fixes while testing 1.12.0

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 7120478f1df89cb9038ddea7f848cad376ca83d7..24ab3f74e5b783becc8106beffeef09a22191cb8 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -90,41 +90,13 @@ class Chimera {
        public:
        
                Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
-               //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;         }
-               //virtual void setWindow(int w)                 {       window = w;                     }
-               //virtual void setIncrement(int i)              {       increment = i;          }
-               //virtual void setNumWanted(int n)              {       numWanted = n;          }
-               //virtual void setKmerSize(int k)                       {       kmerSize = k;           }
-               //virtual void setSVG(int s)                            {       svg = s;                        }
-               //virtual void setName(string n)                        {       name = n;                       }
-               //virtual void setMatch(int m)                  {       match = m;                      }
-               //virtual void setMisMatch(int m)                       {       misMatch = m;           }
-               //virtual void setDivR(float d)                 {       divR = d;                       }
-               //virtual void setParents(int p)                        {       parents = p;            }
-               //virtual void setMinSim(int s)                 {       minSim = s;                     }
-               //virtual void setMinCoverage(int c)            {       minCov = c;                     }
-               //virtual void setMinBS(int b)                  {       minBS = b;                      }
-               //virtual void setMinSNP(int s)                 {       minSNP = s;                     }
-               //virtual void setIters(int i)                  {       iters = i;                      }
                virtual bool getUnaligned()                             {       return unaligned;                       }
-               //virtual void setTemplateFile(string t)        {   templateFileName = t;       templateSeqs = readSeqs(t);  }
                virtual int getLength()                                 {   return length;      }
-               
-               //virtual void setCons(string){};
-               //virtual void setQuantiles(string){};
-               //virtual int doPrep(){ return 0; }
                virtual vector<Sequence*> readSeqs(string);
-               //virtual vector< vector<float> > readQuantiles();
                virtual void setMask(string);
                virtual map<int, int> runFilter(Sequence*);
                virtual string createFilter(vector<Sequence*>, float);
-               
                virtual void printHeader(ostream&){};
                virtual int getChimeras(Sequence*){ return 0; }
                virtual int getChimeras(){ return 0; }
@@ -138,10 +110,9 @@ class Chimera {
        protected:
                
                vector<Sequence*> templateSeqs;
-               bool filter, unaligned; //  correction, svg,
-               int length; //processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters,
-               //float divR;
-               string seqMask, filterString, outputDir, templateFileName; //quanfile, name, 
+               bool filter, unaligned; 
+               int length; 
+               string seqMask, filterString, outputDir, templateFileName; 
                Sequence* getSequence(string);  //find sequence from name       
                MothurOut* m;
 };