X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactcommand.h;h=02fe6e3aa4355a107e76f06d8f8f9a7f0df19118;hp=36288927ac2d5bb575378329c9c0a6b66f1db5c4;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 3628892..02fe6e3 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -26,7 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "rarefaction.single";		}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
 	string getDescription()		{ return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
 
@@ -50,8 +52,8 @@ private:
 	vector<string> groups;
 	string outputDir;
 	
-	vector<string> parseSharedFile(string);
-	vector<string> createGroupFile(vector<string>&);
+	vector<string> parseSharedFile(string, map<string, set<int> >&);
+	vector<string> createGroupFile(vector<string>&, map<int, string>);
 };
 
 #endif