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