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                  initialTreeGroups();
  24                  initialBoot();
  25         }
  26         catch(exception& e) {
  27                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  28                 exit(1);
  29         }
  30         catch(...) {
  31                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  32                 exit(1);
  33         }
  34 }
  35
  36 /********************************************************************/
  37
  38 ValidCalculators::~ValidCalculators() {}
  39
  40 /********************************************************************/
  41
  42 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  43         try {
  44                 //are you looking for a calculator for a single parameter
  45                 if (parameter == "single") {
  46                         //is it valid
  47                         if ((single.find(calculator)) != (single.end())) {
  48                                 return true;
  49                         }else {
  50                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  51                                 for (it = single.begin(); it != single.end(); it++) {
  52                                         cout << it->first << ", ";
  53                                 }
  54                                 cout << endl;
  55                                 return false; }
  56                 //are you looking for a calculator for a shared parameter
  57                 }else if (parameter == "shared") {
  58                         //is it valid
  59                         if ((shared.find(calculator)) != (shared.end())) {
  60                                 return true;
  61                         }else {
  62                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  63                                 for (it = shared.begin(); it != shared.end(); it++) {
  64                                         cout << it->first << ", ";
  65                                 }
  66                                 cout << endl;
  67                                 return false; }
  68                 //are you looking for a calculator for a rarefaction parameter
  69                 }else if (parameter == "rarefaction") {
  70                         //is it valid
  71                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  72                                 return true;
  73                         }else {
  74                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  75                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  76                                         cout << it->first << ", ";
  77                                 }
  78                                 cout << endl;
  79                                 return false; }
  80                 //are you looking for a calculator for a summary parameter
  81                 }else if (parameter == "summary") {
  82                         //is it valid
  83                         if ((summary.find(calculator)) != (summary.end())) {
  84                                 return true;
  85                         }else {
  86                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  87                                 for (it = summary.begin(); it != summary.end(); it++) {
  88                                         cout << it->first << ", ";
  89                                 }
  90                                 cout << endl;
  91                                 return false; }
  92                 //are you looking for a calculator for a sharedsummary parameter
  93                 }else if (parameter == "sharedsummary") {
  94                         //is it valid
  95                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  96                                 return true;
  97                         }else {
  98                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  99                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 100                                         cout << it->first << ", ";
 101                                 }
 102                                 cout << endl;
 103                                 return false; }
 104                 }else if (parameter == "sharedrarefaction") {
 105                         //is it valid
 106                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 107                                 return true;
 108                         }else {
 109                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 110                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 111                                         cout << it->first << ", ";
 112                                 }
 113                                 cout << endl;
 114                                 return false; }
 115                 }else if (parameter == "vennsingle") {
 116                         //is it valid
 117                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 118                                 return true;
 119                         }else {
 120                                 cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
 121                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 122                                         cout << it->first << ", ";
 123                                 }
 124                                 cout << endl;
 125                                 return false; }
 126                 }else if (parameter == "vennshared") {
 127                         //is it valid
 128                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 129                                 return true;
 130                         }else {
 131                                 cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
 132                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 133                                         cout << it->first << ", ";
 134                                 }
 135                                 cout << endl;
 136                                 return false; }
