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["default"]           = "default";
 205         }
 206         catch(exception& e) {
 207                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210         catch(...) {
 211                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214 }
 215
 216 /********************************************************************/
 217 void ValidCalculators::initialShared() {
 218         try {
 219                 shared["sharedsobs"]                    = "sharedsobs";
 220                 shared["sharedchao"]                    = "sharedchao";
 221                 shared["sharedace"]                             = "sharedace";
 222                 shared["jabund"]                                = "jabund";
 223                 shared["sorabund"]                              = "sorabund";
 224                 shared["jclass"]                                = "jclass";
 225                 shared["sorclass"]                              = "sorclass";
 226                 shared["jest"]                                  = "jest";
 227                 shared["sorest"]                                = "sorest";
 228                 shared["thetayc"]                               = "thetayc";
 229                 shared["thetan"]                                = "thetan";
 230                 shared["kstest"]                                = "kstest";
 231                 shared["whittaker"]                         = "whittaker";
 232                 shared["sharednseqs"]                   = "sharednseqs";
 233                 shared["ochiai"]                                = "ochiai";
 234                 shared["anderberg"]                             = "anderberg";
 235                 shared["kulczynski"]                    = "kulczynski";
 236                 shared["kulczynskicody"]                = "kulczynskicody";
 237                 shared["lennon"]                                = "lennon";
 238                 shared["morisitahorn"]                  = "morisitahorn";
 239                 shared["braycurtis"]                    = "braycurtis";
 240                 shared["default"]                   = "default";
 241         }
 242         catch(exception& e) {
 243                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 244                 exit(1);
 245         }
 246         catch(...) {
 247                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 248                 exit(1);
 249         }
 250 }
 251
 252 /********************************************************************/
 253 void ValidCalculators::initialRarefaction() {
 254         try {
 255                 rarefaction["sobs"]                     = "sobs";
 256                 rarefaction["chao"]                     = "chao";
 257                 rarefaction["ace"]                      = "ace";
 258                 rarefaction["jack"]                     = "jack";
 259                 rarefaction["shannon"]          = "shannon";
 260                 rarefaction["npshannon"]        = "npshannon";
 261                 rarefaction["simpson"]          = "simpson";
 262                 rarefaction["bootstrap"]        = "bootstrap";
 263                 rarefaction["nseqs"]            = "nseqs";
 264                 rarefaction["coverage"]         = "coverage";
 265                 rarefaction["default"]      = "default";
 266         }
 267         catch(exception& e) {
 268                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 269                 exit(1);
 270         }
 271         catch(...) {
 272                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 273                 exit(1);
 274         }
 275 }
 276
 277 /********************************************************************/
 278
 279 void ValidCalculators::initialSummary() {
 280         try {
 281                 summary["sobs"]                 = "sobs";
 282                 summary["chao"]                 = "chao";
 283                 summary["ace"]                  = "ace";
 284                 summary["jack"]                 = "jack";
 285                 summary["shannon"]              = "shannon";
 286                 summary["npshannon"]    = "npshannon";
 287                 summary["simpson"]              = "simpson";
 288                 summary["bergerparker"] = "bergerparker";
 289                 summary["geometric"]    = "geometric";
 290                 summary["bootstrap"]    = "bootstrap";
 291                 summary["logseries"]    = "logseries";
 292                 summary["qstat"]        = "qstat";
 293                 summary["bstick"]       = "bstick";
 294                 summary["nseqs"]                = "nseqs";
 295                 summary["goodscoverage"]= "goodscoverage";
 296                 summary["coverage"]             = "coverage";
 297                 summary["default"]          = "default";
 298         }
 299         catch(exception& e) {
 300                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 301                 exit(1);
 302         }
 303         catch(...) {
 304                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 305                 exit(1);
 306         }
 307 }
 308
 309 /********************************************************************/
 310 void ValidCalculators::initialSharedSummary() {
 311         try {
 312                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 313                 sharedsummary["sharedchao"]                             = "sharedchao";
 314                 sharedsummary["sharedace"]                              = "sharedace";
 315                 sharedsummary["jabund"]                                 = "jabund";
 316                 sharedsummary["sorabund"]                       = "sorabund";
 317                 sharedsummary["jclass"]                                 = "jclass";
 318                 sharedsummary["sorclass"]                               = "sorclass";
 319                 sharedsummary["jest"]                                   = "jest";
 320                 sharedsummary["sorest"]                                 = "sorest";
 321                 sharedsummary["thetayc"]                                = "thetayc";
 322                 sharedsummary["thetan"]                                 = "thetan";
 323                 sharedsummary["kstest"]                                 = "kstest";
 324                 sharedsummary["whittaker"]                              = "whittaker";
 325                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 326                 sharedsummary["ochiai"]                                 = "ochiai";
 327                 sharedsummary["anderberg"]                              = "anderberg";
 328                 sharedsummary["kulczynski"]                             = "kulczynski";
 329                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 330                 sharedsummary["lennon"]                                 = "lennon";
 331                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 332                 sharedsummary["braycurtis"]                             = "braycurtis";
 333                 sharedsummary["default"]                                = "default";
 334         }
 335         catch(exception& e) {
 336                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 337                 exit(1);
 338         }
 339         catch(...) {
 340                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 341                 exit(1);
 342         }
 343 }
 344
 345
 346 /********************************************************************/
 347
 348 void ValidCalculators::initialSharedRarefact() {
 349         try {
 350                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 351                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 352                 sharedrarefaction["default"]        = "default";
 353         }
 354         catch(exception& e) {
 355                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 356                 exit(1);
 357         }
 358         catch(...) {
 359                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 360                 exit(1);
 361         }
 362 }
 363
 364
