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 #include "readotu.h"
  16
  17 /* The shared() command:
  18         The shared command can only be executed after a successful read.shared command.
  19         The shared command parses a .list file and separates it into groups.
  20         It outputs a .shared file containing the OTU information for each group.
  21         There are no shared command parameters.  The shared command should be in the following format: shared(). */
  22
  23
  24 class GlobalData;
  25
  26 class SharedCommand : public Command {
  27
  28 public:
  29         SharedCommand(string);
  30         SharedCommand();
  31         ~SharedCommand();
  32         vector<string> getRequiredParameters();
  33         vector<string> getValidParameters();
  34         vector<string> getRequiredFiles();
  35         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  36         int execute();
  37         void help() {}
  38
  39 private:
  40         void printSharedData(vector<SharedRAbundVector*>);
  41         int createMisMatchFile();
  42         int readOrderFile();
  43         bool isValidGroup(string, vector<string>);
  44         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  45         map<string, vector<string> > outputTypes;
  46
  47         GlobalData* globaldata;
  48         ReadOTUFile* read;
  49         SharedListVector* SharedList;
  50         InputData* input;
  51         GroupMap* groupMap;
  52         vector<string> groups, outputNames, order;
  53         ofstream out;
  54         string filename, fileroot, outputDir;
  55         bool firsttime, pickedGroups;
  56         map<string, ofstream*> filehandles;
  57         map<string, ofstream*>::iterator it3;
  58
  59 };
  60
  61 #endif