#include "command.hpp"
+#include "sequence.hpp"
class ChopSeqsCommand : public Command {
public:
- ChopSeqsCommand(string);
+ ChopSeqsCommand(string);
+ ChopSeqsCommand();
~ChopSeqsCommand(){};
- int execute();
- void help();
-
+
+ vector<string> setParameters();
+ string getCommandName() { return "chop.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
+ string getDescription() { return "trim sequence length"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- string fastafile, outputDir;
- bool abort;
- int end;
+ string fastafile, outputDir, keep;
+ bool abort, countGaps, Short;
+ int numbases;
+ vector<string> outputNames;
+
+ string getChopped(Sequence);
};
#endif