created mothurOut class to handle logfiles

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index a83f1edd04c3f8ddfad13887c1dbb78c9341d4f1..42fb0232ad758fed402d6a2db2fe1ca10752b85a 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -43,10 +43,10 @@ Classify(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0), kmerSize(ksize), c
                int start = time(NULL);
                
                if(probFileTest && probFileTest2){      
-                       mothurOut("Reading template probabilities...     "); cout.flush();
+                       m->mothurOut("Reading template probabilities...     "); cout.flush();
                        readProbFile(probFileTest, probFileTest2);      
                }else{
-                       mothurOut("Calculating template probabilities...     "); cout.flush();
+                       m->mothurOut("Calculating template probabilities...     "); cout.flush();
 
                        ofstream out;
                        openOutputFile(probFileName, out);
@@ -88,11 +88,11 @@ Classify(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0), kmerSize(ksize), c
                }
                
                
-               mothurOut("DONE."); mothurOutEndLine();
-               mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); mothurOutEndLine();
+               m->mothurOut("DONE."); m->mothurOutEndLine();
+               m->mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); m->mothurOutEndLine();
        }
        catch(exception& e) {
-               errorOut(e, "Bayesian", "Bayesian");
+               m->errorOut(e, "Bayesian", "Bayesian");
                exit(1);
        }
 }
@@ -122,7 +122,7 @@ string Bayesian::getTaxonomy(Sequence* seq) {
                return tax;     
        }
        catch(exception& e) {
-               errorOut(e, "Bayesian", "getTaxonomy");
+               m->errorOut(e, "Bayesian", "getTaxonomy");
                exit(1);
        }
 }
@@ -196,7 +196,7 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Bayesian", "bootstrapResults");
+               m->errorOut(e, "Bayesian", "bootstrapResults");
                exit(1);
        }
 }
@@ -225,7 +225,7 @@ int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
                return indexofGenus;
        }
        catch(exception& e) {
-               errorOut(e, "Bayesian", "getMostProbableTaxonomy");
+               m->errorOut(e, "Bayesian", "getMostProbableTaxonomy");
                exit(1);
        }
 }
@@ -252,7 +252,7 @@ map<string, int> Bayesian::parseTaxMap(string newTax) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Bayesian", "parseTax");
+               m->errorOut(e, "Bayesian", "parseTax");
                exit(1);
        }
 }
@@ -291,7 +291,7 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum) {
                in.close();
        }
        catch(exception& e) {
-               errorOut(e, "Bayesian", "readProbFile");
+               m->errorOut(e, "Bayesian", "readProbFile");
                exit(1);
        }
 }