binsequencecommand.h

   1 #ifndef BINSEQCOMMAND_H
   2 #define BINSEQCOMMAND_H
   3 /*
   4  *  binsequencecommand.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 4/3/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 /* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
  13
  14 #include "command.hpp"
  15 #include "inputdata.h"
  16 #include "listvector.hpp"
  17 #include "fastamap.h"
  18 #include "groupmap.h"
  19
  20 class BinSeqCommand : public Command {
  21
  22 public:
  23         BinSeqCommand(string);
  24         BinSeqCommand();
  25         ~BinSeqCommand();
  26
  27         vector<string> setParameters();
  28         string getCommandName()                 { return "bin.seqs";                    }
  29         string getCommandCategory()             { return "Sequence Processing"; }
  30         string getHelpString();
  31         string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
  32         string getDescription()         { return "maps sequences to otus"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38
  39         ListVector* list;
  40         InputData* input;
  41         FastaMap* fasta;
  42         GroupMap* groupMap;
  43         bool abort, allLines;
  44         set<string> labels; //holds labels to be used
  45         string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
  46         ofstream out;
  47         ifstream in, inNames;
  48         vector<string> outputNames;
  49
  50         void readNamesFile();
  51         int process(ListVector*);
  52 };
  53
  54 #endif