incorporation of nast-ier code / removed a cout

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index cac96eb158a721ac5fe3d5c68a82d61979fd99e8..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, 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();
                
@@ -43,13 +43,11 @@ class ChimeraSlayer : public Chimera {
                Sequence* querySeq;
                Sequence trimQuery;
                DeCalculator* decalc;
-               map<int, int>  spotMap;
                Database* databaseRight;
                Database* databaseLeft;
-               vector<Sequence*> userTemplate;  //when template=self, the query file is sorted from most abundance to least abundant
-                                                                                //userTemplate grows as the query file is processed by adding sequences that are not chimeric
-               set<string> namesOfChimericSeqs; //only used when template=self
-               
+               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;
@@ -62,7 +60,10 @@ class ChimeraSlayer : public Chimera {
                string getBlock(data_struct, string);
                string getBlock(data_results, data_results, bool, bool, string);
                //int readNameFile(string);
-               int getTemplate(Sequence*);
+               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);
                
 };