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                  initialDistance();
  26         }
  27         catch(exception& e) {
  28                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  29                 exit(1);
  30         }
  31         catch(...) {
  32                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  33                 exit(1);
  34         }
  35 }
  36
  37 /********************************************************************/
  38
  39 ValidCalculators::~ValidCalculators() {}
  40
  41 /********************************************************************/
  42
  43 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  44         try {
  45                 //are you looking for a calculator for a single parameter
  46                 if (parameter == "single") {
  47                         //is it valid
  48                         if ((single.find(calculator)) != (single.end())) {
  49                                 return true;
  50                         }else {
  51                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  52                                 for (it = single.begin(); it != single.end(); it++) {
  53                                         cout << it->first << ", ";
  54                                 }
  55                                 cout << endl;
  56                                 return false; }
  57                 //are you looking for a calculator for a shared parameter
  58                 }else if (parameter == "shared") {
  59                         //is it valid
  60                         if ((shared.find(calculator)) != (shared.end())) {
  61                                 return true;
  62                         }else {
  63                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  64                                 for (it = shared.begin(); it != shared.end(); it++) {
  65                                         cout << it->first << ", ";
  66                                 }
  67                                 cout << endl;
  68                                 return false; }
  69                 //are you looking for a calculator for a rarefaction parameter
  70                 }else if (parameter == "rarefaction") {
  71                         //is it valid
  72                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  73                                 return true;
  74                         }else {
  75                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  76                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  77                                         cout << it->first << ", ";
  78                                 }
  79                                 cout << endl;
  80                                 return false; }
  81                 //are you looking for a calculator for a summary parameter
  82                 }else if (parameter == "summary") {
  83                         //is it valid
  84                         if ((summary.find(calculator)) != (summary.end())) {
  85                                 return true;
  86                         }else {
  87                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  88                                 for (it = summary.begin(); it != summary.end(); it++) {
  89                                         cout << it->first << ", ";
  90                                 }
  91                                 cout << endl;
  92                                 return false; }
  93                 //are you looking for a calculator for a sharedsummary parameter
  94                 }else if (parameter == "sharedsummary") {
  95                         //is it valid
  96                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  97                                 return true;
  98                         }else {
  99                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
 100                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 101                                         cout << it->first << ", ";
 102                                 }
 103                                 cout << endl;
 104                                 return false; }
 105                 }else if (parameter == "sharedrarefaction") {
 106                         //is it valid
 107                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 108                                 return true;
 109                         }else {
 110                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 111                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 112                                         cout << it->first << ", ";
 113                                 }
 114                                 cout << endl;
 115                                 return false; }
 116                 }else if (parameter == "vennsingle") {
 117                         //is it valid
 118                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 119                                 return true;
 120                         }else {
 121                                 cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
 122                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 123                                         cout << it->first << ", ";
 124                                 }
 125                                 cout << endl;
 126                                 return false; }
 127                 }else if (parameter == "vennshared") {
 128                         //is it valid
 129                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 130                                 return true;
 131                         }else {
 132                                 cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
 133                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 134                                         cout << it->first << ", ";
 135                                 }
 136                                 cout << endl;
 137                                 return false; }
 138                 }else if (parameter == "treegroup") {
 139                         //is it valid
 140                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 141                                 return true;
 142                         }else {
 143                                 cout << calculator << " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ";
