removelineagecommand.h

   1 #ifndef REMOVELINEAGECOMMAND_H
   2 #define REMOVELINEAGECOMMAND_H
   3
   4 /*
   5  *  removelineagecommand.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
  18 class RemoveLineageCommand : public Command {
  19
  20         public:
  21
  22                 RemoveLineageCommand(string);
  23                 RemoveLineageCommand();
  24                 ~RemoveLineageCommand(){};
  25
  26                 vector<string> setParameters();
  27                 string getCommandName()                 { return "remove.lineage";                      }
  28                 string getCommandCategory()             { return "Phylotype Analysis";          }
  29
  30         string getHelpString();
  31     string getOutputPattern(string);
  32                 string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
  33                 string getDescription()         { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
  34
  35                 int execute();
  36                 void help() { m->mothurOut(getHelpString()); }
  37
  38         private:
  39                 set<string> names;
  40                 vector<string> outputNames, listOfTaxons;
  41                 string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
  42                 bool abort, dups;
  43         vector<SharedRAbundVector*> lookup;
  44         ListVector* list;
  45
  46                 int readFasta();
  47                 int readName();
  48                 int readGroup();
  49         int readCount();
  50                 int readAlign();
  51                 int readList();
  52                 int readTax();
  53         int readShared();
  54         int readConsTax();
  55         int readConsList();
  56         int getShared();
  57         int getListVector();
  58                 vector< map<string, float> > getTaxons(string);
  59 };
  60
  61 #endif
  62