class ChimeraCcodeCommand : public Command {
public:
ChimeraCcodeCommand(string);
+ ChimeraCcodeCommand();
~ChimeraCcodeCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
-
struct linePair {
unsigned long int start;
- int numSeqs;
- linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
vector<int> processIDS; //processid
vector<linePair*> lines;
Chimera* chimera;
vector<string> fastaFileNames;
vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
};