X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.h;h=4f08d00d7332ae32824464b809744042bd997d7f;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=a5b45468d7059ad2c9e8877376c0154102d05316;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index a5b4546..4f08d00 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "rarefaction.shared";		}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
 	string getDescription()		{ return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
 
@@ -37,18 +38,19 @@ public:
 private:
 	
 	vector<SharedRAbundVector*> lookup;
-	int nIters;
+	int nIters, subsampleSize, iters;
 	string format;
 	float freq;
 	
      map<int, string> file2Group; //index in outputNames[i] -> group
-	bool abort, allLines, jumble, groupMode;
+	bool abort, allLines, jumble, groupMode, subsample;
 	set<string> labels; //holds labels to be used
 	string label, calc, groups, outputDir, sharedfile, designfile;
 	vector<string>  Estimators, Groups, outputNames, Sets;
     
     int process(GroupMap&, string);
     vector<string> createGroupFile(vector<string>&);
+    int subsampleLookup(vector<SharedRAbundVector*>&, string);
 
 };