 365 /********************************************************************/
 366 void ValidCalculators::initialVennSingle() {
 367         try {
 368                 vennsingle["sobs"]              = "sobs";
 369                 vennsingle["chao"]                  = "chao";
 370                 vennsingle["ace"]                       = "ace";
 371                 vennsingle["jack"]                  = "jack";
 372                 vennsingle["default"]           = "default";
 373         }
 374         catch(exception& e) {
 375                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 376                 exit(1);
 377         }
 378         catch(...) {
 379                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 380                 exit(1);
 381         }
 382 }
 383
 384 /********************************************************************/
 385 void ValidCalculators::initialVennShared() {
 386         try {
 387                 vennshared["sharedsobs"]        = "sharedsobs";
 388                 vennshared["sharedchao"]        = "sharedchao";
 389                 vennshared["sharedace"]         = "sharedace";
 390                 vennshared["default"]           = "default";
 391         }
 392         catch(exception& e) {
 393                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 394                 exit(1);
 395         }
 396         catch(...) {
 397                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 398                 exit(1);
 399         }
 400 }
 401
 402 /********************************************************************/
 403 void ValidCalculators::initialTreeGroups() {
 404         try {
 405                 treegroup["jabund"]                                     = "jabund";
 406                 treegroup["sorabund"]                           = "sorabund";
 407                 treegroup["jclass"]                                     = "jclass";
 408                 treegroup["sorclass"]                           = "sorclass";
 409                 treegroup["jest"]                                       = "jest";
 410                 treegroup["sorest"]                                     = "sorest";
 411                 treegroup["thetayc"]                            = "thetayc";
 412                 treegroup["thetan"]                                     = "thetan";
 413                 treegroup["morisitahorn"]                       = "morisitahorn";
 414                 treegroup["braycurtis"]                         = "braycurtis";
 415         }
 416         catch(exception& e) {
 417                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 418                 exit(1);
 419         }
 420         catch(...) {
 421                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 422                 exit(1);
 423         }
 424 }
 425 /********************************************************************/
 426 void ValidCalculators::initialBoot() {
 427         try {
 428                 boot["jabund"]                          = "jabund";
 429                 boot["sorabund"]                        = "sorabund";
 430                 boot["jclass"]                          = "jclass";
 431                 boot["sorclass"]                        = "orclass";
 432                 boot["jest"]                            = "jest";
 433                 boot["sorest"]                          = "sorest";
 434                 boot["thetayc"]                         = "thetayc";
 435                 boot["thetan"]                          = "thetan";
 436                 boot["morisitahorn"]            = "morisitahorn";
 437                 boot["braycurtis"]                      = "braycurtis";
 438         }
 439         catch(exception& e) {
 440                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 441                 exit(1);
 442         }
 443         catch(...) {
 444                 cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 445                 exit(1);
 446         }
 447 }
 448 /********************************************************************/
 449 void ValidCalculators::initialDistance() {
 450         try {
 451                 distance["nogaps"]              = "nogaps";
 452                 distance["eachgap"]             = "eachgap";
 453                 distance["onegap"]              = "onegap";
 454         }
 455         catch(exception& e) {
 456                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 457                 exit(1);
 458         }
 459         catch(...) {
 460                 cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 461                 exit(1);
 462         }
 463 }
 464
 465 /********************************************************************/
 466 void ValidCalculators::printCalc(string parameter, ostream& out) {
 467         try{
 468                 out << "The available estimators for calc are ";
 469                 //are you looking for a calculator for a single parameter
 470                 if (parameter == "single") {
 471                         for (it = single.begin(); it != single.end(); it++) {
 472                                 out << it->first << ", ";
 473                         }
 474                 //are you looking for a calculator for a shared parameter
 475                 }else if (parameter == "shared") {
 476                         for (it = shared.begin(); it != shared.end(); it++) {
 477                                 out << it->first << ", ";
 478                         }
 479                 //are you looking for a calculator for a rarefaction parameter
 480                 }else if (parameter == "rarefaction") {
 481                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 482                                 out << it->first << ", ";
 483                         }
 484                 //are you looking for a calculator for a summary parameter
 485                 }else if (parameter == "summary") {
 486                         for (it = summary.begin(); it != summary.end(); it++) {
 487                                 out << it->first << ", ";
 488                         }
 489                 //are you looking for a calculator for a sharedsummary parameter
 490                 }else if (parameter == "sharedsummary") {
 491                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 492                                 out << it->first << ", ";
 493                         }
 494                 }else if (parameter == "sharedrarefaction") {
 495                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 496                                 out << it->first << ", ";
 497                         }
 498                 }else if (parameter == "vennsingle") {
 499                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 500                                 out << it->first << ", ";
 501                         }
 502                 }else if (parameter == "vennshared") {
 503                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 504                                 out << it->first << ", ";
 505                         }
 506                 }else if (parameter == "treegroup") {
 507                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 508                                 out << it->first << ", ";
 509                         }
 510                 }else if (parameter == "boot") {
 511                         for (it = boot.begin(); it != boot.end(); it++) {
 512                                 out << it->first << ", ";
 513                         }
 514                 }else if (parameter == "distance") {
 515                         for (it = distance.begin(); it != distance.end(); it++) {
 516                                 out << it->first << ", ";
 517                         }
 518                 }
 519
 520                 out << endl;
 521         }
 522         catch(exception& e) {
 523                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 524                 exit(1);
 525         }
 526         catch(...) {
 527                 cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 528                 exit(1);
 529         }
 530
 531 }
 532 /********************************************************************/
 533