X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=3bf36c040231c5f801281f9d553c60bed01101c8;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=c670f37919e7da8ce3e3f3ee5d294cd4d23acd94;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index c670f37..3bf36c0 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -20,18 +20,22 @@ public:
 	FilterSeqsCommand(string);
 	FilterSeqsCommand();
 	~FilterSeqsCommand() {};
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	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;
-		unsigned long int end;
-		linePair(unsigned long int i, unsigned long int j) : start(i), end(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;
@@ -42,7 +46,6 @@ private:
 	int alignmentLength, processors;
 	vector<int> bufferSizes;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 
 	char trump;
 	bool abort;
@@ -56,8 +59,8 @@ 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<unsigned long int>&);
-	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long int>&);	
+	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long long>&);	
 	#endif
 	
 };