created mothurOut class to handle logfiles

[mothur.git] / chimerarealigner.cpp

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index fa9dd566c83014124fa302be6d5505102acdddac..487e7ca8f0425d7ba22e61690a4e0e8bc4758206 100644 (file)
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -12,7 +12,7 @@
 #include "nast.hpp"
 
 //***************************************************************************************************************
-ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int m, int mm) : match(m), misMatch(mm) {  templateSeqs = t;  }
+ChimeraReAligner::ChimeraReAligner(vector<Sequence*> t, int ms, int mm) : match(ms), misMatch(mm) {  templateSeqs = t;   m = MothurOut::getInstance(); }
 //***************************************************************************************************************
 ChimeraReAligner::~ChimeraReAligner() {}       
 //***************************************************************************************************************
@@ -78,7 +78,7 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
                
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraReAligner", "reAlign");
+               m->errorOut(e, "ChimeraReAligner", "reAlign");
                exit(1);
        }
 }
@@ -96,14 +96,14 @@ Sequence* ChimeraReAligner::getSequence(string name) {
                        }
                }
                
-               if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+               if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
                
                temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
                
                return temp;
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraReAligner", "getSequence");
+               m->errorOut(e, "ChimeraReAligner", "getSequence");
                exit(1);
        }
 }