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 <iostream>
  13 #include <fstream>
  14 #include <map>
  15 #include "command.hpp"
  16 #include "sharedlistvector.h"
  17 #include "inputdata.h"
  18 #include "shared.h"
  19 #include "readmatrix.hpp"
  20
  21 /* The shared() command:
  22         The shared command can only be executed after a successful read.shared command.
  23         The shared command parses a .list file and separates it into groups.
  24         It outputs a .shared file containing the OTU information for each group.
  25         There are no shared command parameters.  The shared command should be in the following format: shared(). */
  26
  27
  28 class GlobalData;
  29
  30 class SharedCommand : public Command {
  31
  32 public:
  33         SharedCommand();
  34         ~SharedCommand();
  35         int execute();
  36
  37 private:
  38         void printSharedData();
  39         GlobalData* globaldata;
  40         ReadMatrix* read;
  41         SharedListVector* SharedList;
  42         InputData* input;
  43         Shared* shared;
  44         map<string, SharedRAbundVector*>::iterator it;
  45         ofstream out;
  46         string filename;
  47
  48 };
  49
  50 #endif