continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 366068b43f77cae77f6df9ce82766e253a8789e1..8d7e08d50b37fb92049f52d4d9083030a6acbd5b 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;
 };
@@ -68,6 +68,7 @@ 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 setCons(string){};
                virtual void setQuantiles(string){};
@@ -85,7 +86,7 @@ class Chimera {
        protected:
                
                bool filter, correction;
-               int processors, window, increment, numWanted;
+               int processors, window, increment, numWanted, kmerSize;
                string seqMask, quanfile, filterString;