sharedcommand.h

   1 #ifndef SHAREDCOMMAND_H
   2 #define SHAREDCOMMAND_H
   3 /*
   4  *  sharedcommand.h
   5  *  Dotur
   6  *
   7  *  Created by Sarah Westcott on 1/2/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "sharedlistvector.h"
  14 #include "inputdata.h"
  15
  16 /* The shared() command:
  17         The shared command can only be executed after a successful read.shared command.
  18         The shared command parses a .list file and separates it into groups.
  19         It outputs a .shared file containing the OTU information for each group.
  20         There are no shared command parameters.  The shared command should be in the following format: shared(). */
  21
  22
  23 class SharedCommand : public Command {
  24
  25 public:
  26         SharedCommand(string);
  27         SharedCommand();
  28         ~SharedCommand();
  29
  30         vector<string> setParameters();
  31         string getCommandName()                 { return "make.shared";                         }
  32         string getCommandCategory()             { return "OTU-Based Approaches";        }
  33
  34         string getHelpString();
  35     string getOutputPattern(string);
  36         string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
  37         string getDescription()         { return "make a shared file from a list and group file"; }
  38
  39         int execute();
  40         void help() { m->mothurOut(getHelpString()); }
  41
  42 private:
  43         void printSharedData(vector<SharedRAbundVector*>, ofstream&);
  44         int readOrderFile();
  45         bool isValidGroup(string, vector<string>);
  46         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  47         int ListGroupSameSeqs(vector<string>&, SharedListVector*);
  48     int createSharedFromListGroup(string);
  49     int createSharedFromBiom(string);
  50     string getTag(string&);
  51     vector<string> readRows(string, int&);
  52     int getDims(string, int&, int&);
  53     vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
  54
  55         vector<string> Groups, outputNames, order;
  56         set<string> labels;
  57         string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
  58         bool firsttime, pickedGroups, abort, allLines;
  59         map<string, ofstream*> filehandles;
  60         map<string, ofstream*>::iterator it3;
  61
  62 };
  63
  64 #endif