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 #include "sharedrabundvector.h"
  15 #include "listvector.hpp"
  16
  17 class GetLineageCommand : public Command {
  18
  19         public:
  20
  21                 GetLineageCommand(string);
  22                 GetLineageCommand();
  23                 ~GetLineageCommand(){}
  24
  25                 vector<string> setParameters();
  26                 string getCommandName()                 { return "get.lineage";                         }
  27                 string getCommandCategory()             { return "Phylotype Analysis";          }
  28
  29         string getHelpString();
  30     string getOutputPattern(string);
  31                 string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
  32                 string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
  33
  34
  35                 int execute();
  36                 void help() { m->mothurOut(getHelpString()); }
  37
  38
  39         private:
  40                 set<string> names;
  41                 vector<string> outputNames, listOfTaxons;
  42                 string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
  43                 bool abort, dups;
  44         vector<SharedRAbundVector*> lookup;
  45         ListVector* list;
  46
  47                 int readFasta();
  48                 int readName();
  49         int readCount();
  50                 int readGroup();
  51                 int readAlign();
  52                 int readList();
  53                 int readTax();
  54         int readShared();
  55         int readConsTax();
  56         int readConsList();
  57         int getShared();
  58         int getListVector();
  59                 vector< map<string, float> > getTaxons(string);
  60 };
  61
  62 #endif
  63