consensusseqscommand.h

   1 #ifndef CONSENSUSSEQSCOMMAND_H
   2 #define CONSENSUSSEQSCOMMAND_H
   3
   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
  29         int execute();
  30         void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33
  34         bool abort, allLines;
  35         string fastafile, listfile, namefile, label, outputDir;
  36         set<string> labels;
  37         vector<string> outputNames;
  38         map<string, string> fastaMap;
  39         map<string, string> nameMap;
  40         map<string, string> nameFileMap;
  41         int cutoff;
  42
  43         int readFasta();
  44         int readNames();
  45         int processList(ListVector*&);
  46         string getConsSeq(string, ofstream&, string&, int);
  47         char getBase(vector<int>, int);
  48 };
  49
  50 #endif
  51
  52
  53
  54