test

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 33e514b0f05d424740f2a660066e1ace6d99d40d..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;         }
@@ -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;
+               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;
                        
 
 };