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