X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=f874e9a869d269546c04ce8fd9648786dcc4bab1;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=7d96e31d1eefb534729e421b266092db1536aa46;hpb=c48d91112209b841444923670dca5454da0e2a4d;p=mothur.git diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp index 7d96e31..f874e9a 100644 --- a/pairwiseseqscommand.cpp +++ b/pairwiseseqscommand.cpp @@ -671,14 +671,11 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl 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; } @@ -777,7 +774,9 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st 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; @@ -860,6 +859,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, 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'); @@ -968,6 +969,8 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi 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"; } @@ -1072,7 +1075,9 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi 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";