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         string getOutputFileNameTag(string, string);
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
  30         string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
  31
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37
  38     CountTable ct;
  39         bool abort, allLines;
  40         string fastafile, listfile, namefile, countfile, label, outputDir;
  41         set<string> labels;
  42         vector<string> outputNames;
  43         map<string, string> fastaMap;
  44         map<string, string> nameMap;
  45         map<string, int> nameFileMap;
  46         int cutoff, seqLength;
  47
  48         int readFasta();
  49         int readNames();
  50         int processList(ListVector*&);
  51         string getConsSeq(string, ofstream&, int);
  52         char getBase(vector<int>, int);
  53 };
  54
  55 #endif
  56
  57
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  59