vector<string> setParameters();
string getCommandName() { return "get.rabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+ string getDescription() { return "creates a rabund file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- string filename, listfile, sabundfile, inputfile, format, outputDir;
+ string filename, listfile, sabundfile, inputfile, format, outputDir, countfile;
ofstream out;
- InputData* input;
- RAbundVector* rabund;
vector<string> outputNames;
bool abort, allLines, sorted;
set<string> labels; //holds labels to be used
string label;
-
+ int processList(ofstream& out);
+ int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
};
#endif