X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=3ce4cce4b40cbe331b260f08552fa34bad010d3d;hb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;hp=379209ef382b47a8203895d85710f35926bf188e;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 379209e..3ce4cce 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
 /***********************************************************************/
 
@@ -23,32 +23,36 @@
 class ChimeraSlayer : public Chimera {
 	
 	public:
-		ChimeraSlayer(string, string);	
+		ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
 		~ChimeraSlayer();
 		
-		void getChimeras();
-		void print(ostream&);
-		
-		void setCons(string){};
-		void setQuantiles(string q) {};
+		int getChimeras(Sequence*);
+		int print(ostream&, ostream&);
+		void printHeader(ostream&);
+		int doPrep();
 		
+		#ifdef USE_MPI
+		int print(MPI_File&, MPI_File&);
+		#endif
 		
 	private:
+		Sequence* querySeq;
 		DeCalculator* decalc;
 		Maligner* maligner;
 		Slayer* slayer;
-		vector<linePair*> lines;
-		vector<Sequence*> querySeqs;
-		vector<Sequence*> templateSeqs;
-		vector< map<int, int> > spotMap;
+		map<int, int>  spotMap;
+		Database* databaseRight;
+		Database* databaseLeft;
 		
-		vector< vector<data_struct> > chimeraResults;
-		vector<string> chimeraFlags;
-				
-		string fastafile, templateFile;
+		vector<data_struct>  chimeraResults;
+		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&);
+		string getBlock(data_struct);
 		
-		Sequence* getSequence(string);  //find sequence from name
-		void printBlock(data_struct, ostream&, int i);
 };
 
 /************************************************************************/