X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=90f6b62f83fea0bc4abc980baacccb362e216554;hb=4de093e3b92bdab1579565cb2873553412f6671e;hp=d201ccb5f1baa2c628f217c7c763523e832d70eb;hpb=7b80945ef716dd72d00563a5a4d692394f7f84c3;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index d201ccb..90f6b62 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -14,22 +14,24 @@
 #include "command.hpp"
 #include "chimera.h"
 
-
 /***********************************************************/
 
 class ChimeraSlayerCommand : public Command {
 public:
 	ChimeraSlayerCommand(string);
 	ChimeraSlayerCommand();
-	~ChimeraSlayerCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~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"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 	
-		
 private:
 
 	struct linePair {
@@ -44,19 +46,19 @@ private:
 	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&, MPI_File&, vector<unsigned long int>&);
 	#endif
 
 	bool abort, realign, trim, trimera;
-	string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
+	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;
-	map<string, vector<string> > outputTypes;
 	vector<string> fastaFileNames;
 	vector<string> nameFileNames;