SequenceDB alignDB;
pairwiseData(){}
- pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, int tid) {
+ pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, float cu, int tid) {
outputFileName = ofn;
m = mout;
start = st;
alignDB = DB;
count = 0;
output = op;
+ cutoff = cu;
threadID = tid;
}
};
ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
-
- pDataArray->count = pDataArray->end;
int startTime = time(NULL);
if((pDataArray->output == "lt") && pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
+ pDataArray->count = 0;
for(int i=pDataArray->start;i<pDataArray->end;i++){
+ pDataArray->count++;
if(pDataArray->output == "lt") {
string name = pDataArray->alignDB.get(i).getName();