X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.h;h=4f08d00d7332ae32824464b809744042bd997d7f;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=1a2d944894feabe26b4103e5431c0da08c6574b4;hpb=ffc44592ff7ae94f14f9e21f87198e33d323cd1d;p=mothur.git

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 1a2d944..4f08d00 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "rarefaction.shared";		}
 	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.shared"; }
 	string getDescription()		{ return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
 
@@ -36,16 +38,19 @@ public:
 private:
 	
 	vector<SharedRAbundVector*> lookup;
-	int nIters;
+	int nIters, subsampleSize, iters;
 	string format;
 	float freq;
 	
-	bool abort, allLines, jumble;
+     map<int, string> file2Group; //index in outputNames[i] -> group
+	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);
 
 };