errorchecking.h

   1 #ifndef ERRORCHECKING_H
   2 #define ERRORCHECKING_H
   3 /*
   4  *  errorchecking.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 "mothur.h"
  13 #include "globaldata.hpp"
  14 #include "validcommands.h"
  15 #include "validparameter.h"
  16
  17
  18 class ErrorCheck {
  19         public:
  20                 ErrorCheck();
  21                 ~ErrorCheck();
  22                 bool checkInput(string);
  23
  24         private:
  25                 GlobalData* globaldata;
  26                 ValidCommands* validCommand;
  27                 ValidParameters* validParameter;
  28                 void validateReadFiles();
  29                 void validateReadDist();
  30                 void validateReadPhil();
  31                 void validateParseFiles();
  32                 void validateTreeFiles();
  33                 void validateBinFiles();
  34                 void validateSeqsFiles();
  35                 void clear();
  36                 void refresh();
  37                 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, cutoff, format;
  38                 string precision, method, fileroot, label, line, iters, jumble, freq, single, rarefaction, shared, summary, randomtree, abund, sorted, trump, soft, filter, scale, ends, processors, size;
  39                 string candidatefile, search, ksize, align, match, mismatch, gapopen, gapextend;
  40                 string commandName, optionText;
  41                 bool errorFree;
  42
  43                 vector<string> sharedGroups;
  44 };
  45 #endif