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 #include "counttable.h"
  20
  21
  22 class SubSampleCommand : public Command {
  23
  24 public:
  25         SubSampleCommand(string);
  26         SubSampleCommand();
  27         ~SubSampleCommand() {}
  28
  29         vector<string> setParameters();
  30         string getCommandName()                 { return "sub.sample";  }
  31         string getCommandCategory()             { return "Sequence Processing";         }
  32
  33         string getHelpString();
  34     string getOutputPattern(string);
  35         string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
  36         string getDescription()         { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
  37
  38         int execute();
  39         void help() { m->mothurOut(getHelpString()); }
  40
  41 private:
  42         bool abort, pickedGroups, allLines, persample;
  43         string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile, taxonomyfile;
  44         set<string> labels; //holds labels to be used
  45         string groups, label, outputDir;
  46         vector<string> Groups, outputNames;
  47         int size;
  48         vector<string> names;
  49         map<string, vector<string> > nameMap;
  50     CountTable ct;
  51
  52         int getSubSampleShared();
  53         int getSubSampleList();
  54         int getSubSampleRabund();
  55         int getSubSampleSabund();
  56         int getSubSampleFasta();
  57         int processShared(vector<SharedRAbundVector*>&);
  58         int processRabund(RAbundVector*&, ofstream&);
  59         int processSabund(SAbundVector*&, ofstream&);
  60         int processList(ListVector*&, ofstream&, set<string>&);
  61         int getNames();
  62         int readNames();
  63     int getTax(set<string>&);
  64
  65 };
  66
  67 #endif
  68