X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=e4615ee8787d481dfad122bd8120ae35e130cdb6;hb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;hp=4095b86a4b0855e31b05bbfd775504801cc4ed1f;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 4095b86..e4615ee 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,7 +15,7 @@
 #include "maligner.h"
 #include "slayer.h"
 
-/***********************************************************************/
+//***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
@@ -23,12 +23,17 @@
 class ChimeraSlayer : public Chimera {
 	
 	public:
-		ChimeraSlayer(string);	
+		ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
 		~ChimeraSlayer();
 		
 		int getChimeras(Sequence*);
-		void print(ostream&);
+		int print(ostream&, ostream&);
 		void printHeader(ostream&);
+		int doPrep();
+		
+		#ifdef USE_MPI
+		int print(MPI_File&, MPI_File&);
+		#endif
 		
 	private:
 		Sequence* querySeq;
@@ -36,12 +41,18 @@ class ChimeraSlayer : public Chimera {
 		Maligner* maligner;
 		Slayer* slayer;
 		map<int, int>  spotMap;
+		Database* databaseRight;
+		Database* databaseLeft;
 		
 		vector<data_struct>  chimeraResults;
-		string chimeraFlags, searchMethod;
-		string fastafile;
+		string chimeraFlags, searchMethod, fastafile;
+		bool realign;
+		int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+		float divR;
 	
-		void printBlock(data_struct, ostream&);
+		void printBlock(data_struct, string, ostream&);
+		string getBlock(data_struct, string);
+		
 };
 
 /************************************************************************/