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 "readotu.h"
  18 #include "fastamap.h"
  19 #include "groupmap.h"
  20
  21
  22 class GlobalData;
  23
  24 class BinSeqCommand : public Command {
  25
  26 public:
  27         BinSeqCommand(string);
  28         BinSeqCommand();
  29         ~BinSeqCommand();
  30         vector<string> getRequiredParameters();
  31         vector<string> getValidParameters();
  32         vector<string> getRequiredFiles();
  33         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  34         int execute();
  35         void help();
  36
  37 private:
  38         GlobalData* globaldata;
  39         ListVector* list;
  40         ReadOTUFile* read;
  41         InputData* input;
  42         FastaMap* fasta;
  43         GroupMap* groupMap;
  44         bool abort, allLines;
  45         set<string> labels; //holds labels to be used
  46         string filename, fastafile, namesfile, groupfile, label, outputDir;
  47         ofstream out;
  48         ifstream in, inNames;
  49         vector<string> outputNames;
  50         map<string, vector<string> > outputTypes;
  51
  52         void readNamesFile();
  53         int process(ListVector*);
  54 };
  55
  56 #endif