X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedchao1.cpp;h=8d47ad2fca1d307bd150a985224b1099e492626a;hp=402e0d9f1911bb0b19d27fc0aeac661826c1683d;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 402e0d9..8d47ad2 100644
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -27,10 +27,9 @@ 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++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//get bin values and calc shared 
 			bool sharedByAll = true;
 			temp.clear();
@@ -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;
@@ -84,12 +85,12 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
 			delete f2leaves[i];
 		}
 		
-
+		
 		data[0] = Chao;
 		return data;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "getValues");
+		m->errorOut(e, "SharedChao1", "getValues");
 		exit(1);
 	}
 }
@@ -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];
 		
@@ -146,7 +138,8 @@ void SharedChao1::initialTree(int n) {
 		setCoef(f2root, 0);
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "initialTree");
+		if ((toString(e.what()) == "vector::_M_fill_insert") || (toString(e.what()) == "St9bad_alloc")) { m->mothurOut("You are using " + toString(n) + " groups which creates 2^" + toString(n+1) + " nodes. Try reducing the number of groups you selected. "); m->mothurOutEndLine(); exit(1); }
+		m->errorOut(e, "SharedChao1", "initialTree");
 		exit(1);
 	}
 }
@@ -159,7 +152,7 @@ void SharedChao1::updateTree(vector<int> bin) {
 		updateBranchf2(f2root, bin, 0); 
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "updateTree");
+		m->errorOut(e, "SharedChao1", "updateTree");
 		exit(1);
 	}
 }
@@ -181,7 +174,7 @@ void SharedChao1::updateBranchf1(IntNode* node, vector<int> bin, int index) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "updateBranchf1");		
+		m->errorOut(e, "SharedChao1", "updateBranchf1");		
 		exit(1);
 	}
 }
@@ -203,7 +196,7 @@ void SharedChao1::updateBranchf2(IntNode* node, vector<int> bin, int index) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "updateBranchf2");	
+		m->errorOut(e, "SharedChao1", "updateBranchf2");	
 		exit(1);
 	}
 }
@@ -220,7 +213,7 @@ void SharedChao1::setCoef(IntNode* node, int coef) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "setCoef");	
+		m->errorOut(e, "SharedChao1", "setCoef");	
 		exit(1);
 	}
 }
@@ -229,10 +222,10 @@ void SharedChao1::setCoef(IntNode* node, int coef) {
 //for debugging purposes
 void SharedChao1::printTree() {
 	
-	mothurOut("F1 leaves"); mothurOutEndLine();
+	m->mothurOut("F1 leaves"); m->mothurOutEndLine();
 	printBranch(f1root);
 	
-	mothurOut("F2 leaves"); mothurOutEndLine();
+	m->mothurOut("F2 leaves"); m->mothurOutEndLine();
 	printBranch(f2root);
 
 
@@ -246,13 +239,13 @@ void SharedChao1::printBranch(IntNode* node) {
 			printBranch(node->left);
 			printBranch(node->right);
 		}else { //you are a leaf
-			mothurOut(toString(node->lvalue)); mothurOutEndLine();
-			mothurOut(toString(node->rvalue)); mothurOutEndLine();
+			m->mothurOut(toString(node->lvalue)); m->mothurOutEndLine();
+			m->mothurOut(toString(node->rvalue)); m->mothurOutEndLine();
 		}
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedChao1", "printBranch");	
+		m->errorOut(e, "SharedChao1", "printBranch");	
 		exit(1);
 	}
 }