created mothurOut class to handle logfiles

[mothur.git] / knn.cpp

diff --git a/knn.cpp b/knn.cpp
index 706d2435117513d4a7149e0cc2a670e0e18dc7bb..c11626a082ac9003785fd937e87b922e3bf8025a 100644 (file)
--- a/knn.cpp
+++ b/knn.cpp
@@ -28,23 +28,23 @@ string Knn::getTaxonomy(Sequence* seq) {
                
                        //is this sequence in the taxonomy file
                        if (it == taxonomy.end()) { //error not in file
-                               mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file.  It will be eliminated as a match to sequence " + seq->getName() + "."); mothurOutEndLine();
+                               m->mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file.  It will be eliminated as a match to sequence " + seq->getName() + "."); m->mothurOutEndLine();
                        }else{   closestNames.push_back(it->first);     }
                }
                
                if (closestNames.size() == 0) {
-                       mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); mothurOutEndLine();
+                       m->mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); m->mothurOutEndLine();
                        tax = "bad seq";
                }else{
                        tax = findCommonTaxonomy(closestNames);
-                       if (tax == "") { mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); mothurOutEndLine(); tax = "bad seq"; }
+                       if (tax == "") { m->mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); m->mothurOutEndLine(); tax = "bad seq"; }
                }
                
                simpleTax = tax;
                return tax;     
        }
        catch(exception& e) {
-               errorOut(e, "Knn", "getTaxonomy");
+               m->errorOut(e, "Knn", "getTaxonomy");
                exit(1);
        }
 }
@@ -92,7 +92,7 @@ string Knn::findCommonTaxonomy(vector<string> closest)  {
                return common;
        }
        catch(exception& e) {
-               errorOut(e, "Knn", "findCommonTaxonomy");
+               m->errorOut(e, "Knn", "findCommonTaxonomy");
                exit(1);
        }
 }