*
*/
-
-
#include "command.hpp"
#include "groupmap.h"
#include "listvector.hpp"
RemoveOtusCommand(string);
RemoveOtusCommand();
~RemoveOtusCommand(){}
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "remove.otus"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
+ string getDescription() { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
string accnosfile, groupfile, listfile, outputDir, groups, label;
bool abort;
vector<string> outputNames, Groups;
- map<string, vector<string> > outputTypes;
GroupMap* groupMap;
- void readAccnos();
int readListGroup();
int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);