X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=35ff7627552d2e2d15fe4e03adcd9c634e8b8b3c;hb=f5ef644ce76074de08b2bbb64097619b2b16d60d;hp=7c20fb912bd321a121a410da45ed9abc87fce474;hpb=0c78e45408d8c099bc51579225ebfc227f7523b2;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 7c20fb9..35ff762 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,42 +14,53 @@
 #include "command.hpp"
 #include "chimera.h"
 
-
 /***********************************************************/
 
 class ChimeraSlayerCommand : public Command {
 public:
 	ChimeraSlayerCommand(string);
-	~ChimeraSlayerCommand();
-	int execute();
-	void help();
+	ChimeraSlayerCommand();
+	~ChimeraSlayerCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "chimera.slayer";		}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getHelpString();	
+	string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 	
-		
 private:
 
 	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(j) {}
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
 	};
+
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
 	
-	int driver(linePair*, string, string, string);
-	int createProcesses(string, string, string);
+	int driver(linePair*, string, string, string, string);
+	int createProcesses(string, string, string, string);
+	int divideInHalf(Sequence, string&, string&);
+	map<string, int> sortFastaFile(string, string);
 		
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
 	#endif
 
-	bool abort, realign;
-	string fastafile, templatefile, outputDir, search;
+	bool abort, realign, trim, trimera;
+	string fastafile, templatefile, outputDir, search, namefile;
 	int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
 	float divR;
 	Chimera* chimera;
 	
 	vector<string> outputNames;
 	vector<string> fastaFileNames;
+	vector<string> nameFileNames;
 	
 };