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["shen"]          = "shen";
 208                 single["default"]           = "default";
 209         }
 210         catch(exception& e) {
 211                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214         catch(...) {
 215                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 216                 exit(1);
 217         }
 218 }
 219
 220 /********************************************************************/
 221 void ValidCalculators::initialShared() {
 222         try {
 223                 shared["sharedsobs"]                    = "sharedsobs";
 224                 shared["sharedchao"]                    = "sharedchao";
 225                 shared["sharedace"]                             = "sharedace";
 226                 shared["jabund"]                                = "jabund";
 227                 shared["sorabund"]                              = "sorabund";
 228                 shared["jclass"]                                = "jclass";
 229                 shared["sorclass"]                              = "sorclass";
 230                 shared["jest"]                                  = "jest";
 231                 shared["sorest"]                                = "sorest";
 232                 shared["thetayc"]                               = "thetayc";
 233                 shared["thetan"]                                = "thetan";
 234                 shared["kstest"]                                = "kstest";
 235                 shared["whittaker"]                         = "whittaker";
 236                 shared["sharednseqs"]                   = "sharednseqs";
 237                 shared["ochiai"]                                = "ochiai";
 238                 shared["anderberg"]                             = "anderberg";
 239                 shared["kulczynski"]                    = "kulczynski";
 240                 shared["kulczynskicody"]                = "kulczynskicody";
 241                 shared["lennon"]                                = "lennon";
 242                 shared["morisitahorn"]                  = "morisitahorn";
 243                 shared["braycurtis"]                    = "braycurtis";
 244                 shared["default"]                   = "default";
 245         }
 246         catch(exception& e) {
 247                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 248                 exit(1);
 249         }
 250         catch(...) {
 251                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 252                 exit(1);
 253         }
 254 }
 255
 256 /********************************************************************/
 257 void ValidCalculators::initialRarefaction() {
 258         try {
 259                 rarefaction["sobs"]                     = "sobs";
 260                 rarefaction["chao"]                     = "chao";
 261                 rarefaction["ace"]                      = "ace";
 262                 rarefaction["jack"]                     = "jack";
 263                 rarefaction["shannon"]          = "shannon";
 264                 rarefaction["npshannon"]        = "npshannon";
 265                 rarefaction["simpson"]          = "simpson";
 266                 rarefaction["bootstrap"]        = "bootstrap";
 267                 rarefaction["nseqs"]            = "nseqs";
 268                 rarefaction["coverage"]         = "coverage";
 269                 rarefaction["default"]      = "default";
 270         }
 271         catch(exception& e) {
 272                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 273                 exit(1);
 274         }
 275         catch(...) {
 276                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 277                 exit(1);
 278         }
 279 }
 280
 281 /********************************************************************/
 282
 283 void ValidCalculators::initialSummary() {
 284         try {
 285                 summary["sobs"]                 = "sobs";
 286                 summary["chao"]                 = "chao";
 287                 summary["ace"]                  = "ace";
 288                 summary["jack"]                 = "jack";
 289                 summary["shannon"]              = "shannon";
 290                 summary["npshannon"]    = "npshannon";
 291                 summary["simpson"]              = "simpson";
 292                 summary["bergerparker"] = "bergerparker";
 293                 summary["geometric"]    = "geometric";
 294                 summary["bootstrap"]    = "bootstrap";
 295                 summary["logseries"]    = "logseries";
 296                 summary["qstat"]        = "qstat";
 297                 summary["bstick"]       = "bstick";
 298                 summary["nseqs"]                = "nseqs";
 299                 summary["goodscoverage"]= "goodscoverage";
 300                 summary["coverage"]             = "coverage";
 301                 summary["efron"]        = "efron";
 302                 summary["boneh"]        = "boneh";
 303                 summary["solow"]        = "solow";
 304                 summary["shen"]         = "shen";
 305                 summary["default"]          = "default";
 306         }
 307         catch(exception& e) {
 308                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 309                 exit(1);
 310         }
 311         catch(...) {
 312                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 313                 exit(1);
 314         }
 315 }
 316
 317 /********************************************************************/
 318 void ValidCalculators::initialSharedSummary() {
 319         try {
 320                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 321                 sharedsummary["sharedchao"]                             = "sharedchao";
 322                 sharedsummary["sharedace"]                              = "sharedace";
 323                 sharedsummary["jabund"]                                 = "jabund";
 324                 sharedsummary["sorabund"]                       = "sorabund";
 325                 sharedsummary["jclass"]                                 = "jclass";
 326                 sharedsummary["sorclass"]                               = "sorclass";
 327                 sharedsummary["jest"]                                   = "jest";
 328                 sharedsummary["sorest"]                                 = "sorest";
 329                 sharedsummary["thetayc"]                                = "thetayc";
 330                 sharedsummary["thetan"]                                 = "thetan";
 331                 sharedsummary["kstest"]                                 = "kstest";
 332                 sharedsummary["whittaker"]                              = "whittaker";
 333                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 334                 sharedsummary["ochiai"]                                 = "ochiai";
 335                 sharedsummary["anderberg"]                              = "anderberg";
 336                 sharedsummary["kulczynski"]                             = "kulczynski";
 337                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 338                 sharedsummary["lennon"]                                 = "lennon";
 339                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 340                 sharedsummary["braycurtis"]                             = "braycurtis";
 341                 sharedsummary["default"]                                = "default";
 342         }
 343         catch(exception& e) {
 344                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 345                 exit(1);
 346         }
 347         catch(...) {
 348                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 349                 exit(1);
 350         }
 351 }
 352
 353
 354 /********************************************************************/
 355
 356 void ValidCalculators::initialSharedRarefact() {
 357         try {
 358                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 359                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 360                 sharedrarefaction["default"]        = "default";
 361         }
 362         catch(exception& e) {
