summarycommand.h

   1 #ifndef SUMMARYCOMMAND_H
   2 #define SUMMARYCOMMAND_H
   3 /*
   4  *  summarycommand.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 "sabundvector.hpp"
  14 #include "inputdata.h"
  15 #include "calculator.h"
  16 #include "validcalculator.h"
  17
  18 class SummaryCommand : public Command {
  19
  20 public:
  21         SummaryCommand(string);
  22         SummaryCommand();
  23         ~SummaryCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "summary.single";                      }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
  32         string getDescription()         { return "generate summary file that has the calculator value for each line in the OTU data"; }
  33
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         vector<Calculator*> sumCalculators;
  40         InputData* input;
  41         SAbundVector* sabund;
  42         int abund, size, iters, subsampleSize;
  43
  44         bool abort, allLines, groupMode, subsample;
  45         set<string> labels; //holds labels to be used
  46         string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
  47         vector<string>  Estimators;
  48         vector<string> inputFileNames, outputNames;
  49         vector<string> groups;
  50
  51         vector<string> parseSharedFile(string);
  52         vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
  53     int process(SAbundVector*&, ofstream&, ofstream&);
  54
  55
  56 };
  57 #endif