added modify names parameter to set.dir

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index a210574002969c411be4d9e9c705af9d88c980f0..4f08d00d7332ae32824464b809744042bd997d7f 100644 (file)
--- 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"; }
 
@@ -36,18 +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);
 
 };