summarysharedcommand.h

   1 #ifndef SUMMARYSHAREDCOMMAND_H
   2 #define SUMMARYSHAREDCOMMAND_H
   3 /*
   4  *  summarysharedcommand.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 "sharedrabundvector.h"
  15 #include "inputdata.h"
  16 #include "calculator.h"
  17 #include "validcalculator.h"
  18
  19 class SummarySharedCommand : public Command {
  20
  21 public:
  22         SummarySharedCommand(string);
  23         SummarySharedCommand();
  24         ~SummarySharedCommand() {}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "summary.shared";                      }
  28         string getCommandCategory()             { return "OTU-Based Approaches";        }
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35
  36 private:
  37         struct linePair {
  38                 int start;
  39                 int end;
  40         };
  41         vector<linePair> lines;
  42         vector<Calculator*> sumCalculators;
  43         InputData* input;
  44
  45         bool abort, allLines, mult, all, createPhylip;
  46         set<string> labels; //holds labels to be used
  47         string label, calc, groups, sharedfile;
  48         vector<string>  Estimators, Groups, outputNames;
  49         vector<SharedRAbundVector*> lookup;
  50         string format, outputDir;
  51         int numGroups, processors;
  52         int process(vector<SharedRAbundVector*>, string, string);
  53         int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
  54
  55 };
  56
  57 #endif