incorporation of nast-ier code / removed a cout

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 3e76297b038b9eeafab2c04e5428a2091814a07d..ded0f89b1cb57c88c66777405d1c0d8de9df088d 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -23,7 +23,7 @@ class ChimeraSlayer : public Chimera {
        
        public:
                ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
-               ChimeraSlayer(string, string, bool, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
 
                ~ChimeraSlayer();
                
@@ -41,16 +41,16 @@ class ChimeraSlayer : public Chimera {
                
        private:
                Sequence* querySeq;
-               Sequence* trimQuery;
+               Sequence trimQuery;
                DeCalculator* decalc;
-               map<int, int>  spotMap;
                Database* databaseRight;
                Database* databaseLeft;
-               map<string, vector<string> > nameMapRank;  //sequence name to rank so you can construct a template of the abundant sequences if the user uses itself as template
-               
+               map<string, int> priority; //for template=self, seqname, seqAligned, abundance
+               set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
+       
                vector<data_struct>  chimeraResults;
                data_results printResults;
-               string chimeraFlags, searchMethod, fastafile, includeAbunds;
+               string chimeraFlags, searchMethod, fastafile;
                bool realign, trimChimera;
                int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
                float divR;
@@ -59,8 +59,11 @@ class ChimeraSlayer : public Chimera {
                void printBlock(data_results, data_results, bool, bool, string, ostream&);
                string getBlock(data_struct, string);
                string getBlock(data_results, data_results, bool, bool, string);
-               int readNameFile(string);
-               vector<Sequence*> getTemplate(Sequence*);
+               //int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
+               vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
+               vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
+               vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);
                
 };