X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=4bf6759dcda1d4eccda99658780a1e9d819bcece;hb=4de093e3b92bdab1579565cb2873553412f6671e;hp=6abf06a6fcf11bba1a714c6b3efdfd2be37b7285;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 6abf06a..4bf6759 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -16,14 +16,23 @@
 class SeqSummaryCommand : public Command {
 public:
 	SeqSummaryCommand(string);
-	~SeqSummaryCommand();
-	int execute();
-	void help();
+	SeqSummaryCommand();
+	~SeqSummaryCommand(){}
 	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 private:
 	bool abort;
-	string fastafile, outputDir;
+	string fastafile, outputDir, namefile;
 	int processors;
+	vector<string> outputNames;
+	map<string, int> nameMap;
 	
 	struct linePair {
 		unsigned long int start;