public:
ClusterFragmentsCommand(string);
+ ClusterFragmentsCommand();
~ClusterFragmentsCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
map<string, string> names; //represents the names file first column maps to second column
map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
map<string, int>::iterator itSize;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
int readFASTA();
void readNameFile();