modified chimera.slayer template=self

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 3e76297b038b9eeafab2c04e5428a2091814a07d..cac96eb158a721ac5fe3d5c68a82d61979fd99e8 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, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
 
                ~ChimeraSlayer();
                
@@ -41,16 +41,18 @@ 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
+               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
                
                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 +61,8 @@ 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);
+               int getTemplate(Sequence*);
                
 };