validcalculator.cpp

   1 /*
   2  *  validcalculator.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 "validcalculator.h"
  11
  12 /********************************************************************/
  13 ValidCalculators::ValidCalculators() {
  14         try {
  15                  initialSingle();
  16                  initialShared();
  17                  initialRarefaction();
  18                  initialSharedRarefact();
  19                  initialSummary();
  20                  initialSharedSummary();
  21         }
  22         catch(exception& e) {
  23                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26         catch(...) {
  27                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  28                 exit(1);
  29         }
  30 }
  31
  32 /********************************************************************/
  33
  34 ValidCalculators::~ValidCalculators() {}
  35
  36 /********************************************************************/
  37
  38 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  39         try {
  40                 //are you looking for a calculator for a single parameter
  41                 if (parameter == "single") {
  42                         //is it valid
  43                         if ((single.find(calculator)) != (single.end())) {
  44                                 return true;
  45                         }else {
  46                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  47                                 for (it = single.begin(); it != single.end(); it++) {
  48                                         cout << it->first << ", ";
  49                                 }
  50                                 cout << endl;
  51                                 return false; }
  52                 //are you looking for a calculator for a shared parameter
  53                 }else if (parameter == "shared") {
  54                         //is it valid
  55                         if ((shared.find(calculator)) != (shared.end())) {
  56                                 return true;
  57                         }else {
  58                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  59                                 for (it = shared.begin(); it != shared.end(); it++) {
  60                                         cout << it->first << ", ";
  61                                 }
  62                                 cout << endl;
  63                                 return false; }
  64                 //are you looking for a calculator for a rarefaction parameter
  65                 }else if (parameter == "rarefaction") {
  66                         //is it valid
  67                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  68                                 return true;
  69                         }else {
  70                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  71                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  72                                         cout << it->first << ", ";
  73                                 }
  74                                 cout << endl;
  75                                 return false; }
  76                 //are you looking for a calculator for a summary parameter
  77                 }else if (parameter == "summary") {
  78                         //is it valid
  79                         if ((summary.find(calculator)) != (summary.end())) {
  80                                 return true;
  81                         }else {
  82                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  83                                 for (it = summary.begin(); it != summary.end(); it++) {
  84                                         cout << it->first << ", ";
  85                                 }
  86                                 cout << endl;
  87                                 return false; }
  88                 //are you looking for a calculator for a sharedsummary parameter
  89                 }else if (parameter == "sharedsummary") {
  90                         //is it valid
  91                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  92                                 return true;
  93                         }else {
  94                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  95                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
  96                                         cout << it->first << ", ";
  97                                 }
  98                                 cout << endl;
  99                                 return false; }
 100                 }else if (parameter == "sharedrarefaction") {
 101                         //is it valid
 102                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 103                                 return true;
 104                         }else {
 105                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 106                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 107                                         cout << it->first << ", ";
 108                                 }
 109                                 cout << endl;
 110                                 return false; }
 111                 //not a valid paramter
 112                 }else { return false; }
 113
 114         }
 115         catch(exception& e) {
 116                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 117                 exit(1);
 118         }
 119         catch(...) {
 120                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 121                 exit(1);
 122         }
 123 }
 124
 125 /********************************************************************/
 126 void ValidCalculators::initialSingle() {
 127         try {
 128
 129                 single["sobs"]          = "sobs";
 130                 single["chao"]              = "chao";
 131                 single["ace"]               = "ace";
 132                 single["jack"]              = "jack";
 133                 single["shannon"]           = "shannon";
 134                 single["npshannon"]     = "npshannon";
 135                 single["simpson"]           = "simpson";
 136                 single["bergerparker"]  = "bergerparker";
 137                 single["bootstrap"]     = "bootstrap";
 138                 single["geom"]          = "geom";
 139                 single["logsd"]         = "logsd";
 140                 single["qstat"]         = "qstat";
 141                 single["bstick"]        = "bstick";
 142                 single["nseqs"]         = "nseqs";
 143                 single["default"]           = "default";
 144
 145         }
 146         catch(exception& e) {
 147                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 148                 exit(1);
 149         }
 150         catch(...) {
 151                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 152                 exit(1);
 153         }
 154 }
 155
 156 /********************************************************************/
 157 void ValidCalculators::initialShared() {
 158         try {
 159                 shared["sharedsobs"]                    = "sharedsobs";
 160                 shared["sharedchao"]                    = "sharedchao";
 161                 shared["sharedace"]                             = "sharedace";
