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"; }
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);
};