X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=d201ccb5f1baa2c628f217c7c763523e832d70eb;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=95541b2b6aac8a636242dba385c1114267416bb4;hpb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 95541b2..d201ccb 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -20,7 +20,12 @@
 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();
 	
@@ -29,27 +34,31 @@ 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&);
 		
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	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, includeAbunds;
 	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;
 	
 };