test

[mothur.git] / sharedchao1.cpp

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 402e0d9f1911bb0b19d27fc0aeac661826c1683d..c19f0322c1358ba6718485a24933578c02bd5a3f 100644 (file)
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -27,9 +27,8 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                // the coeffient is 2.  Note: we only set the coeffient in f2 values.
                
                //create and initialize trees to 0.
-               initialTree(numGroups); 
+               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;
@@ -46,11 +45,11 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                        }
                }
 
-                       
+               
                //calculate chao1, (numleaves-1) because numleaves contains the ++ values.
-               bool bias;
+               bool bias = false;
                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 +59,7 @@ 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 +73,7 @@ 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 +85,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                        delete f2leaves[i];
                }
                
-
+               
                data[0] = Chao;
                return data;
        }
@@ -106,39 +107,30 @@ void SharedChao1::initialTree(int n) {
                
                f1leaves.resize(numNodes);
                f2leaves.resize(numNodes);
-               
+       
                //initialize leaf values
                for (int i = 0; i < numLeaves; i++) {
-                       f1leaves[i] = new IntNode;
-                       f1leaves[i]->lvalue = 0;
-                       f1leaves[i]->rvalue = 0;
-                       f1leaves[i]->left = NULL;
-                       f1leaves[i]->right = NULL;
-                       
-                       f2leaves[i] = new IntNode;
-                       f2leaves[i]->lvalue = 0;
-                       f2leaves[i]->rvalue = 0;
-                       f2leaves[i]->left = NULL;
-                       f2leaves[i]->right = NULL;
+                       f1leaves[i] = new IntNode(0, 0, NULL, NULL);
+                       f2leaves[i] = new IntNode(0, 0, NULL, NULL);
                }
                
                //set pointers to children
                for (int j = numLeaves; j < numNodes; j++) {
-                       f1leaves[j] = new IntNode;
+                       f1leaves[j] = new IntNode();
                        f1leaves[j]->left = f1leaves[countleft];
                        f1leaves[j]->right = f1leaves[countright];
                                                
-                       f2leaves[j] = new IntNode;
+                       f2leaves[j] = new IntNode();
                        f2leaves[j]->left = f2leaves[countleft];
                        f2leaves[j]->right =f2leaves[countright];
-                                               
+                       
                        countleft = countleft + 2;
                        countright = countright + 2;
                }
                
                //point to root
                f1root = f1leaves[numNodes-1];
-               
+       
                //point to root
                f2root = f2leaves[numNodes-1];
                
@@ -146,6 +138,7 @@ void SharedChao1::initialTree(int n) {
                setCoef(f2root, 0);
        }
        catch(exception& e) {
+               if ((toString(e.what()) == "vector::_M_fill_insert") || (toString(e.what()) == "St9bad_alloc")) { mothurOut("You are using " + toString(n) + " groups which creates 2^" + toString(n+1) + " nodes. Try reducing the number of groups you selected. "); mothurOutEndLine(); exit(1); }
                errorOut(e, "SharedChao1", "initialTree");
                exit(1);
        }