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                  initialVennSingle();
  22                  initialVennShared();
  23         }
  24         catch(exception& e) {
  25                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  26                 exit(1);
  27         }
  28         catch(...) {
  29                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32 }
  33
  34 /********************************************************************/
  35
  36 ValidCalculators::~ValidCalculators() {}
  37
  38 /********************************************************************/
  39
  40 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  41         try {
  42                 //are you looking for a calculator for a single parameter
  43                 if (parameter == "single") {
  44                         //is it valid
  45                         if ((single.find(calculator)) != (single.end())) {
  46                                 return true;
  47                         }else {
  48                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  49                                 for (it = single.begin(); it != single.end(); it++) {
  50                                         cout << it->first << ", ";
  51                                 }
  52                                 cout << endl;
  53                                 return false; }
  54                 //are you looking for a calculator for a shared parameter
  55                 }else if (parameter == "shared") {
  56                         //is it valid
  57                         if ((shared.find(calculator)) != (shared.end())) {
  58                                 return true;
  59                         }else {
  60                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  61                                 for (it = shared.begin(); it != shared.end(); it++) {
  62                                         cout << it->first << ", ";
  63                                 }
  64                                 cout << endl;
  65                                 return false; }
  66                 //are you looking for a calculator for a rarefaction parameter
  67                 }else if (parameter == "rarefaction") {
  68                         //is it valid
  69                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  70                                 return true;
  71                         }else {
  72                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  73                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  74                                         cout << it->first << ", ";
  75                                 }
  76                                 cout << endl;
  77                                 return false; }
  78                 //are you looking for a calculator for a summary parameter
  79                 }else if (parameter == "summary") {
  80                         //is it valid
  81                         if ((summary.find(calculator)) != (summary.end())) {
  82                                 return true;
  83                         }else {
  84                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  85                                 for (it = summary.begin(); it != summary.end(); it++) {
  86                                         cout << it->first << ", ";
  87                                 }
  88                                 cout << endl;
  89                                 return false; }
  90                 //are you looking for a calculator for a sharedsummary parameter
  91                 }else if (parameter == "sharedsummary") {
  92                         //is it valid
  93                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  94                                 return true;
  95                         }else {
  96                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  97                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
  98                                         cout << it->first << ", ";
  99                                 }
 100                                 cout << endl;
 101                                 return false; }
 102                 }else if (parameter == "sharedrarefaction") {
 103                         //is it valid
 104                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 105                                 return true;
 106                         }else {
 107                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 108                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 109                                         cout << it->first << ", ";
 110                                 }
 111                                 cout << endl;
 112                                 return false; }
 113                 }else if (parameter == "vennsingle") {
 114                         //is it valid
 115                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 116                                 return true;
 117                         }else {
 118                                 cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
 119                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 120                                         cout << it->first << ", ";
 121                                 }
 122                                 cout << endl;
 123                                 return false; }
 124                 }else if (parameter == "vennshared") {
 125                         //is it valid
 126                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 127                                 return true;
 128                         }else {
 129                                 cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
 130                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 131                                         cout << it->first << ", ";
 132                                 }
 133                                 cout << endl;
 134                                 return false; }
 135                 //not a valid parameter
 136                 }else { return false; }
 137
 138         }
 139         catch(exception& e) {
 140                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 141                 exit(1);
 142         }
 143         catch(...) {
 144                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 145                 exit(1);
 146         }
 147 }
 148
 149 /********************************************************************/
 150 void ValidCalculators::initialSingle() {
 151         try {
 152                 single["sobs"]          = "sobs";
 153                 single["chao"]              = "chao";
 154                 single["ace"]               = "ace";
 155                 single["jack"]              = "jack";
 156                 single["shannon"]           = "shannon";
 157                 single["npshannon"]     = "npshannon";
 158                 single["simpson"]           = "simpson";
 159                 single["bergerparker"]  = "bergerparker";
 160                 single["bootstrap"]     = "bootstrap";
 161                 single["geom"]          = "geom";
 162                 single["logsd"]         = "logsd";
 163                 single["qstat"]         = "qstat";
 164                 single["bstick"]        = "bstick";
 165                 single["nseqs"]         = "nseqs";
 166                 single["default"]           = "default";
 167         }
 168         catch(exception& e) {
 169                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172         catch(...) {
 173                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176 }
 177
 178 /********************************************************************/
 179 void ValidCalculators::initialShared() {
 180         try {
 181                 shared["sharedsobs"]                    = "sharedsobs";
 182                 shared["sharedchao"]                    = "sharedchao";
 183                 shared["sharedace"]                             = "sharedace";
 184                 shared["sharedjabund"]                  = "sharedjabund";
 185                 shared["sharedsorensonabund"]   = "sharedsorensonabund";
 186                 shared["sharedjclass"]                  = "sharedjclass";
 187                 shared["sharedsorclass"]                = "sharedsorclass";
 188                 shared["sharedjest"]                    = "sharedjest";
