fixed bugs in venn and aligner

[mothur.git] / sharedchao1.cpp

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 402e0d9f1911bb0b19d27fc0aeac661826c1683d..803e95368240b15e8bee33ff4b22842fa168519d 100644 (file)
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -29,7 +29,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                //create and initialize trees to 0.
                initialTree(numGroups); 
                
-               //loop through vectors calculating the f11, f1A, f2A, f1B, f2B, S12 values
+               
                for (int i = 0; i < shared[0]->size(); i++) {
                        //get bin values and calc shared 
                        bool sharedByAll = true;
@@ -50,7 +50,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                //calculate chao1, (numleaves-1) because numleaves contains the ++ values.
                bool bias;
                for(int i=0;i<numLeaves;i++){
-                       if (f2leaves[i]->lvalue == 0) { bias = true;}// break;}
+                       if ((f2leaves[i]->lvalue == 0) || (f2leaves[i]->rvalue == 0))  { bias = true;  }// break;}
                }
 
                if(bias){
@@ -60,6 +60,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                                if (i != (numLeaves-1)) {
                                        rightvalue = (float)(f1leaves[i]->rvalue * (f1leaves[i]->rvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * (f2leaves[i]->rvalue + 1));
                                }else{
+                                       //add in sobs
                                        rightvalue = (float)(f1leaves[i]->rvalue);
                                }
                                Chao += leftvalue + rightvalue;
@@ -73,6 +74,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                                if (i != (numLeaves-1)) {
                                        rightvalue = (float)(f1leaves[i]->rvalue * f1leaves[i]->rvalue) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * f2leaves[i]->rvalue);
                                }else{
+                                       //add in sobs
                                        rightvalue = (float)(f1leaves[i]->rvalue);
                                }
                                Chao += leftvalue + rightvalue;
@@ -84,7 +86,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                        delete f2leaves[i];
                }
                
-
+               
                data[0] = Chao;
                return data;
        }