vector<string> setParameters();
string getCommandName() { return "summary.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
vector<Calculator*> sumCalculators;
InputData* input;
- bool abort, allLines, mult, all, createPhylip;
+ bool abort, allLines, mult, all, createPhylip, subsample;
set<string> labels; //holds labels to be used
- string label, calc, groups, sharedfile;
+ string label, calc, groups, sharedfile, output;
vector<string> Estimators, Groups, outputNames;
vector<SharedRAbundVector*> lookup;
string format, outputDir;
- int numGroups, processors;
+ int numGroups, processors, subsampleSize, iters;
int process(vector<SharedRAbundVector*>, string, string);
int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
+ int printSims(ostream&, vector< vector<double> >&);
};