sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 47adc9a55b4ba929796fca2993138b89584bdee1..94ae125962c85c2cc0b7f100bf5178b89da89bdd 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -465,40 +465,28 @@ int UnifracWeightedCommand::getAverageSTDMatrices(vector< vector<double> >& dist
         //we need to find the average distance and standard deviation for each groups distance
         
         //finds sum
-        vector<double> averages; averages.resize(numComp, 0); 
-        for (int thisIter = 0; thisIter < subsampleIters; thisIter++) {
-            for (int i = 0; i < dists[thisIter].size(); i++) {  
-                averages[i] += dists[thisIter][i];
-            }
-        }
-        
-        //finds average.
-        for (int i = 0; i < averages.size(); i++) {  averages[i] /= (float) subsampleIters; }
+        vector<double> averages = m->getAverages(dists);        
         
         //find standard deviation
-        vector<double> stdDev; stdDev.resize(numComp, 0);
-                
-        for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
-            for (int j = 0; j < dists[thisIter].size(); j++) {
-                stdDev[j] += ((dists[thisIter][j] - averages[j]) * (dists[thisIter][j] - averages[j]));
-            }
-        }
-        for (int i = 0; i < stdDev.size(); i++) {  
-            stdDev[i] /= (float) subsampleIters; 
-            stdDev[i] = sqrt(stdDev[i]);
-        }
+        vector<double> stdDev = m->getStandardDeviation(dists, averages);
         
         //make matrix with scores in it
-        vector< vector<double> > avedists;     avedists.resize(m->getNumGroups());
+        vector< vector<double> > avedists;     //avedists.resize(m->getNumGroups());
         for (int i = 0; i < m->getNumGroups(); i++) {
-            avedists[i].resize(m->getNumGroups(), 0.0);
+            vector<double> temp;
+            for (int j = 0; j < m->getNumGroups(); j++) { temp.push_back(0.0); }
+            avedists.push_back(temp);
         }
         
         //make matrix with scores in it
-        vector< vector<double> > stddists;     stddists.resize(m->getNumGroups());
+        vector< vector<double> > stddists;     //stddists.resize(m->getNumGroups());
         for (int i = 0; i < m->getNumGroups(); i++) {
-            stddists[i].resize(m->getNumGroups(), 0.0);
+            vector<double> temp;
+            for (int j = 0; j < m->getNumGroups(); j++) { temp.push_back(0.0); }
+            //stddists[i].resize(m->getNumGroups(), 0.0);
+            stddists.push_back(temp);
         }
+
         
         //flip it so you can print it
         int count = 0;