X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.h;h=09de39fddfe89bc48fd9397a4e0fffc5e32d495a;hb=cbbf2f185fc7289910bb69421095c1de024c5225;hp=0bf8a4528025eafc3f0e16955e08fbf4553ea13b;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102;p=mothur.git

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 0bf8a45..09de39f 100644
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -26,9 +26,12 @@ 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"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -38,10 +41,10 @@ private:
 	OrderVector* order;
 	InputData* input;
 	Rarefact* rCurve;
-	int nIters, abund, processors;
+	int nIters, abund, processors, alpha;
 	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 +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