 363                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. 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 initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 368                 exit(1);
 369         }
 370 }
 371
 372
 373 /********************************************************************/
 374 void ValidCalculators::initialVennSingle() {
 375         try {
 376                 vennsingle["sobs"]              = "sobs";
 377                 vennsingle["chao"]                  = "chao";
 378                 vennsingle["ace"]                       = "ace";
 379                 vennsingle["jack"]                  = "jack";
 380                 vennsingle["default"]           = "default";
 381         }
 382         catch(exception& e) {
 383                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 384                 exit(1);
 385         }
 386         catch(...) {
 387                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 388                 exit(1);
 389         }
 390 }
 391
 392 /********************************************************************/
 393 void ValidCalculators::initialVennShared() {
 394         try {
 395                 vennshared["sharedsobs"]        = "sharedsobs";
 396                 vennshared["sharedchao"]        = "sharedchao";
 397                 vennshared["sharedace"]         = "sharedace";
 398                 vennshared["default"]           = "default";
 399         }
 400         catch(exception& e) {
 401                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 402                 exit(1);
 403         }
 404         catch(...) {
 405                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 406                 exit(1);
 407         }
 408 }
 409
 410 /********************************************************************/
 411 void ValidCalculators::initialTreeGroups() {
 412         try {
 413                 treegroup["jabund"]                                     = "jabund";
 414                 treegroup["sorabund"]                           = "sorabund";
 415                 treegroup["jclass"]                                     = "jclass";
 416                 treegroup["sorclass"]                           = "sorclass";
 417                 treegroup["jest"]                                       = "jest";
 418                 treegroup["sorest"]                                     = "sorest";
 419                 treegroup["thetayc"]                            = "thetayc";
 420                 treegroup["thetan"]                                     = "thetan";
 421                 treegroup["morisitahorn"]                       = "morisitahorn";
 422                 treegroup["braycurtis"]                         = "braycurtis";
 423         }
 424         catch(exception& e) {
 425                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 426                 exit(1);
 427         }
 428         catch(...) {
 429                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 430                 exit(1);
 431         }
 432 }
 433 /********************************************************************/
 434 void ValidCalculators::initialBoot() {
 435         try {
 436                 boot["jabund"]                          = "jabund";
 437                 boot["sorabund"]                        = "sorabund";
 438                 boot["jclass"]                          = "jclass";
 439                 boot["sorclass"]                        = "orclass";
 440                 boot["jest"]                            = "jest";
 441                 boot["sorest"]                          = "sorest";
 442                 boot["thetayc"]                         = "thetayc";
 443                 boot["thetan"]                          = "thetan";
 444                 boot["morisitahorn"]            = "morisitahorn";
 445                 boot["braycurtis"]                      = "braycurtis";
 446         }
 447         catch(exception& e) {
 448                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 449                 exit(1);
 450         }
 451         catch(...) {
 452                 cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 453                 exit(1);
 454         }
 455 }
 456 /********************************************************************/
 457 void ValidCalculators::initialDistance() {
 458         try {
 459                 distance["nogaps"]              = "nogaps";
 460                 distance["eachgap"]             = "eachgap";
 461                 distance["onegap"]              = "onegap";
 462         }
 463         catch(exception& e) {
 464                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 465                 exit(1);
 466         }
 467         catch(...) {
 468                 cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 469                 exit(1);
 470         }
 471 }
 472
 473 /********************************************************************/
 474 void ValidCalculators::printCalc(string parameter, ostream& out) {
 475         try{
 476                 out << "The available estimators for calc are ";
 477                 //are you looking for a calculator for a single parameter
 478                 if (parameter == "single") {
 479                         for (it = single.begin(); it != single.end(); it++) {
 480                                 out << it->first << ", ";
 481                         }
 482                 //are you looking for a calculator for a shared parameter
 483                 }else if (parameter == "shared") {
 484                         for (it = shared.begin(); it != shared.end(); it++) {
 485                                 out << it->first << ", ";
 486                         }
 487                 //are you looking for a calculator for a rarefaction parameter
 488                 }else if (parameter == "rarefaction") {
 489                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 490                                 out << it->first << ", ";
 491                         }
 492                 //are you looking for a calculator for a summary parameter
 493                 }else if (parameter == "summary") {
 494                         for (it = summary.begin(); it != summary.end(); it++) {
 495                                 out << it->first << ", ";
 496                         }
 497                 //are you looking for a calculator for a sharedsummary parameter
 498                 }else if (parameter == "sharedsummary") {
 499                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 500                                 out << it->first << ", ";
 501                         }
 502                 }else if (parameter == "sharedrarefaction") {
 503                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 504                                 out << it->first << ", ";
 505                         }
 506                 }else if (parameter == "vennsingle") {
 507                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 508                                 out << it->first << ", ";
 509                         }
 510                 }else if (parameter == "vennshared") {
 511                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 512                                 out << it->first << ", ";
 513                         }
 514                 }else if (parameter == "treegroup") {
 515                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 516                                 out << it->first << ", ";
 517                         }
 518                 }else if (parameter == "boot") {
 519                         for (it = boot.begin(); it != boot.end(); it++) {
 520                                 out << it->first << ", ";
 521                         }
 522                 }else if (parameter == "distance") {
 523                         for (it = distance.begin(); it != distance.end(); it++) {
 524                                 out << it->first << ", ";
 525                         }
 526                 }
 527
 528                 out << endl;
 529         }
 530         catch(exception& e) {
 531                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 532                 exit(1);
 533         }
 534         catch(...) {
 535                 cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 536                 exit(1);
 537         }
 538
 539 }
 540 /********************************************************************/
 541