alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
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 (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
if(dist <= cutoff){
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- outFile << dist << '\t';
+ outFile << dist << '\t';
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outFile << endl;
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
+
+ if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
if(dist <= cutoff){
outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
+
+ if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
outputString += toString(dist) + "\t";
}
distCalculator->calcDist(seqI, seqJ);
double dist = distCalculator->getDist();
- outputString += toString(dist) + "\t";
+ outputString += toString(dist) + "\t";
+
+ if (m->debug) { cout << ("[DEBUG]: " + seqI.getName() + '\t' + alignment->getSeqAAln() + '\n' + seqJ.getName() + alignment->getSeqBAln() + '\n' + "distance = " + toString(dist) + "\n"); }
}
outputString += "\n";