removed various build warnings

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index f9b34298a6fc6eddb364f0148f8c44b3e6900aac..d1732cd0dc37ba3db1edcfdb3835413d3ddaf559 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1160,7 +1160,6 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
                double clusterCutoff = cutoff;
                while (matrix->getSmallDist() <= clusterCutoff && matrix->getNNodes() > 0){
                        cluster->update(clusterCutoff);
-                       float dist = matrix->getSmallDist();
                }
                
                list->setLabel(toString(cutoff));
@@ -1411,7 +1410,6 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
                                for(int j=0;j<nSeqsPerOTU[i];j++){
                                        int index = cumNumSeqs[i] + j;
                                        int nI = seqIndex[index];
-                                       int nIU = mapSeqToUnique[nI];
                                        
                                        double tauValue = singleTau[seqNumber[index]];
                                        
@@ -1483,7 +1481,6 @@ double ShhherCommand::getNewWeights(){
                        
                        for(int j=0;j<nSeqsPerOTU[i];j++){
                                int index = cumNumSeqs[i] + j;
-                               int nI = seqIndex[index];
                                double tauValue = singleTau[seqNumber[index]];
                                weight[i] += tauValue;
                        }
@@ -1902,7 +1899,6 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
                vector<vector<int> > qualities(numOTUs);
                vector<double> pr(HOMOPS, 0);
                
-               int index = 0;
                
                for(int i=0;i<numOTUs;i++){
                        int index = 0;