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         string getHelpString();
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         void printSharedData(vector<SharedRAbundVector*>);
  40         int createMisMatchFile();
  41         int readOrderFile();
  42         bool isValidGroup(string, vector<string>);
  43         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  44
  45         SharedListVector* SharedList;
  46         InputData* input;
  47         GroupMap* groupMap;
  48         vector<string> Groups, outputNames, order;
  49         set<string> labels;
  50         ofstream out;
  51         string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
  52         bool firsttime, pickedGroups, abort, allLines;
  53         map<string, ofstream*> filehandles;
  54         map<string, ofstream*>::iterator it3;
  55
  56 };
  57
  58 #endif