test

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 2d6ac0b2a7495bbf2408e38b18f52e0c0c330dcc..8b3b0eb713beb96cc391f18a733029298508145a 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -59,8 +59,8 @@ class Chimera {
        public:
        
                Chimera(){};
-               Chimera(string);
                Chimera(string, string);
+               Chimera(string, string, string);
                virtual ~Chimera(){};
                virtual void setFilter(bool f)                  {       filter = f;                     }
                virtual void setCorrection(bool c)              {       correction = c;         }
@@ -76,7 +76,7 @@ class Chimera {
                virtual void setDivR(float d)                   {       divR = d;                       }
                virtual void setParents(int p)                  {       parents = p;            }
                virtual void setMinSim(int s)                   {       minSim = s;                     }
-               virtual void setPrint(int p)                    {       printAll = p;           }
+               virtual void setIters(int i)                    {       iters = i;                      }
 
                
                virtual void setCons(string){};
@@ -89,15 +89,15 @@ class Chimera {
                
                
                //pure functions
-               virtual void getChimeras() = 0; 
+               virtual int getChimeras() = 0;  
                virtual void print(ostream&) = 0;       
                
        protected:
                
-               bool filter, correction, svg, printAll;
-               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents;
+               bool filter, correction, svg, unaligned;
+               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents, iters;
                float divR;
-               string seqMask, quanfile, filterString, name;
+               string seqMask, quanfile, filterString, name, outputDir;
                        
 
 };