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         vector<string> getRequiredParameters();
  23         vector<string> getValidParameters();
  24         vector<string> getRequiredFiles();
  25         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  26         int execute();
  27         void help();
  28
  29 private:
  30
  31         bool abort, allLines;
  32         string fastafile, listfile, namefile, label, outputDir;
  33         set<string> labels;
  34         vector<string> outputNames;
  35         map<string, vector<string> > outputTypes;
  36         map<string, string> fastaMap;
  37         map<string, string> nameMap;
  38         map<string, string> nameFileMap;
  39
  40         int readFasta();
  41         int readNames();
  42         int processList(ListVector*&);
  43         string getConsSeq(string, ofstream&, string&, int);
  44         char getBase(vector<int>);
  45 };
  46
  47 #endif
  48
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  51