string extension = toString(i) + ".temp";
// Allocate memory for thread data.
- pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
+ pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, cutoff, i);
pDataArray.push_back(tempDist);
processIDS.push_back(i);
seqI.setAligned(alignment->getSeqAAln());
seqJ.setAligned(alignment->getSeqBAln());
-
+ //cout << seqI.getName() << '\t' << seqJ.getName() << endl;
+ //cout << alignment->getSeqAAln() << endl << alignment->getSeqBAln() << endl;
+
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
-
+
+ //cout << "dist = " << dist << endl;
+
if(dist <= cutoff){
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}