X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraslayer.h;fp=chimeraslayer.h;h=0000000000000000000000000000000000000000;hp=c409c503da43a78f707d83a448372d9ef03595d7;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76

diff --git a/chimeraslayer.h b/chimeraslayer.h
deleted file mode 100644
index c409c50..0000000
--- a/chimeraslayer.h
+++ /dev/null
@@ -1,79 +0,0 @@
-#ifndef CHIMERASLAYER_H
-#define CHIMERASLAYER_H
-
-/*
- *  chimeraslayer.h
- *  Mothur
- *
- *  Created by westcott on 9/25/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "chimera.h"
-#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, 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();
-		
-		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);
-		#endif
-		
-	private:
-		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);
-		
-};
-
-/************************************************************************/
-
-#endif
-
-