X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;fp=filterseqscommand.h;h=75e7895c6ef2d4a532dfae9d37ea4fc035243b75;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=c670f37919e7da8ce3e3f3ee5d294cd4d23acd94;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index c670f37..75e7895 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -20,12 +20,14 @@ 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();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	struct linePair {
@@ -42,7 +44,6 @@ private:
 	int alignmentLength, processors;
 	vector<int> bufferSizes;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 
 	char trump;
 	bool abort;