alignmentLength = query->getAlignLength(); //x
int queryUnalignedLength = query->getNumBases(); //y
-
buildTemplateProfile(parents);
createAlignMatrix(queryUnalignedLength, alignmentLength);
else if(seq[j] == 'C') { profile[j].C++; }
else if(seq[j] == '-') { profile[j].Gap++; }
else if(seq[j] == '.') { profile[j].Gap++; }
- else { profile[j].A++; }
+// else { profile[j].A++; }
}
}
for(int i=alignmentLength-1;i>=0;i--){
flipSeq += queryAlignment[i];
}
-
+
return flipSeq;
}
catch(exception& e) {