removerarecommand.h

   1 #ifndef REMOVERARECOMMAND_H
   2 #define REMOVERARECOMMAND_H
   3
   4 /*
   5  *  removerarecommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 1/21/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "listvector.hpp"
  16
  17 class RemoveRareCommand : public Command {
  18
  19 public:
  20
  21         RemoveRareCommand(string);
  22         RemoveRareCommand();
  23         ~RemoveRareCommand(){}
  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         string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
  33         int nseqs, allLines;
  34         bool abort, byGroup;
  35         vector<string> outputNames, Groups;
  36         set<string> labels;
  37         map<string, vector<string> > outputTypes;
  38
  39         int processSabund();
  40         int processRabund();
  41         int processList();
  42         int processShared();
  43
  44 };
  45
  46 #endif
  47
  48
  49
  50