X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.h;h=a9ed223b112cdb50876024c893257549e159481f;hb=45b880733289694b2a23c9dc8a774aa626458f81;hp=c3d71c920ee2d84e8c6a2738e21cbcb840d4a8c5;hpb=0c78e45408d8c099bc51579225ebfc227f7523b2;p=mothur.git

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index c3d71c9..a9ed223 100644
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,17 +20,21 @@
 class ChimeraCcodeCommand : public Command {
 public:
 	ChimeraCcodeCommand(string);
+	ChimeraCcodeCommand();
 	~ChimeraCcodeCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
 		
 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 +43,7 @@ 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;
@@ -48,6 +52,7 @@ private:
 	Chimera* chimera;
 	vector<string> fastaFileNames;
 	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 	
 	
 };