added logfile feature

[mothur.git] / sharedchao1.cpp

diff --git a/sharedchao1.cpp b/sharedchao1.cpp
index 8dff314b2b7ab3d913d73d4437cd3b82cefd863c..402e0d9f1911bb0b19d27fc0aeac661826c1683d 100644 (file)
--- a/sharedchao1.cpp
+++ b/sharedchao1.cpp
@@ -41,15 +41,12 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                        
                        //they are shared
                        if (sharedByAll == true) { 
-                               // cout << "temp = ";
-                               // for (int h = 0; h < temp.size(); h++) { cout << temp[h] << " "; } cout << endl;
                                //find f1 and f2values
                                updateTree(temp);
                        }
                }
 
                        
-               //cout << "Entering " << endl;
                //calculate chao1, (numleaves-1) because numleaves contains the ++ values.
                bool bias;
                for(int i=0;i<numLeaves;i++){
@@ -87,18 +84,14 @@ EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
                        delete f2leaves[i];
                }
                
-       //      cout << "exiting " << endl;
+
                data[0] = Chao;
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedChao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -153,13 +146,9 @@ void SharedChao1::initialTree(int n) {
                setCoef(f2root, 0);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function initialTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "initialTree");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedChao1 class function initialTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -170,13 +159,9 @@ void SharedChao1::updateTree(vector<int> bin) {
                updateBranchf2(f2root, bin, 0); 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function updateTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "updateTree");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedChao1 class function updateTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -196,13 +181,9 @@ void SharedChao1::updateBranchf1(IntNode* node, vector<int> bin, int index) {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function updateBranchf1. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "updateBranchf1");           
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedChao1 class function updateBranchf1. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -222,13 +203,9 @@ void SharedChao1::updateBranchf2(IntNode* node, vector<int> bin, int index) {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function updateBranchf2. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "updateBranchf2");   
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedChao1 class function updateBranchf2. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
@@ -243,23 +220,19 @@ void SharedChao1::setCoef(IntNode* node, int coef) {
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function getCoef. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "setCoef");  
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedChao1 class function getCoef. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/
 //for debugging purposes
 void SharedChao1::printTree() {
        
-       cout << "F1 leaves" << endl;
+       mothurOut("F1 leaves"); mothurOutEndLine();
        printBranch(f1root);
        
-       cout << "F2 leaves" << endl;
+       mothurOut("F2 leaves"); mothurOutEndLine();
        printBranch(f2root);
 
 
@@ -273,19 +246,15 @@ void SharedChao1::printBranch(IntNode* node) {
                        printBranch(node->left);
                        printBranch(node->right);
                }else { //you are a leaf
-                       cout << node->lvalue << endl;
-                       cout << node->rvalue << endl;
+                       mothurOut(toString(node->lvalue)); mothurOutEndLine();
+                       mothurOut(toString(node->rvalue)); mothurOutEndLine();
                }
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedChao1", "printBranch");      
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /*****************************************************************/