public:
ChimeraPintailCommand(string);
+ ChimeraPintailCommand();
~ChimeraPintailCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
int processors, window, increment, numSeqs, templateSeqsLength;
Chimera* chimera;
vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
vector<string> fastaFileNames;