X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.h;h=6e81812e469772b18a737930354f1bdf943a9ef9;hb=1e0359c041eedc99670c93d824a2cf7fa72577cc;hp=89dc6aa7144175a6130743fe97fec9eac466c350;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;p=mothur.git

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 89dc6aa..6e81812 100644
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -21,7 +21,12 @@
 class ChimeraCheckCommand : public Command {
 public:
 	ChimeraCheckCommand(string);
+	ChimeraCheckCommand();
 	~ChimeraCheckCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();
 	
@@ -30,9 +35,10 @@ 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;
 	
@@ -40,7 +46,7 @@ private:
 	int createProcesses(string, string);
 		
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
 	#endif
 
 	bool abort, svg;
@@ -50,6 +56,7 @@ private:
 	vector<string> fastaFileNames;
 	vector<string> nameFileNames;
 	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 		
 };