+++ /dev/null
-#ifndef REMOVEOTUSCOMMAND_H
-#define REMOVEOTUSCOMMAND_H
-
-/*
- * removeotuscommand.h
- * Mothur
- *
- * Created by westcott on 11/12/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "groupmap.h"
-#include "listvector.hpp"
-
-class RemoveOtusCommand : public Command {
-
-public:
-
- RemoveOtusCommand(string);
- RemoveOtusCommand();
- ~RemoveOtusCommand(){}
-
- vector<string> setParameters();
- string getCommandName() { return "remove.otus"; }
- string getCommandCategory() { return "OTU-Based Approaches"; }
- string getHelpString();
- 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;
- GroupMap* groupMap;
-
- void readAccnos();
- int readListGroup();
- int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
-
-};
-
-#endif
-
-
-
-