public:
GetSharedOTUCommand(string);
+ GetSharedOTUCommand();
~GetSharedOTUCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
GroupMap* groupMap;
set<string> labels;
- string fastafile, label, groups, listfile, groupfile, output;
- bool abort, allLines;
+ string fastafile, label, groups, listfile, groupfile, output, userGroups, outputDir;
+ bool abort, allLines, unique;
vector<string> Groups;
map<string, string> groupFinder;
map<string, string>::iterator it;
vector<Sequence> seqs;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
- void process(ListVector*);
+ int process(ListVector*);
};
//**********************************************************************************************************************