chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index f8006c41382919b311e8fd8b590f31e9b8bfaad1..bf9cf7f8166884e1dda08f0de7a1989bec961c65 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -23,12 +23,13 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, bool);    
+               ChimeraSlayer(string, bool, string);    
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
                void print(ostream&);
                void printHeader(ostream&);
+               void doPrep();
                
        private:
                Sequence* querySeq;
@@ -36,13 +37,15 @@ class ChimeraSlayer : public Chimera {
                Maligner* maligner;
                Slayer* slayer;
                map<int, int>  spotMap;
+               Database* databaseRight;
+               Database* databaseLeft;
                
                vector<data_struct>  chimeraResults;
-               string chimeraFlags, searchMethod;
-               string fastafile;
+               string chimeraFlags, searchMethod, fastafile;
                bool realign;
        
                void printBlock(data_struct, ostream&);
+               
 };
 
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