X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=09de39fddfe89bc48fd9397a4e0fffc5e32d495a;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=6aaa3de401e07f653abcd29cff4e98c868a94e4b;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 6aaa3de..09de39f 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"; }
 
@@ -39,7 +41,7 @@ private:
 	OrderVector* order;
 	InputData* input;
 	Rarefact* rCurve;
-	int nIters, abund, processors;
+	int nIters, abund, processors, alpha;
 	float freq;
 	
 	bool abort, allLines, groupMode;
@@ -50,7 +52,7 @@ private:
 	vector<string> groups;
 	string outputDir;
 	
-	vector<string> parseSharedFile(string);
+	vector<string> parseSharedFile(string, map<string, set<int> >&);
 	vector<string> createGroupFile(vector<string>&, map<int, string>);
 };