X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraccodecommand.h;h=52bf07d01f6a411b870e119f82ef97f7b6f45cbd;hp=5989eb25e0c5c1488e8bdf69e03157bbe1e7e6fd;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index 5989eb2..52bf07d 100644
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,17 +20,27 @@
 class ChimeraCcodeCommand : public Command {
 public:
 	ChimeraCcodeCommand(string);
-	~ChimeraCcodeCommand();
-	int execute();
-	void help();
+	ChimeraCcodeCommand();
+	~ChimeraCcodeCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "chimera.ccode";		}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
+	
+	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 long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
 	};
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
@@ -39,17 +49,15 @@ private:
 	int createProcesses(string, 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&, vector<unsigned long long>&);
 	#endif
 
-	bool abort, filter;
+	bool abort, filter, save;
 	string fastafile, templatefile, outputDir, maskfile;
 	int processors, window, numwanted, numSeqs, templateSeqsLength;
 	Chimera* chimera;
 	vector<string> fastaFileNames;
 	vector<string> outputNames;
-	
-	
 };
 
 /***********************************************************/