subsamplecommand.h

   1 #ifndef SUBSAMPLECOMMAND_H
   2 #define SUBSAMPLECOMMAND_H
   3
   4 /*
   5  *  subsamplecommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 10/27/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "sharedrabundvector.h"
  15 #include "listvector.hpp"
  16 #include "rabundvector.hpp"
  17 #include "inputdata.h"
  18 #include "sequence.hpp"
  19
  20
  21 class SubSampleCommand : public Command {
  22
  23 public:
  24         SubSampleCommand(string);
  25         SubSampleCommand();
  26         ~SubSampleCommand() {}
  27
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "sub.sample";  }
  30         string getCommandCategory()             { return "General";             }
  31         string getHelpString();
  32         string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38         bool abort, pickedGroups, allLines, persample;
  39         string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
  40         set<string> labels; //holds labels to be used
  41         string groups, label, outputDir;
  42         vector<string> Groups, outputNames;
  43         int size;
  44         vector<string> names;
  45         map<string, vector<string> > nameMap;
  46
  47         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  48         int getSubSampleShared();
  49         int getSubSampleList();
  50         int getSubSampleRabund();
  51         int getSubSampleSabund();
  52         int getSubSampleFasta();
  53         int processShared(vector<SharedRAbundVector*>&, ofstream&);
  54         int processRabund(RAbundVector*&, ofstream&);
  55         int processSabund(SAbundVector*&, ofstream&);
  56         int processList(ListVector*&, ofstream&, set<string>&);
  57         int getNames();
  58         int readNames();
  59
  60 };
  61
  62 #endif
  63