 144                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 145                                         cout << it->first << ", ";
 146                                 }
 147                                 cout << endl;
 148                                 return false; }
 149                 }else if (parameter == "boot") {
 150                         //is it valid
 151                         if ((boot.find(calculator)) != (boot.end())) {
 152                                 return true;
 153                         }else {
 154                                 cout << calculator << " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ";
 155                                 for (it = boot.begin(); it != boot.end(); it++) {
 156                                         cout << it->first << ", ";
 157                                 }
 158                                 cout << endl;
 159                                 return false; }
 160                 }else if (parameter == "distance") {
 161                         //is it valid
 162                         if ((distance.find(calculator)) != (distance.end())) {
 163                                 return true;
 164                         }else {
 165                                 cout << calculator << " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ";
 166                                 for (it = distance.begin(); it != distance.end(); it++) {
 167                                         cout << it->first << ", ";
 168                                 }
 169                                 cout << endl;
 170                                 return false; }
 171                 //not a valid parameter
 172                 }else { return false; }
 173
 174         }
 175         catch(exception& e) {
 176                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179         catch(...) {
 180                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 181                 exit(1);
 182         }
 183 }
 184
 185 /********************************************************************/
 186 void ValidCalculators::initialSingle() {
 187         try {
 188                 single["sobs"]          = "sobs";
 189                 single["chao"]              = "chao";
 190                 single["ace"]               = "ace";
 191                 single["jack"]              = "jack";
 192                 single["shannon"]           = "shannon";
 193                 single["npshannon"]     = "npshannon";
 194                 single["simpson"]           = "simpson";
 195                 single["bergerparker"]  = "bergerparker";
 196                 single["bootstrap"]     = "bootstrap";
 197                 single["geometric"]     = "geometric";
 198                 single["logseries"]         = "logseries";
 199                 single["qstat"]         = "qstat";
 200                 single["bstick"]        = "bstick";
 201                 single["goodscoverage"] = "goodscoverage";
 202                 single["nseqs"]                 = "nseqs";
 203                 single["coverage"]              = "coverage";
 204                 single["efron"]         = "efron";
 205                 single["boneh"]         = "boneh";
 206                 single["solow"]         = "solow";
 207                 single["default"]           = "default";
 208         }
 209         catch(exception& e) {
 210                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 211                 exit(1);
 212         }
 213         catch(...) {
 214                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 215                 exit(1);
 216         }
 217 }
 218
 219 /********************************************************************/
 220 void ValidCalculators::initialShared() {
 221         try {
 222                 shared["sharedsobs"]                    = "sharedsobs";
 223                 shared["sharedchao"]                    = "sharedchao";
 224                 shared["sharedace"]                             = "sharedace";
 225                 shared["jabund"]                                = "jabund";
 226                 shared["sorabund"]                              = "sorabund";
 227                 shared["jclass"]                                = "jclass";
 228                 shared["sorclass"]                              = "sorclass";
 229                 shared["jest"]                                  = "jest";
 230                 shared["sorest"]                                = "sorest";
 231                 shared["thetayc"]                               = "thetayc";
 232                 shared["thetan"]                                = "thetan";
 233                 shared["kstest"]                                = "kstest";
 234                 shared["whittaker"]                         = "whittaker";
 235                 shared["sharednseqs"]                   = "sharednseqs";
 236                 shared["ochiai"]                                = "ochiai";
 237                 shared["anderberg"]                             = "anderberg";
 238                 shared["kulczynski"]                    = "kulczynski";
 239                 shared["kulczynskicody"]                = "kulczynskicody";
 240                 shared["lennon"]                                = "lennon";
 241                 shared["morisitahorn"]                  = "morisitahorn";
 242                 shared["braycurtis"]                    = "braycurtis";
 243                 shared["default"]                   = "default";
 244         }
 245         catch(exception& e) {
 246                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 247                 exit(1);
 248         }
 249         catch(...) {
 250                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 251                 exit(1);
 252         }
 253 }
 254
 255 /********************************************************************/
 256 void ValidCalculators::initialRarefaction() {
 257         try {
 258                 rarefaction["sobs"]                     = "sobs";
 259                 rarefaction["chao"]                     = "chao";
 260                 rarefaction["ace"]                      = "ace";
 261                 rarefaction["jack"]                     = "jack";
 262                 rarefaction["shannon"]          = "shannon";
 263                 rarefaction["npshannon"]        = "npshannon";
 264                 rarefaction["simpson"]          = "simpson";
 265                 rarefaction["bootstrap"]        = "bootstrap";
