class PreClusterCommand : public Command {
public:
- PreClusterCommand(string);
+ PreClusterCommand(string);
+ PreClusterCommand();
~PreClusterCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
map<string, int>::iterator itSize;
// map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
int readFASTA();
void readNameFile();