X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.h;h=af73e132001d1e80bf239362b5541cd08c99d85e;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=54d0495fdc8a1ac5063c8c01ff24970cea2b02fb;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 54d0495..af73e13 100644
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -25,9 +25,11 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "rarefaction.shared";		}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Rarefaction.shared"; }
-	
+	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"; }
+
 	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
@@ -35,17 +37,19 @@ public:
 private:
 	
 	vector<SharedRAbundVector*> lookup;
-	InputData* input;
-	Rarefact* rCurve;
-	vector<Display*> rDisplays;
-	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;
-	vector<string>  Estimators, Groups, outputNames;
+	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);
 
 };