chimeracode

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 617ba7ee9557eb6ad54f65b4aa99f323fd5afd86..4095b86a4b0855e31b05bbfd775504801cc4ed1f 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -23,29 +23,25 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string);  
+               ChimeraSlayer(string);  
                ~ChimeraSlayer();
                
-               void getChimeras();
+               int getChimeras(Sequence*);
                void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) {};
-               
+               void printHeader(ostream&);
                
        private:
+               Sequence* querySeq;
                DeCalculator* decalc;
                Maligner* maligner;
                Slayer* slayer;
-               vector<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
-                               
-               string fastafile, templateFile;
+               map<int, int>  spotMap;
                
-               Sequence* getSequence(string);  //find sequence from name
-                       
-                               
+               vector<data_struct>  chimeraResults;
+               string chimeraFlags, searchMethod;
+               string fastafile;
+       
+               void printBlock(data_struct, ostream&);
 };
 
 /************************************************************************/