 162                 shared["sharedjabund"]                  = "sharedjabund";
 163                 shared["sharedsorensonabund"]   = "sharedsorensonabund";
 164                 shared["sharedjclass"]                  = "sharedjclass";
 165                 shared["sharedsorclass"]                = "sharedsorclass";
 166                 shared["sharedjest"]                    = "sharedjest";
 167                 shared["sharedsorest"]                  = "sharedsorest";
 168                 shared["sharedthetayc"]                 = "sharedthetayc";
 169                 shared["sharedthetan"]                  = "sharedthetan";
 170                 shared["sharedkstest"]          = "sharedkstest";
 171                 shared["sharedbdiversity"]      = "sharedbdiversity";
 172                 shared["sharednseqs"]                   = "sharednseqs";
 173                 shared["sharedochiai"]                  = "sharedochiai";
 174                 shared["sharedanderberg"]               = "sharedanderberg";
 175                 shared["sharedkulczynski"]              = "sharedkulczynski";
 176                 shared["sharedkulczynskicody"]  = "sharedkulczynskicody";
 177                 shared["sharedlennon"]                  = "sharedlennon";
 178                 shared["sharedmorisitahorn"]    = "sharedmorisitahorn";
 179                 shared["sharedbraycurtis"]              = "sharedbraycurtis";
 180                 shared["default"]                   = "default";
 181         }
 182         catch(exception& e) {
 183                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 184                 exit(1);
 185         }
 186         catch(...) {
 187                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 188                 exit(1);
 189         }
 190 }
 191
 192 /********************************************************************/
 193 void ValidCalculators::initialRarefaction() {
 194         try {
 195                 rarefaction["sobs"]                     = "sobs";
 196                 rarefaction["chao"]                     = "chao";
 197                 rarefaction["ace"]                      = "ace";
 198                 rarefaction["jack"]                     = "jack";
 199                 rarefaction["shannon"]          = "shannon";
 200                 rarefaction["npshannon"]        = "npshannon";
 201                 rarefaction["simpson"]          = "simpson";
 202                 rarefaction["bootstrap"]        = "bootstrap";
 203                 rarefaction["nseqs"]            = "nseqs";
 204                 rarefaction["default"]      = "default";
 205         }
 206         catch(exception& e) {
 207                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210         catch(...) {
 211                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214 }
 215
 216 /********************************************************************/
 217
 218 void ValidCalculators::initialSummary() {
 219         try {
 220                 summary["sobs"]                 = "sobs";
 221                 summary["chao"]                 = "chao";
 222                 summary["ace"]                  = "ace";
 223                 summary["jack"]                 = "jack";
 224                 summary["shannon"]              = "shannon";
 225                 summary["npshannon"]    = "npshannon";
 226                 summary["simpson"]              = "simpson";
 227                 summary["bergerparker"] = "bergerparker";
 228                 summary["geom"]         = "geom";
 229                 summary["bootstrap"]    = "bootstrap";
 230                 summary["logsd"]        = "logsd";
 231                 summary["qstat"]        = "qstat";
 232                 summary["bstick"]       = "bstick";
 233                 summary["nseqs"]                = "nseqs";
 234                 summary["default"]          = "default";
 235         }
 236         catch(exception& e) {
 237                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 238                 exit(1);
 239         }
 240         catch(...) {
 241                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 242                 exit(1);
 243         }
 244 }
 245
 246 /********************************************************************/
 247 void ValidCalculators::initialSharedSummary() {
 248         try {
 249                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 250                 sharedsummary["sharedchao"]                             = "sharedchao";
 251                 sharedsummary["sharedace"]                              = "sharedace";
 252                 sharedsummary["sharedjabund"]                   = "sharedjabund";
 253                 sharedsummary["sharedsorensonabund"]    = "sharedsorensonabund";
 254                 sharedsummary["sharedjclass"]                   = "sharedjclass";
 255                 sharedsummary["sharedsorclass"]                 = "sharedsorclass";
 256                 sharedsummary["sharedjest"]                             = "sharedjest";
 257                 sharedsummary["sharedsorest"]                   = "sharedsorest";
 258                 sharedsummary["sharedthetayc"]                  = "sharedthetayc";
 259                 sharedsummary["sharedthetan"]                   = "sharedthetan";
 260                 sharedsummary["sharedkstest"]           = "sharedkstest";
 261                 sharedsummary["sharedbdiversity"]       = "sharedbdiversity";
 262                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 263                 sharedsummary["sharedochiai"]                   = "sharedochiai";
 264                 sharedsummary["sharedanderberg"]                = "sharedanderberg";
 265                 sharedsummary["sharedkulczynski"]               = "sharedkulczynski";
 266                 sharedsummary["sharedkulczynskicody"]   = "sharedkulczynskicody";
 267                 sharedsummary["sharedlennon"]                   = "sharedlennon";
 268                 sharedsummary["sharedmorisitahorn"]             = "sharedmorisitahorn";
 269                 sharedsummary["sharedbraycurtis"]               = "sharedbraycurtis";
 270                 sharedsummary["default"]                                = "default";
 271         }
 272         catch(exception& e) {
 273                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 274                 exit(1);
 275         }
 276         catch(...) {
 277                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 278                 exit(1);
 279         }
 280 }
 281
 282
 283 /********************************************************************/
 284
 285 void ValidCalculators::initialSharedRarefact() {
 286         try {
 287                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 288                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 289                 sharedrarefaction["default"]        = "default";
 290         }
 291         catch(exception& e) {
 292                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 293                 exit(1);
 294         }
 295         catch(...) {
 296                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 297                 exit(1);
 298         }
 299 }
 300
 301 /********************************************************************/
 302
 303
 304