X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraslayer.h;h=7bf663afeadeb3517daf4f9bfa25135fbf872cab;hp=a305b5bfd09601220b15a44fd0ad18ee6b42a09d;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=58cc09a375d1e1afceef3b036574ff21394ccc4d

diff --git a/chimeraslayer.h b/chimeraslayer.h
index a305b5b..7bf663a 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,40 +15,61 @@
 #include "maligner.h"
 #include "slayer.h"
 
-/***********************************************************************/
+
+
+//***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
-
 class ChimeraSlayer : public Chimera {
 	
 	public:
-		ChimeraSlayer(string, string);	
+		ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+		ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+		ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int, bool);
+
 		~ChimeraSlayer();
 		
-		void getChimeras();
-		void print(ostream&);
-		
-		void setCons(string){};
-		void setQuantiles(string q) {};
+		int getChimeras(Sequence*);
+		Sequence print(ostream&, ostream&);
+		Sequence print(ostream&, ostream&, data_results, data_results);
+		void printHeader(ostream&);
+		int doPrep();
+		int getNumNoParents() { return numNoParents; }
+		data_results getResults() { return printResults; }
 		
+		#ifdef USE_MPI
+		Sequence print(MPI_File&, MPI_File&);
+		Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&);
+		#endif
 		
 	private:
-		DeCalculator* decalc;
-		Maligner* maligner;
-		Slayer* slayer;
-		vector<linePair*> lines;
-		vector<Sequence*> querySeqs;
-		vector<Sequence*> templateSeqs;
-		
-		vector< vector<data_struct> > chimeraResults;
-		vector<string> chimeraFlags;
-				
-		string fastafile, templateFile;
+		Sequence querySeq;
+		Sequence trimQuery;
+		DeCalculator decalc;
+		Database* databaseRight;
+		Database* databaseLeft;
+		map<string, int> priority; //for template=self, seqname, seqAligned, abundance
+		set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
+		int numNoParents, threadID;
+	
+		vector<data_struct>  chimeraResults;
+		data_results printResults;
+		string chimeraFlags, searchMethod, fastafile, blastlocation;
+		bool realign, trimChimera;
+		int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+		float divR;
+	
+		void printBlock(data_struct, string, ostream&);
+		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, vector<Sequence*>&);
+		vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
+		vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
+		vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
 		
-		Sequence* getSequence(string);  //find sequence from name
-			
-				
 };
 
 /************************************************************************/