X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trialSwap2.cpp;h=9959443c9ffbb0c411dfcd0fc6dd6920fbe6f5c8;hp=71c3027db2c8bbe97265cb40af839c6a81a17b33;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ccf2fedbb600a362777a11501bb56c9c7746068e

diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index 71c3027..9959443 100644
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -50,9 +50,10 @@ double TrialSwap2::calc_c_score (vector<vector<int> > &co_matrix, vector<int> ro
             }
         }
         
-        cscore = cscore/(double)(nrows*(nrows-1)/2);
+        //cscore = cscore/(double)(nrows*(nrows-1)/2);  //not normalized
         //cout << "normalized c score: " << normcscore/nonzeros << endl;
-        
+        cscore = normcscore/(double)nonzeros;
+
         return cscore;
     }
     catch(exception& e) {
@@ -148,7 +149,7 @@ int TrialSwap2::calc_combo (int nrows, int ncols, vector<vector<int> > &nullmatr
 {
     try {
         //need to transpose so we can compare rows (row-major order)
-        int tmpnrows = nrows;
+        //int tmpnrows = nrows;
         vector<vector<int> > tmpmatrix;
         
         vector<int> tmprow;