 137                 }else if (parameter == "treegroup") {
 138                         //is it valid
 139                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 140                                 return true;
 141                         }else {
 142                                 cout << calculator << " is not a valid estimator for the tree.shared command in shared mode and will be disregarded. Valid estimators are ";
 143                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 144                                         cout << it->first << ", ";
 145                                 }
 146                                 cout << endl;
 147                                 return false; }
 148                 }else if (parameter == "boot") {
 149                         //is it valid
 150                         if ((boot.find(calculator)) != (boot.end())) {
 151                                 return true;
 152                         }else {
 153                                 cout << calculator << " is not a valid estimator for the bootstrap.shared command in shared mode and will be disregarded. Valid estimators are ";
 154                                 for (it = boot.begin(); it != boot.end(); it++) {
 155                                         cout << it->first << ", ";
 156                                 }
 157                                 cout << endl;
 158                                 return false; }
 159                 //not a valid parameter
 160                 }else { return false; }
 161
 162         }
 163         catch(exception& e) {
 164                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167         catch(...) {
 168                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 169                 exit(1);
 170         }
 171 }
 172
 173 /********************************************************************/
 174 void ValidCalculators::initialSingle() {
 175         try {
 176                 single["sobs"]          = "sobs";
 177                 single["chao"]              = "chao";
 178                 single["ace"]               = "ace";
 179                 single["jack"]              = "jack";
 180                 single["shannon"]           = "shannon";
 181                 single["npshannon"]     = "npshannon";
 182                 single["simpson"]           = "simpson";
 183                 single["bergerparker"]  = "bergerparker";
 184                 single["bootstrap"]     = "bootstrap";
 185                 single["geometric"]     = "geometric";
 186                 single["logseries"]         = "logseries";
 187                 single["qstat"]         = "qstat";
 188                 single["bstick"]        = "bstick";
 189                 single["goodscoverage"] = "goodscoverage";
 190                 single["nseqs"]                 = "nseqs";
 191                 single["coverage"]              = "coverage";
 192                 single["default"]           = "default";
 193         }
 194         catch(exception& e) {
 195                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198         catch(...) {
 199                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202 }
 203
 204 /********************************************************************/
 205 void ValidCalculators::initialShared() {
 206         try {
 207                 shared["sharedsobs"]                    = "sharedsobs";
 208                 shared["sharedchao"]                    = "sharedchao";
 209                 shared["sharedace"]                             = "sharedace";
 210                 shared["jabund"]                                = "jabund";
 211                 shared["sorabund"]                      = "sorabund";
 212                 shared["jclass"]                                = "jclass";
 213                 shared["sorclass"]                              = "sorclass";
 214                 shared["jest"]                                  = "jest";
 215                 shared["sorest"]                                = "sorest";
 216                 shared["thetayc"]                               = "thetayc";
 217                 shared["thetan"]                                = "thetan";
 218                 shared["kstest"]                                = "kstest";
 219                 shared["whittaker"]                         = "whittaker";
 220                 shared["sharednseqs"]                   = "sharednseqs";
 221                 shared["ochiai"]                                = "ochiai";
 222                 shared["anderberg"]                             = "anderberg";
 223                 shared["kulczynski"]                    = "kulczynski";
 224                 shared["kulczynskicody"]                = "kulczynskicody";
 225                 shared["lennon"]                                = "lennon";
 226                 shared["morisitahorn"]                  = "morisitahorn";
 227                 shared["braycurtis"]                    = "braycurtis";
 228                 shared["default"]                   = "default";
 229         }
 230         catch(exception& e) {
 231                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 232                 exit(1);
 233         }
 234         catch(...) {
 235                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 236                 exit(1);
 237         }
 238 }
 239
 240 /********************************************************************/
 241 void ValidCalculators::initialRarefaction() {
 242         try {
 243                 rarefaction["sobs"]                     = "sobs";
 244                 rarefaction["chao"]                     = "chao";
 245                 rarefaction["ace"]                      = "ace";
 246                 rarefaction["jack"]                     = "jack";
 247                 rarefaction["shannon"]          = "shannon";
 248                 rarefaction["npshannon"]        = "npshannon";
 249                 rarefaction["simpson"]          = "simpson";
 250                 rarefaction["bootstrap"]        = "bootstrap";
 251                 rarefaction["nseqs"]            = "nseqs";
