X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=d19a396410f2e2c9850f9b20a93d65c03000bac2;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=d8f8f0905ba3c3e8c09dfb8ec83ec34f817db89e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d8f8f09..d19a396 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -19,7 +19,6 @@
 #include "readmatrix.hpp"
 #include "formatmatrix.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
@@ -43,7 +42,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.oturep";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
+	string getDescription()		{ return "gets a representative sequence for each OTU"; }
+
 	
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
@@ -78,6 +81,7 @@ private:
 	SeqMap getMap(int);
 	string findRep(vector<string>); 	// returns the name of the "representative" sequence of given bin or subset of a bin, for groups
 	int processNames(string, string);
+	int processFastaNames(string, string);
 };
 
 #endif