#include "command.hpp"
+#include "sequence.hpp"
class ChopSeqsCommand : public Command {
public:
- ChopSeqsCommand(string);
+ ChopSeqsCommand(string);
+ ChopSeqsCommand();
~ChopSeqsCommand(){};
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
- string fastafile, outputDir;
- bool abort;
- int end;
+ string fastafile, outputDir, keep;
+ bool abort, countGaps, Short;
+ int numbases;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+
+ string getChopped(Sequence);
+
+
};
#endif