X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=0e77a277e6ad7cda962a4c9476945f6b2aa6b557;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=58e6819bf07ef6d63d6fbf8f4bb92a2f154bf163;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 58e6819..0e77a27 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -27,8 +27,9 @@ public:
 	string getCommandName()			{ return "rarefaction.single";		}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Rarefaction.single"; }
-	
+	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"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -41,7 +42,7 @@ 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;
@@ -49,7 +50,8 @@ 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