X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=3bf36c040231c5f801281f9d553c60bed01101c8;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=2ec152bb557eb27970c3660136b1b879f658949d;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 2ec152b..3bf36c0 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -18,16 +18,26 @@ class FilterSeqsCommand : public Command {
 
 public:
 	FilterSeqsCommand(string);
+	FilterSeqsCommand();
 	~FilterSeqsCommand() {};
-	int execute();	
-	void help();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "filter.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }
+	string getDescription()		{ return "removes columns from alignments based on a criteria defined by the user"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	struct linePair {
-		unsigned long int start;
-		int num;
-		linePair(unsigned long int i, long int j) : start(i), num(j) {}
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
 	};
+
 	vector<linePair*> lines;
 	vector<int> processIDS;
 
@@ -49,11 +59,9 @@ private:
 	int driverRunFilter(string, string, string, linePair*);
 	int driverCreateFilter(Filters& F, string filename, linePair* line);
 	#ifdef USE_MPI
-	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<long>&);
-	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&);	
+	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long long>&);	
 	#endif
-	int setLines(string);
-	
 	
 };