getgroupscommand.h

   1 #ifndef GETGROUPSCOMMAND_H
   2 #define GETGROUPSCOMMAND_H
   3
   4 /*
   5  *  getgroupscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/10/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "groupmap.h"
  16
  17 class GetGroupsCommand : public Command {
  18
  19 public:
  20
  21         GetGroupsCommand(string);
  22         GetGroupsCommand();
  23         ~GetGroupsCommand(){}
  24         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32         set<string> names;
  33         string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
  34         bool abort;
  35         vector<string> outputNames, Groups;
  36         map<string, vector<string> > outputTypes;
  37         GroupMap* groupMap;
  38
  39         int readFasta();
  40         int readName();
  41         int readGroup();
  42         void readAccnos();
  43         int readList();
  44         int readTax();
  45         int fillNames();
  46
  47 };
  48
  49 #endif
  50
  51
  52