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