X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimeraslayer.h;h=ded0f89b1cb57c88c66777405d1c0d8de9df088d;hb=1e8d08e96f4fe99604a6b3502568de464bf60891;hp=3ce4cce4b40cbe331b260f08552fa34bad010d3d;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 3ce4cce..ded0f89 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -19,39 +19,51 @@
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
-
 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, map<string, int>&, 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&);
+		Sequence* print(ostream&, ostream&, data_results, data_results);
 		void printHeader(ostream&);
 		int doPrep();
+		data_results getResults() { return printResults; }
 		
 		#ifdef USE_MPI
-		int print(MPI_File&, MPI_File&);
+		Sequence* print(MPI_File&, MPI_File&);
+		Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
 		#endif
 		
 	private:
 		Sequence* querySeq;
+		Sequence trimQuery;
 		DeCalculator* decalc;
-		Maligner* maligner;
-		Slayer* slayer;
-		map<int, int>  spotMap;
 		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
+	
 		vector<data_struct>  chimeraResults;
+		data_results printResults;
 		string chimeraFlags, searchMethod, fastafile;
-		bool realign;
+		bool realign, trimChimera;
 		int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
 		float divR;
 	
-		void printBlock(data_struct, ostream&);
-		string getBlock(data_struct);
+		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);
 		
 };