public:
SplitAbundCommand(string);
+ SplitAbundCommand();
~SplitAbundCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
int splitList(ListVector*);
int splitNames(); //namefile
int writeNames();
- int writeList(ListVector*);
+ int writeList(ListVector*, string);
int writeAccnos(string);
int parseGroup(string);
int parseFasta(string);
int createNameMap(ListVector*);
vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
ListVector* list;
GroupMap* groupMap;
InputData* input;
vector<string> Groups;
bool abort, allLines, accnos;
int cutoff;
- map<string, bool> wroteListFile;
+ //map<string, bool> wroteListFile;
map<string, string> nameMap;