vector<string> setParameters();
string getCommandName() { return "summary.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
+ string getDescription() { return "generate summary file that has the calculator value for each line in the OTU data"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
vector<Calculator*> sumCalculators;
InputData* input;
SAbundVector* sabund;
- int abund, size;
+ int abund, size, iters, subsampleSize;
- bool abort, allLines, groupMode;
+ bool abort, allLines, groupMode, subsample;
set<string> labels; //holds labels to be used
string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
vector<string> groups;
vector<string> parseSharedFile(string);
- string createGroupSummaryFile(int, int, vector<string>&);
+ vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+ int process(SAbundVector*&, ofstream&, ofstream&);
};