getlineagecommand.h

   1 #ifndef GETLINEAGECOMMAND_H
   2 #define GETLINEAGECOMMAND_H
   3
   4 /*
   5  *  getlineagecommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/24/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 class GetLineageCommand : public Command {
  16
  17         public:
  18
  19                 GetLineageCommand(string);
  20                 GetLineageCommand();
  21                 ~GetLineageCommand(){};
  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                 set<string> names;
  31                 vector<string> outputNames;
  32                 string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
  33                 bool abort, dups;
  34                 map<string, vector<string> > outputTypes;
  35
  36                 int readFasta();
  37                 int readName();
  38                 int readGroup();
  39                 int readAlign();
  40                 int readList();
  41                 int readTax();
  42                 string removeConfidences(string);
  43 };
  44
  45 #endif
  46