 266                 rarefaction["nseqs"]            = "nseqs";
 267                 rarefaction["coverage"]         = "coverage";
 268                 rarefaction["default"]      = "default";
 269         }
 270         catch(exception& e) {
 271                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 272                 exit(1);
 273         }
 274         catch(...) {
 275                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 276                 exit(1);
 277         }
 278 }
 279
 280 /********************************************************************/
 281
 282 void ValidCalculators::initialSummary() {
 283         try {
 284                 summary["sobs"]                 = "sobs";
 285                 summary["chao"]                 = "chao";
 286                 summary["ace"]                  = "ace";
 287                 summary["jack"]                 = "jack";
 288                 summary["shannon"]              = "shannon";
 289                 summary["npshannon"]    = "npshannon";
 290                 summary["simpson"]              = "simpson";
 291                 summary["bergerparker"] = "bergerparker";
 292                 summary["geometric"]    = "geometric";
 293                 summary["bootstrap"]    = "bootstrap";
 294                 summary["logseries"]    = "logseries";
 295                 summary["qstat"]        = "qstat";
 296                 summary["bstick"]       = "bstick";
 297                 summary["nseqs"]                = "nseqs";
 298                 summary["goodscoverage"]= "goodscoverage";
 299                 summary["coverage"]             = "coverage";
 300                 summary["efron"]        = "efron";
 301                 summary["boneh"]        = "boneh";
 302                 summary["solow"]        = "solow";
 303                 summary["default"]          = "default";
 304         }
 305         catch(exception& e) {
 306                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 307                 exit(1);
 308         }
 309         catch(...) {
 310                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 311                 exit(1);
 312         }
 313 }
 314
 315 /********************************************************************/
 316 void ValidCalculators::initialSharedSummary() {
 317         try {
 318                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 319                 sharedsummary["sharedchao"]                             = "sharedchao";
 320                 sharedsummary["sharedace"]                              = "sharedace";
 321                 sharedsummary["jabund"]                                 = "jabund";
 322                 sharedsummary["sorabund"]                       = "sorabund";
 323                 sharedsummary["jclass"]                                 = "jclass";
 324                 sharedsummary["sorclass"]                               = "sorclass";
 325                 sharedsummary["jest"]                                   = "jest";
 326                 sharedsummary["sorest"]                                 = "sorest";
 327                 sharedsummary["thetayc"]                                = "thetayc";
 328                 sharedsummary["thetan"]                                 = "thetan";
 329                 sharedsummary["kstest"]                                 = "kstest";
 330                 sharedsummary["whittaker"]                              = "whittaker";
 331                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 332                 sharedsummary["ochiai"]                                 = "ochiai";
 333                 sharedsummary["anderberg"]                              = "anderberg";
 334                 sharedsummary["kulczynski"]                             = "kulczynski";
 335                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 336                 sharedsummary["lennon"]                                 = "lennon";
 337                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 338                 sharedsummary["braycurtis"]                             = "braycurtis";
 339                 sharedsummary["default"]                                = "default";
 340         }
 341         catch(exception& e) {
 342                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 343                 exit(1);
 344         }
 345         catch(...) {
 346                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 347                 exit(1);
 348         }
 349 }
 350
 351
 352 /********************************************************************/
 353
 354 void ValidCalculators::initialSharedRarefact() {
 355         try {
 356                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 357                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 358                 sharedrarefaction["default"]        = "default";
 359         }
 360         catch(exception& e) {
 361                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 362                 exit(1);
 363         }
 364         catch(...) {
 365                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 366                 exit(1);
 367         }
 368 }
 369
 370
 371 /********************************************************************/
 372 void ValidCalculators::initialVennSingle() {
 373         try {
 374                 vennsingle["sobs"]              = "sobs";
 375                 vennsingle["chao"]                  = "chao";
 376                 vennsingle["ace"]                       = "ace";
 377                 vennsingle["jack"]                  = "jack";
 378                 vennsingle["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::initialVennShared() {
 392         try {
 393                 vennshared["sharedsobs"]        = "sharedsobs";
 394                 vennshared["sharedchao"]        = "sharedchao";
 395                 vennshared["sharedace"]         = "sharedace";
 396                 vennshared["default"]           = "default";
 397         }
 398         catch(exception& e) {
 399                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 400                 exit(1);
 401         }
 402         catch(...) {
 403                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 404                 exit(1);
 405         }
 406 }
 407
 408 /********************************************************************/
 409 void ValidCalculators::initialTreeGroups() {
 410         try {
 411                 treegroup["jabund"]                                     = "jabund";
