public:
GetOTURepCommand(string);
+ GetOTURepCommand();
~GetOTURepCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
vector<SeqMap> seqVec; // contains maps with sequence index and distance
// for all distances related to a certain sequence
vector<int> rowPositions;
+ map<string, vector<string> > outputTypes;
void readNamesFile();
int process(ListVector*);