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 "readotu.h"
  18 #include "validcalculator.h"
  19
  20 class GlobalData;
  21
  22 class SummarySharedCommand : public Command {
  23
  24 public:
  25         SummarySharedCommand(string);
  26         SummarySharedCommand();
  27         ~SummarySharedCommand();
  28         vector<string> getRequiredParameters();
  29         vector<string> getValidParameters();
  30         vector<string> getRequiredFiles();
  31         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  32         int execute();
  33         void help();
  34
  35 private:
  36         struct linePair {
  37                 int start;
  38                 int end;
  39         };
  40         vector<linePair> lines;
  41         GlobalData* globaldata;
  42         ReadOTUFile* read;
  43         vector<Calculator*> sumCalculators;
  44         InputData* input;
  45         ValidCalculators* validCalculator;
  46
  47         bool abort, allLines, mult, all, createPhylip;
  48         set<string> labels; //holds labels to be used
  49         string label, calc, groups;
  50         vector<string>  Estimators, Groups, outputNames;
  51         map<string, vector<string> > outputTypes;
  52         vector<SharedRAbundVector*> lookup;
  53         string format, outputDir;
  54         int numGroups, processors;
  55         int process(vector<SharedRAbundVector*>, string, string);
  56         int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
  57
  58 };
  59
  60 #endif