created mothurOut class to handle logfiles

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index f893d63ed9c57e7d53d84843cb3b647cc9dd89d6..f6a5180975b134d7c5928dca4343e0a1f62074da 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -88,11 +88,11 @@ class Chimera {
 
        public:
        
-               Chimera(){};
-               Chimera(string);
-               Chimera(string, bool, string);
-               Chimera(string, string);
-               virtual ~Chimera(){};
+               Chimera(){ m = MothurOut::getInstance(); }
+               Chimera(string) { m = MothurOut::getInstance(); }
+               Chimera(string, bool, string) { m = MothurOut::getInstance(); }
+               Chimera(string, string) { m = MothurOut::getInstance(); }
+               virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
                virtual void setFilter(bool f)                  {       filter = f;                     }
                virtual void setCorrection(bool c)              {       correction = c;         }
                virtual void setProcessors(int p)               {       processors = p;         }
@@ -111,9 +111,8 @@ class Chimera {
                virtual void setMinBS(int b)                    {       minBS = b;                      }
                virtual void setMinSNP(int s)                   {       minSNP = s;                     }
                virtual void setIters(int i)                    {       iters = i;                      }
-               virtual void setTemplateSeqs(vector<Sequence*> t)       {       templateSeqs = t;       }
                virtual bool getUnaligned()                             {       return unaligned;                       }
-               virtual void setTemplateFile(string t)  {   templateFileName = t;       }
+               virtual void setTemplateFile(string t)  {   templateFileName = t;       templateSeqs = readSeqs(t);  }
                virtual int getLength()                                 {   return length;      }
                
                virtual void setCons(string){};
@@ -139,6 +138,7 @@ class Chimera {
                float divR;
                string seqMask, quanfile, filterString, name, outputDir, templateFileName;
                Sequence* getSequence(string);  //find sequence from name       
+               MothurOut* m;
 };
 
 /***********************************************************************/