collectsharedcommand.h

   1 #ifndef COLLECTSHAREDCOMMAND_H
   2 #define COLLECTSHAREDCOMMAND_H
   3 /*
   4  *  collectsharedcommand.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
  13 #include "command.hpp"
  14 #include "sharedordervector.h"
  15 #include "sharedlistvector.h"
  16 #include "inputdata.h"
  17 #include "groupmap.h"
  18 #include "collect.h"
  19 #include "display.h"
  20 #include "readotu.h"
  21 #include "validcalculator.h"
  22 #include "sharedutilities.h"
  23
  24 class GlobalData;
  25
  26 class CollectSharedCommand : public Command {
  27
  28 public:
  29         CollectSharedCommand(string);
  30         CollectSharedCommand();
  31         ~CollectSharedCommand();
  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         GlobalData* globaldata;
  41         SharedUtil* util;
  42         GroupMap* groupmap;
  43         SharedListVector* SharedList;
  44         ReadOTUFile* read;
  45         SharedOrderVector* order;
  46         InputData* input;
  47         ValidCalculators* validCalculator;
  48         Collect* cCurve;
  49         vector<Display*> cDisplays;
  50         float freq;
  51         string format;
  52
  53         bool abort, allLines, all;
  54         set<string> labels; //holds labels to be used
  55         string label, calc, groups, outputDir;
  56         vector<string>  Estimators, Groups, outputNames;
  57         map<string, vector<string> > outputTypes;
  58
  59
  60 };
  61
  62 #endif