X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=6ca0310d109c117cf5205ac0725e79338540676a;hb=64581f6d0e63e67d4e119601bea695ebb3f52a13;hp=c2d9c45cfa931e9510981a4ff0c82c1d1e0fa890;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index c2d9c45..6ca0310 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,42 +14,51 @@
 #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();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 	
-		
 private:
 
 	struct linePair {
 		unsigned long int start;
-		int numSeqs;
-		linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+		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&);
+	string 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;
 	
 };