working on chimera change to add trim feature, fixed bug in print of distance file...

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index e4615ee8787d481dfad122bd8120ae35e130cdb6..1e03d9281e7a194f34bde73065c1916f66bec469 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,6 +15,8 @@
 #include "maligner.h"
 #include "slayer.h"
 
+
+
 //***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
@@ -23,35 +25,39 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               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();
                
                int getChimeras(Sequence*);
-               int print(ostream&, ostream&);
+               Sequence* print(ostream&, ostream&);
                void printHeader(ostream&);
                int doPrep();
                
                #ifdef USE_MPI
-               int print(MPI_File&, MPI_File&);
+               Sequence* print(MPI_File&, MPI_File&);
                #endif
                
        private:
                Sequence* querySeq;
+               Sequence* trimQuery;
                DeCalculator* decalc;
-               Maligner* maligner;
-               Slayer* slayer;
                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<data_struct>  chimeraResults;
-               string chimeraFlags, searchMethod, fastafile;
-               bool realign;
+               string chimeraFlags, searchMethod, fastafile, includeAbunds;
+               bool realign, trimChimera;
                int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
                float divR;
        
                void printBlock(data_struct, string, ostream&);
                string getBlock(data_struct, string);
+               int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence*);
                
 };