This contains Pat's bug fixes and updates. It represents mothur v.1.3.0

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 7d1f6a0308b5358b2ef39ef70579d866fafca6da..6fee651cb8963680ec294051e671cfc57b9c6135 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -20,12 +20,12 @@ DistanceCommand::DistanceCommand(){
        try {
                globaldata = GlobalData::getInstance();
                validCalculator = new ValidCalculators();
-               ends = globaldata->getEnds();
+               countends = globaldata->getCountEnds();
                convert(globaldata->getProcessors(), processors);
                convert(globaldata->getCutOff(), cutoff);
                
                int i;
-               if (ends != "T") {
+               if (countends == "T") {
                        for (i=0; i<globaldata->Estimators.size(); i++) {
                                if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) { 
                                        if (globaldata->Estimators[i] == "nogaps") { 
@@ -83,7 +83,8 @@ int DistanceCommand::execute(){
                seqDB = readSeqs->getDB();
        
                int numSeqs = seqDB->getNumSeqs();
-               
+               cutoff += 0.005;
+
                string distFile = getRootName(globaldata->getFastaFile()) + "dist";
                
                remove(distFile.c_str());
@@ -201,10 +202,6 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
                for(int i=startLine;i<endLine;i++){
                
                        for(int j=0;j<i;j++){
-//cout << "unaligned" << endl;
-//cout << align->get(i).getUnaligned() << "  " << align->get(j).getUnaligned() << endl;
-//cout << "aligned" << endl;
-//cout << align->get(i).getAligned() << "  " << align->get(j).getAligned() << endl;
                                distCalculator->calcDist(align->get(i), align->get(j));
                                double dist = distCalculator->getDist();