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 getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
string fastafile, outputDir, keep;
- bool abort;
+ bool abort, countGaps, Short;
int numbases;
+ vector<string> outputNames;
string getChopped(Sequence);
-
};
#endif