 412                 treegroup["sorabund"]                           = "sorabund";
 413                 treegroup["jclass"]                                     = "jclass";
 414                 treegroup["sorclass"]                           = "sorclass";
 415                 treegroup["jest"]                                       = "jest";
 416                 treegroup["sorest"]                                     = "sorest";
 417                 treegroup["thetayc"]                            = "thetayc";
 418                 treegroup["thetan"]                                     = "thetan";
 419                 treegroup["morisitahorn"]                       = "morisitahorn";
 420                 treegroup["braycurtis"]                         = "braycurtis";
 421         }
 422         catch(exception& e) {
 423                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 424                 exit(1);
 425         }
 426         catch(...) {
 427                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 428                 exit(1);
 429         }
 430 }
 431 /********************************************************************/
 432 void ValidCalculators::initialBoot() {
 433         try {
 434                 boot["jabund"]                          = "jabund";
 435                 boot["sorabund"]                        = "sorabund";
 436                 boot["jclass"]                          = "jclass";
 437                 boot["sorclass"]                        = "orclass";
 438                 boot["jest"]                            = "jest";
 439                 boot["sorest"]                          = "sorest";
 440                 boot["thetayc"]                         = "thetayc";
 441                 boot["thetan"]                          = "thetan";
 442                 boot["morisitahorn"]            = "morisitahorn";
 443                 boot["braycurtis"]                      = "braycurtis";
 444         }
 445         catch(exception& e) {
 446                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 447                 exit(1);
 448         }
 449         catch(...) {
 450                 cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 451                 exit(1);
 452         }
 453 }
 454 /********************************************************************/
 455 void ValidCalculators::initialDistance() {
 456         try {
 457                 distance["nogaps"]              = "nogaps";
 458                 distance["eachgap"]             = "eachgap";
 459                 distance["onegap"]              = "onegap";
 460         }
 461         catch(exception& e) {
 462                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 463                 exit(1);
 464         }
 465         catch(...) {
 466                 cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 467                 exit(1);
 468         }
 469 }
 470
 471 /********************************************************************/
 472 void ValidCalculators::printCalc(string parameter, ostream& out) {
 473         try{
 474                 out << "The available estimators for calc are ";
 475                 //are you looking for a calculator for a single parameter
 476                 if (parameter == "single") {
 477                         for (it = single.begin(); it != single.end(); it++) {
 478                                 out << it->first << ", ";
 479                         }
 480                 //are you looking for a calculator for a shared parameter
 481                 }else if (parameter == "shared") {
 482                         for (it = shared.begin(); it != shared.end(); it++) {
 483                                 out << it->first << ", ";
 484                         }
 485                 //are you looking for a calculator for a rarefaction parameter
 486                 }else if (parameter == "rarefaction") {
 487                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 488                                 out << it->first << ", ";
 489                         }
 490                 //are you looking for a calculator for a summary parameter
 491                 }else if (parameter == "summary") {
 492                         for (it = summary.begin(); it != summary.end(); it++) {
 493                                 out << it->first << ", ";
 494                         }
 495                 //are you looking for a calculator for a sharedsummary parameter
 496                 }else if (parameter == "sharedsummary") {
 497                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 498                                 out << it->first << ", ";
 499                         }
 500                 }else if (parameter == "sharedrarefaction") {
 501                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 502                                 out << it->first << ", ";
 503                         }
 504                 }else if (parameter == "vennsingle") {
 505                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 506                                 out << it->first << ", ";
 507                         }
 508                 }else if (parameter == "vennshared") {
 509                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 510                                 out << it->first << ", ";
 511                         }
 512                 }else if (parameter == "treegroup") {
 513                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 514                                 out << it->first << ", ";
 515                         }
 516                 }else if (parameter == "boot") {
 517                         for (it = boot.begin(); it != boot.end(); it++) {
 518                                 out << it->first << ", ";
 519                         }
 520                 }else if (parameter == "distance") {
 521                         for (it = distance.begin(); it != distance.end(); it++) {
 522                                 out << it->first << ", ";
 523                         }
 524                 }
 525
 526                 out << endl;
 527         }
 528         catch(exception& e) {
 529                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 530                 exit(1);
 531         }
 532         catch(...) {
 533                 cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 534                 exit(1);
 535         }
 536
 537 }
 538 /********************************************************************/
 539