public:
SetCurrentCommand(string);
SetCurrentCommand();
- ~SetCurrentCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~SetCurrentCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "set.current"; }
+ string getCommandCategory() { return "General"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
+ string getDescription() { return "set current files for mothur"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
bool abort;
string clearTypes;
vector<string> types;
- string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+ string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
};