optimizing classify.seqs calculating of template probabilities.

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index b4bce3e172d141ab5e1fdcea1c59bd35b25dadab..9c7e1ed34fcffebaf73f4499bd6637d0d36c2b68 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -26,6 +26,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "rarefaction.single";          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        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"; }
@@ -42,7 +43,7 @@ private:
        int nIters, abund, processors;
        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;
@@ -50,7 +51,8 @@ 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