added amova command

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index f9b34298a6fc6eddb364f0148f8c44b3e6900aac..ffddb8cfc9de4dd92feb4966dd8d31477e1363fa 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -838,10 +838,10 @@ void ShhherCommand::getJointLookUp(){
                for(int i=0;i<NUMBINS;i++){
                        for(int j=0;j<NUMBINS;j++){             
                                
-                               float minSum = 10000000000;
+                               double minSum = 100000000;
                                
                                for(int k=0;k<HOMOPS;k++){
-                                       float sum = singleLookUp[k * NUMBINS + i] + singleLookUp[k * NUMBINS + j];
+                                       double sum = singleLookUp[k * NUMBINS + i] + singleLookUp[k * NUMBINS + j];
                                        
                                        if(sum < minSum)        {       minSum = sum;           }
                                }       
@@ -857,9 +857,11 @@ void ShhherCommand::getJointLookUp(){
 
 /**************************************************************************************************/
 
-float ShhherCommand::getProbIntensity(int intIntensity){                          
+double ShhherCommand::getProbIntensity(int intIntensity){                          
        try{
-               float minNegLogProb = 10000000000; 
+
+               double minNegLogProb = 100000000; 
+
                
                for(int i=0;i<HOMOPS;i++){//loop signal strength
                        float negLogProb = singleLookUp[i * NUMBINS + intIntensity];
@@ -1160,7 +1162,6 @@ 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 +1412,6 @@ 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 +1483,6 @@ 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 +1901,6 @@ 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;