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         string getDescription()         { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         struct linePair {
  39                 int start;
  40                 int end;
  41         };
  42         vector<linePair> lines;
  43         vector<Calculator*> sumCalculators;
  44         InputData* input;
  45
  46         bool abort, allLines, mult, all, createPhylip;
  47         set<string> labels; //holds labels to be used
  48         string label, calc, groups, sharedfile;
  49         vector<string>  Estimators, Groups, outputNames;
  50         vector<SharedRAbundVector*> lookup;
  51         string format, outputDir;
  52         int numGroups, processors;
  53         int process(vector<SharedRAbundVector*>, string, string);
  54         int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
  55
  56 };
  57
  58 #endif