X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.h;h=36584e091537138c8d1ab853ee99be68cbc5bcec;hb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;hp=c3d71c920ee2d84e8c6a2738e21cbcb840d4a8c5;hpb=0c78e45408d8c099bc51579225ebfc227f7523b2;p=mothur.git

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index c3d71c9..36584e0 100644
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,17 +20,24 @@
 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 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"; }
+	
+	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;
@@ -39,7 +46,7 @@ private:
 	int createProcesses(string, 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&, vector<unsigned long int>&);
 	#endif
 
 	bool abort, filter;
@@ -48,8 +55,6 @@ private:
 	Chimera* chimera;
 	vector<string> fastaFileNames;
 	vector<string> outputNames;
-	
-	
 };
 
 /***********************************************************/