source/consensusseqscommand.h

   1 #ifndef CONSENSUSSEQSCOMMAND_H
   2 #define CONSENSUSSEQSCOMMAND_H
   3 //test
   4 /*
   5  *  consensusseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/23/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "listvector.hpp"
  16
  17 class ConsensusSeqsCommand : public Command {
  18 public:
  19         ConsensusSeqsCommand(string);
  20         ConsensusSeqsCommand();
  21         ~ConsensusSeqsCommand(){}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "consensus.seqs";              }
  25         string getCommandCategory()             { return "Sequence Processing"; }
  26         string getHelpString();
  27         string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
  28         string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
  29
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35
  36         bool abort, allLines;
  37         string fastafile, listfile, namefile, label, outputDir;
  38         set<string> labels;
  39         vector<string> outputNames;
  40         map<string, string> fastaMap;
  41         map<string, string> nameMap;
  42         map<string, string> nameFileMap;
  43         int cutoff;
  44
  45         int readFasta();
  46         int readNames();
  47         int processList(ListVector*&);
  48         string getConsSeq(string, ofstream&, string&, int);
  49         char getBase(vector<int>, int);
  50 };
  51
  52 #endif
  53
  54
  55
  56