validparameter.cpp

   1 /*
   2  *  validparameter.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/5/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "validparameter.h"
  11
  12 /***********************************************************************/
  13
  14 ValidParameters::ValidParameters() {
  15         try {
  16
  17                 parameters["phylip"]            = "phylip";
  18                 parameters["column"]            = "column";
  19                 parameters["list"]                      = "list";
  20                 parameters["rabund"]            = "rabund";
  21                 parameters["sabund"]            = "sabund";
  22                 parameters["name"]                      = "name";
  23                 parameters["group"]                     = "group";
  24                 parameters["order"]                     = "order";
  25                 parameters["fasta"]                     = "fasta";
  26                 parameters["tree"]                      = "tree";
  27                 parameters["fileroot"]                  = "fileroot";
  28                 parameters["cutoff"]                    = "cutoff";
  29                 parameters["method"]                    = "method";
  30                 parameters["format"]                    = "format";
  31                 parameters["precision"]                 = "precision";
  32                 parameters["label"]                             = "label";
  33                 parameters["line"]                              = "line";
  34                 parameters["iters"]                             = "iters";
  35                 parameters["jumble"]                    = "jumble";
  36                 parameters["freq"]                              = "freq";
  37                 parameters["single"]                    = "single";
  38                 parameters["rarefaction"]               = "rarefaction";
  39                 parameters["sharedrarefaction"] = "sharedrarefaction";
  40                 parameters["shared"]                    = "shared";
  41                 parameters["summary"]                   = "summary";
  42                 parameters["sharedsummary"]             = "sharedsummary";
  43                 parameters["random"]                    = "random";
  44                 parameters["groups"]                    = "groups";
  45                 parameters["calc"]                              = "calc";
  46
  47         }
  48         catch(exception& e) {
  49                 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  50                 exit(1);
  51         }
  52         catch(...) {
  53                 cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56 }
  57
  58 /***********************************************************************/
  59
  60 ValidParameters::~ValidParameters() {}
  61
  62 /***********************************************************************/
  63 bool ValidParameters::isValidParameter(string parameter) {
  64         try {
  65
  66                 //is the parameter in the map
  67                 if ((parameters.find(parameter)) != (parameters.end())) {
  68                         return true;
  69                 }else{
  70                         cout << parameter << " is not a valid parameter in Mothur. Valid parameters are " << endl;
  71                         for (it = parameters.begin(); it != parameters.end(); it++) {
  72                                 cout << it->first << ", ";
  73                         }
  74                         cout << endl;
  75
  76                         return false;
  77                 }
  78
  79         }
  80         catch(exception& e) {
  81                 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  82                 exit(1);
  83         }
  84         catch(...) {
  85                 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  86                 exit(1);
  87         }
  88 }
  89
  90 /***********************************************************************/