changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 0bf8a4528025eafc3f0e16955e08fbf4553ea13b..0e77a277e6ad7cda962a4c9476945f6b2aa6b557 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -28,7 +28,8 @@ public:
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        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"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -41,7 +42,7 @@ 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;
@@ -49,7 +50,8 @@ 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