test

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 366068b43f77cae77f6df9ce82766e253a8789e1..8b3b0eb713beb96cc391f18a733029298508145a 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -39,8 +39,8 @@ inline bool compareSeqDist(SeqDist left, SeqDist right){
 //********************************************************************************************************************
 
 struct sim {
-               Sequence* leftParent;
-               Sequence* rightParent; 
+               string leftParent;
+               string rightParent; 
                float score;  
                int midpoint;
 };
@@ -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;         }
@@ -68,6 +68,16 @@ class Chimera {
                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 setIters(int i)                    {       iters = i;                      }
+
                
                virtual void setCons(string){};
                virtual void setQuantiles(string){};
@@ -79,14 +89,15 @@ class Chimera {
                
                
                //pure functions
-               virtual void getChimeras() = 0; 
+               virtual int getChimeras() = 0;  
                virtual void print(ostream&) = 0;       
                
        protected:
                
-               bool filter, correction;
-               int processors, window, increment, numWanted;
-               string seqMask, quanfile, filterString;
+               bool filter, correction, svg, unaligned;
+               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents, iters;
+               float divR;
+               string seqMask, quanfile, filterString, name, outputDir;
                        
 
 };