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 #include "counttable.h"
  17
  18 class ConsensusSeqsCommand : public Command {
  19 public:
  20         ConsensusSeqsCommand(string);
  21         ConsensusSeqsCommand();
  22         ~ConsensusSeqsCommand(){}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "consensus.seqs";              }
  26         string getCommandCategory()             { return "Sequence Processing"; }
  27
  28         string getHelpString();
  29     string getOutputPattern(string);
  30         string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
  31         string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
  32
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38
  39     CountTable ct;
  40         bool abort, allLines;
  41         string fastafile, listfile, namefile, countfile, label, outputDir;
  42         set<string> labels;
  43         vector<string> outputNames;
  44         map<string, string> fastaMap;
  45         map<string, string> nameMap;
  46         map<string, int> nameFileMap;
  47         int cutoff, seqLength;
  48
  49         int readFasta();
  50         int readNames();
  51         int processList(ListVector*&);
  52         string getConsSeq(string, ofstream&, int);
  53         char getBase(vector<int>, int);
  54 };
  55
  56 #endif
  57
  58
  59
  60