added modify names parameter to set.dir

[mothur.git] / sharedchao1.cpp

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index cbb519241bd98e85823ef1fc25f33701dbeb84e9..8d47ad2fca1d307bd150a985224b1099e492626a 100644 (file)
--- 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);
                
-               
-               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();
@@ -46,9 +45,9 @@ 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 || f2leaves[i]->rvalue == 0) { bias = true;}// break;}
                }
@@ -91,7 +90,7 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                return data;
        }
        catch(exception& e) {
-               errorOut(e, "SharedChao1", "getValues");
+               m->errorOut(e, "SharedChao1", "getValues");
                exit(1);
        }
 }
@@ -108,39 +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];
                
@@ -148,7 +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);
        }
 }
@@ -161,7 +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);
        }
 }
@@ -183,7 +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);
        }
 }
@@ -205,7 +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);
        }
 }
@@ -222,7 +213,7 @@ void SharedChao1::setCoef(IntNode* node, int coef) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "SharedChao1", "setCoef");  
+               m->errorOut(e, "SharedChao1", "setCoef");       
                exit(1);
        }
 }
@@ -231,10 +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);
 
 
@@ -248,13 +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);
        }
 }