X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=1e03d9281e7a194f34bde73065c1916f66bec469;hb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d;hp=e4615ee8787d481dfad122bd8120ae35e130cdb6;hpb=a0f87c2ae6414af28d4e70b1e6830401eac21bef;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index e4615ee..1e03d92 100644
--- 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*);
 		
 };