 189                 shared["sharedsorest"]                  = "sharedsorest";
 190                 shared["sharedthetayc"]                 = "sharedthetayc";
 191                 shared["sharedthetan"]                  = "sharedthetan";
 192                 shared["sharedkstest"]          = "sharedkstest";
 193                 shared["sharedbdiversity"]      = "sharedbdiversity";
 194                 shared["sharednseqs"]                   = "sharednseqs";
 195                 shared["sharedochiai"]                  = "sharedochiai";
 196                 shared["sharedanderberg"]               = "sharedanderberg";
 197                 shared["sharedkulczynski"]              = "sharedkulczynski";
 198                 shared["sharedkulczynskicody"]  = "sharedkulczynskicody";
 199                 shared["sharedlennon"]                  = "sharedlennon";
 200                 shared["sharedmorisitahorn"]    = "sharedmorisitahorn";
 201                 shared["sharedbraycurtis"]              = "sharedbraycurtis";
 202                 shared["default"]                   = "default";
 203         }
 204         catch(exception& e) {
 205                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 206                 exit(1);
 207         }
 208         catch(...) {
 209                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 210                 exit(1);
 211         }
 212 }
 213
 214 /********************************************************************/
 215 void ValidCalculators::initialRarefaction() {
 216         try {
 217                 rarefaction["sobs"]                     = "sobs";
 218                 rarefaction["chao"]                     = "chao";
 219                 rarefaction["ace"]                      = "ace";
 220                 rarefaction["jack"]                     = "jack";
 221                 rarefaction["shannon"]          = "shannon";
 222                 rarefaction["npshannon"]        = "npshannon";
 223                 rarefaction["simpson"]          = "simpson";
 224                 rarefaction["bootstrap"]        = "bootstrap";
 225                 rarefaction["nseqs"]            = "nseqs";
 226                 rarefaction["default"]      = "default";
 227         }
 228         catch(exception& e) {
 229                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 230                 exit(1);
 231         }
 232         catch(...) {
 233                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 234                 exit(1);
 235         }
 236 }
 237
 238 /********************************************************************/
 239
 240 void ValidCalculators::initialSummary() {
 241         try {
 242                 summary["sobs"]                 = "sobs";
 243                 summary["chao"]                 = "chao";
 244                 summary["ace"]                  = "ace";
 245                 summary["jack"]                 = "jack";
 246                 summary["shannon"]              = "shannon";
 247                 summary["npshannon"]    = "npshannon";
 248                 summary["simpson"]              = "simpson";
 249                 summary["bergerparker"] = "bergerparker";
 250                 summary["geom"]         = "geom";
 251                 summary["bootstrap"]    = "bootstrap";
 252                 summary["logsd"]        = "logsd";
 253                 summary["qstat"]        = "qstat";
 254                 summary["bstick"]       = "bstick";
 255                 summary["nseqs"]                = "nseqs";
 256                 summary["default"]          = "default";
 257         }
 258         catch(exception& e) {
 259                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 260                 exit(1);
 261         }
 262         catch(...) {
 263                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 264                 exit(1);
 265         }
 266 }
 267
 268 /********************************************************************/
 269 void ValidCalculators::initialSharedSummary() {
 270         try {
 271                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 272                 sharedsummary["sharedchao"]                             = "sharedchao";
 273                 sharedsummary["sharedace"]                              = "sharedace";
 274                 sharedsummary["sharedjabund"]                   = "sharedjabund";
 275                 sharedsummary["sharedsorensonabund"]    = "sharedsorensonabund";
 276                 sharedsummary["sharedjclass"]                   = "sharedjclass";
 277                 sharedsummary["sharedsorclass"]                 = "sharedsorclass";
 278                 sharedsummary["sharedjest"]                             = "sharedjest";
 279                 sharedsummary["sharedsorest"]                   = "sharedsorest";
 280                 sharedsummary["sharedthetayc"]                  = "sharedthetayc";
 281                 sharedsummary["sharedthetan"]                   = "sharedthetan";
 282                 sharedsummary["sharedkstest"]           = "sharedkstest";
 283                 sharedsummary["sharedbdiversity"]       = "sharedbdiversity";
 284                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 285                 sharedsummary["sharedochiai"]                   = "sharedochiai";
 286                 sharedsummary["sharedanderberg"]                = "sharedanderberg";
 287                 sharedsummary["sharedkulczynski"]               = "sharedkulczynski";
 288                 sharedsummary["sharedkulczynskicody"]   = "sharedkulczynskicody";
 289                 sharedsummary["sharedlennon"]                   = "sharedlennon";
 290                 sharedsummary["sharedmorisitahorn"]             = "sharedmorisitahorn";
 291                 sharedsummary["sharedbraycurtis"]               = "sharedbraycurtis";
 292                 sharedsummary["default"]                                = "default";
 293         }
 294         catch(exception& e) {
 295                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 296                 exit(1);
 297         }
 298         catch(...) {
 299                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 300                 exit(1);
 301         }
 302 }
 303
 304
 305 /********************************************************************/
 306
 307 void ValidCalculators::initialSharedRarefact() {
 308         try {
 309                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 310                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 311                 sharedrarefaction["default"]        = "default";
 312         }
 313         catch(exception& e) {
 314                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 315                 exit(1);
 316         }
 317         catch(...) {
 318                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 319                 exit(1);
 320         }
 321 }
 322
 323
 324 /********************************************************************/
 325 void ValidCalculators::initialVennSingle() {
 326         try {
 327                 vennsingle["sobs"]              = "sobs";
 328                 vennsingle["chao"]                  = "chao";
 329                 vennsingle["ace"]                               = "ace";
 330                 vennsingle["jack"]                  = "jack";
 331                 vennsingle["default"]                   = "default";
 332         }
 333         catch(exception& e) {
 334                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 335                 exit(1);
 336         }
 337         catch(...) {
 338                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 339                 exit(1);
 340         }
 341 }
 342
 343 /********************************************************************/
 344 void ValidCalculators::initialVennShared() {
 345         try {
 346                 vennshared["sharedsobs"]        = "sharedsobs";
 347                 vennshared["sharedchao"]        = "sharedchao";
 348                 vennshared["sharedace"]         = "sharedace";
 349                 vennshared["default"]           = "default";
 350         }
 351         catch(exception& e) {
 352                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 353                 exit(1);
 354         }
 355         catch(...) {
 356                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 357                 exit(1);
 358         }
 359 }
 360
 361 /********************************************************************/
 362
 363
 364