X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactcommand.h;h=02fe6e3aa4355a107e76f06d8f8f9a7f0df19118;hp=b4bce3e172d141ab5e1fdcea1c59bd35b25dadab;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf

diff --git a/rarefactcommand.h b/rarefactcommand.h
index b4bce3e..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"; }
 
@@ -42,7 +44,7 @@ private:
 	int nIters, abund, processors;
 	float freq;
 	
-	bool abort, allLines;
+	bool abort, allLines, groupMode;
 	set<string> labels; //holds labels to be used
 	string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
 	vector<string>  Estimators;
@@ -50,7 +52,8 @@ 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>);
 };
 
 #endif