - could be a chrom/contig/transcript - from pszSpecies
UINT32 TargLoci, // loci within target sequence at which SNPs observed
etSeqBase TargRefBase, // loci has this reference base
char *pszProbeSpecies, // reads were aligned from this cultivar or species
UINT32 ProbeCntA, // number instances probe base A aligned to TargRefBase
UINT32 ProbeCntC, // number instances probe base C aligned to TargRefBase
UINT32 ProbeCntG, // number instances probe base G aligned to TargRefBase
UINT32 ProbeCntT, // number instances probe base T aligned to TargRefBase
UINT32 ProbeCntN) // number instances probe base U aligned to TargRefBase
{
UINT8 TargID;
UINT8 ProbeID;
UINT32 TargSeqID;
int Rslt;
TargID = AddSpecies(pszTargSpecies,true);
if(TargID == 0 || TargID != m_RefSpeciesID)
return(-1);
ProbeID = AddSpecies(pszProbeSpecies,false);
if(ProbeID == 0 || ProbeID == m_RefSpeciesID)
return(-1);
TargSeqID = AddTargSeq(pszTargSeq);
if(TargSeqID == 0)
return(-1);
if((Rslt = AddLoci(TargID,TargSeqID,TargLoci,TargRefBase,ProbeID,ProbeCntA,ProbeCntC,ProbeCntG,ProbeCntT,ProbeCntN)) < 0)
return(Rslt);
return(Rslt);
}
avtSpeciesMetaData::avtSpeciesMetaData(const std::string &n,
const std::string &meshn, const std::string &matn,
int nummat, const intVector &ns, const std::vector<stringVector> &sn)
: AttributeSubject(avtSpeciesMetaData::TypeMapFormatString)
{
// Initialize all.
*this = avtSpeciesMetaData();
// Override members
name = n;
originalName = name;
meshName = meshn;
materialName = matn;
numMaterials = nummat;
ClearSpecies();
for (size_t i=0; i<ns.size(); i++)
AddSpecies(avtMatSpeciesMetaData(ns[i], sn[i]));
validVariable = true;
}
