public:
ChimeraBellerophonCommand(string);
ChimeraBellerophonCommand();
- ~ChimeraBellerophonCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map< string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ChimeraBellerophonCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "chimera.bellerophon"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
+ string getDescription() { return "detect chimeric sequences"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
int processors, window, increment, numSeqs;
Chimera* chimera;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
vector<string> fastaFileNames;
};