 252                 rarefaction["coverage"]         = "coverage";
 253                 rarefaction["default"]      = "default";
 254         }
 255         catch(exception& e) {
 256                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 257                 exit(1);
 258         }
 259         catch(...) {
 260                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 261                 exit(1);
 262         }
 263 }
 264
 265 /********************************************************************/
 266
 267 void ValidCalculators::initialSummary() {
 268         try {
 269                 summary["sobs"]                 = "sobs";
 270                 summary["chao"]                 = "chao";
 271                 summary["ace"]                  = "ace";
 272                 summary["jack"]                 = "jack";
 273                 summary["shannon"]              = "shannon";
 274                 summary["npshannon"]    = "npshannon";
 275                 summary["simpson"]              = "simpson";
 276                 summary["bergerparker"] = "bergerparker";
 277                 summary["geometric"]    = "geometric";
 278                 summary["bootstrap"]    = "bootstrap";
 279                 summary["logseries"]    = "logseries";
 280                 summary["qstat"]        = "qstat";
 281                 summary["bstick"]       = "bstick";
 282                 summary["nseqs"]                = "nseqs";
 283                 summary["goodscoverage"]= "goodscoverage";
 284                 summary["coverage"]             = "coverage";
 285                 summary["default"]          = "default";
 286         }
 287         catch(exception& e) {
 288                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 289                 exit(1);
 290         }
 291         catch(...) {
 292                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 293                 exit(1);
 294         }
 295 }
 296
 297 /********************************************************************/
 298 void ValidCalculators::initialSharedSummary() {
 299         try {
 300                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 301                 sharedsummary["sharedchao"]                             = "sharedchao";
 302                 sharedsummary["sharedace"]                              = "sharedace";
 303                 sharedsummary["jabund"]                                 = "jabund";
 304                 sharedsummary["sorabund"]                       = "sorabund";
 305                 sharedsummary["jclass"]                                 = "jclass";
 306                 sharedsummary["sorclass"]                               = "sorclass";
 307                 sharedsummary["jest"]                                   = "jest";
 308                 sharedsummary["sorest"]                                 = "sorest";
 309                 sharedsummary["thetayc"]                                = "thetayc";
 310                 sharedsummary["thetan"]                                 = "thetan";
 311                 sharedsummary["kstest"]                                 = "kstest";
 312                 sharedsummary["whittaker"]                              = "whittaker";
 313                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 314                 sharedsummary["ochiai"]                                 = "ochiai";
 315                 sharedsummary["anderberg"]                              = "anderberg";
 316                 sharedsummary["kulczynski"]                             = "kulczynski";
 317                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 318                 sharedsummary["lennon"]                                 = "lennon";
 319                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 320                 sharedsummary["braycurtis"]                             = "braycurtis";
 321                 sharedsummary["default"]                                = "default";
 322         }
 323         catch(exception& e) {
 324                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 325                 exit(1);
 326         }
 327         catch(...) {
 328                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 329                 exit(1);
 330         }
 331 }
 332
 333
 334 /********************************************************************/
 335
 336 void ValidCalculators::initialSharedRarefact() {
 337         try {
 338                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 339                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 340                 sharedrarefaction["default"]        = "default";
 341         }
 342         catch(exception& e) {
 343                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 344                 exit(1);
 345         }
 346         catch(...) {
 347                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 348                 exit(1);
 349         }
 350 }
 351
 352
 353 /********************************************************************/
 354 void ValidCalculators::initialVennSingle() {
 355         try {
 356                 vennsingle["sobs"]              = "sobs";
 357                 vennsingle["chao"]                  = "chao";
 358                 vennsingle["ace"]                       = "ace";
 359                 vennsingle["jack"]                  = "jack";
 360                 vennsingle["default"]           = "default";
 361         }
 362         catch(exception& e) {
 363                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 364                 exit(1);
 365         }
 366         catch(...) {
 367                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 368                 exit(1);
 369         }
 370 }
 371
 372 /********************************************************************/
 373 void ValidCalculators::initialVennShared() {
 374         try {
 375                 vennshared["sharedsobs"]        = "sharedsobs";
 376                 vennshared["sharedchao"]        = "sharedchao";
 377                 vennshared["sharedace"]         = "sharedace";
 378                 vennshared["default"]           = "default";
