added logfile feature

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 9a8706e82499fb80f9c2a55d61bc92c7b2399839..db6ed1d862d4ee3d9a4037b672ee63cdcacd03a6 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -91,7 +91,6 @@ EstOutput Parsimony::getValues(Tree* t) {
                
                        //create pgroups that reflect the groups the user want to use
                        for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
-//                             cout << i << "..." << endl;
                                copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
                        }
                
@@ -105,13 +104,6 @@ EstOutput Parsimony::getValues(Tree* t) {
                                int rcSize = copyTree->tree[rc].pGroups.size();
                                int lcSize = copyTree->tree[lc].pGroups.size();
                                
-//                             cout << i+1 << '\t' << lc+1 << '\t' << rc+1 << ":\t";
-                               
-//                             for(it=copyTree->tree[i].pGroups.begin();it!=copyTree->tree[i].pGroups.end();it++){
-//                                     cout << it->first << '\t';
-//                             }
-                               
-//                             cout << " : " << iSize << '\t' << rcSize << '\t' << lcSize << '\t';
                                        
                                //if isize are 0 then that branch is to be ignored
                                if (iSize == 0) { }
@@ -120,12 +112,10 @@ EstOutput Parsimony::getValues(Tree* t) {
                                else if(iSize > rcSize || iSize > lcSize){
                                        score++;
                                }
-//                             cout << score << endl;
                        } 
                
                        data[count] = score;
-                       string hold;
-//                     cin >> hold;
+
                }
                
                delete copyTree;
@@ -133,14 +123,9 @@ EstOutput Parsimony::getValues(Tree* t) {
                return data;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "Parsimony", "getValues");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
 }
 
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