 379         }
 380         catch(exception& e) {
 381                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 382                 exit(1);
 383         }
 384         catch(...) {
 385                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 386                 exit(1);
 387         }
 388 }
 389
 390 /********************************************************************/
 391 void ValidCalculators::initialTreeGroups() {
 392         try {
 393                 treegroup["jabund"]                                     = "jabund";
 394                 treegroup["sorabund"]                   = "sorabund";
 395                 treegroup["jclass"]                                     = "jclass";
 396                 treegroup["sorclass"]                           = "sorclass";
 397                 treegroup["jest"]                                       = "jest";
 398                 treegroup["sorest"]                                     = "sorest";
 399                 treegroup["thetayc"]                            = "thetayc";
 400                 treegroup["thetan"]                                     = "thetan";
 401                 treegroup["morisitahorn"]                       = "morisitahorn";
 402                 treegroup["braycurtis"]                 = "braycurtis";
 403         }
 404         catch(exception& e) {
 405                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 406                 exit(1);
 407         }
 408         catch(...) {
 409                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 410                 exit(1);
 411         }
 412 }
 413 /********************************************************************/
 414 void ValidCalculators::initialBoot() {
 415         try {
 416                 boot["jabund"]                          = "jabund";
 417                 boot["sorabund"]                = "sorabund";
 418                 boot["jclass"]                          = "jclass";
 419                 boot["sorclass"]                        = "orclass";
 420                 boot["jest"]                            = "jest";
 421                 boot["sorest"]                          = "sorest";
 422                 boot["thetayc"]                         = "thetayc";
 423                 boot["thetan"]                          = "thetan";
 424                 boot["morisitahorn"]            = "morisitahorn";
 425                 boot["braycurtis"]                      = "braycurtis";
 426         }
 427         catch(exception& e) {
 428                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 429                 exit(1);
 430         }
 431         catch(...) {
 432                 cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 433                 exit(1);
 434         }
 435 }
 436
 437 /********************************************************************/
 438 void ValidCalculators::printCalc(string parameter, ostream& out) {
 439         try{
 440                 out << "The available estimators for calc are ";
 441                 //are you looking for a calculator for a single parameter
 442                 if (parameter == "single") {
 443                         for (it = single.begin(); it != single.end(); it++) {
 444                                 out << it->first << ", ";
 445                         }
 446                 //are you looking for a calculator for a shared parameter
 447                 }else if (parameter == "shared") {
 448                         for (it = shared.begin(); it != shared.end(); it++) {
 449                                 out << it->first << ", ";
 450                         }
 451                 //are you looking for a calculator for a rarefaction parameter
 452                 }else if (parameter == "rarefaction") {
 453                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 454                                 out << it->first << ", ";
 455                         }
 456                 //are you looking for a calculator for a summary parameter
 457                 }else if (parameter == "summary") {
 458                         for (it = summary.begin(); it != summary.end(); it++) {
 459                                 out << it->first << ", ";
 460                         }
 461                 //are you looking for a calculator for a sharedsummary parameter
 462                 }else if (parameter == "sharedsummary") {
 463                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 464                                 out << it->first << ", ";
 465                         }
 466                 }else if (parameter == "sharedrarefaction") {
 467                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 468                                 out << it->first << ", ";
 469                         }
 470                 }else if (parameter == "vennsingle") {
 471                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 472                                 out << it->first << ", ";
 473                         }
 474                 }else if (parameter == "vennshared") {
 475                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 476                                 out << it->first << ", ";
 477                         }
 478                 }else if (parameter == "treegroup") {
 479                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 480                                 out << it->first << ", ";
 481                         }
 482                 }else if (parameter == "boot") {
 483                         for (it = boot.begin(); it != boot.end(); it++) {
 484                                 out << it->first << ", ";
 485                         }
 486                 }
 487                 out << endl;
 488         }
 489         catch(exception& e) {
 490                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 491                 exit(1);
 492         }
 493         catch(...) {
 494                 cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 495                 exit(1);
 496         }
 497
 498 }
 499 /********************************************************************/
 500