validcalculator.cpp

   1 /*
   2  *  validcalculator.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/5/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "validcalculator.h"
  11
  12 /********************************************************************/
  13 ValidCalculators::ValidCalculators() {
  14         try {
  15                  initialSingle();
  16                  initialShared();
  17                  initialRarefaction();
  18                  initialSharedRarefact();
  19                  initialSummary();
  20                  initialSharedSummary();
  21                  initialVennSingle();
  22                  initialVennShared();
  23                  initialTreeGroups();
  24                  initialBoot();
  25         }
  26         catch(exception& e) {
  27                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  28                 exit(1);
  29         }
  30         catch(...) {
  31                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  32                 exit(1);
  33         }
  34 }
  35
  36 /********************************************************************/
  37
  38 ValidCalculators::~ValidCalculators() {}
  39
  40 /********************************************************************/
  41
  42 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  43         try {
  44                 //are you looking for a calculator for a single parameter
  45                 if (parameter == "single") {
  46                         //is it valid
  47                         if ((single.find(calculator)) != (single.end())) {
  48                                 return true;
  49                         }else {
  50                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  51                                 for (it = single.begin(); it != single.end(); it++) {
  52                                         cout << it->first << ", ";
  53                                 }
  54                                 cout << endl;
  55                                 return false; }
  56                 //are you looking for a calculator for a shared parameter
  57                 }else if (parameter == "shared") {
  58                         //is it valid
  59                         if ((shared.find(calculator)) != (shared.end())) {
  60                                 return true;
  61                         }else {
  62                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  63                                 for (it = shared.begin(); it != shared.end(); it++) {
  64                                         cout << it->first << ", ";
  65                                 }
  66                                 cout << endl;
  67                                 return false; }
  68                 //are you looking for a calculator for a rarefaction parameter
  69                 }else if (parameter == "rarefaction") {
  70                         //is it valid
  71                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  72                                 return true;
  73                         }else {
  74                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  75                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  76                                         cout << it->first << ", ";
  77                                 }
  78                                 cout << endl;
  79                                 return false; }
  80                 //are you looking for a calculator for a summary parameter
  81                 }else if (parameter == "summary") {
  82                         //is it valid
  83                         if ((summary.find(calculator)) != (summary.end())) {
  84                                 return true;
  85                         }else {
  86                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  87                                 for (it = summary.begin(); it != summary.end(); it++) {
  88                                         cout << it->first << ", ";
  89                                 }
  90                                 cout << endl;
  91                                 return false; }
  92                 //are you looking for a calculator for a sharedsummary parameter
  93                 }else if (parameter == "sharedsummary") {
  94                         //is it valid
  95                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  96                                 return true;
  97                         }else {
  98                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  99                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 100                                         cout << it->first << ", ";
 101                                 }
 102                                 cout << endl;
 103                                 return false; }
 104                 }else if (parameter == "sharedrarefaction") {
 105                         //is it valid
 106                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 107                                 return true;
 108                         }else {
 109                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 110                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 111                                         cout << it->first << ", ";
 112                                 }
 113                                 cout << endl;
 114                                 return false; }
 115                 }else if (parameter == "vennsingle") {
 116                         //is it valid
 117                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 118                                 return true;
 119                         }else {
 120                                 cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
 121                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 122                                         cout << it->first << ", ";
 123                                 }
 124                                 cout << endl;
 125                                 return false; }
 126                 }else if (parameter == "vennshared") {
 127                         //is it valid
 128                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 129                                 return true;
 130                         }else {
 131                                 cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
 132                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 133                                         cout << it->first << ", ";
 134                                 }
 135                                 cout << endl;
 136                                 return false; }
 137                 }else if (parameter == "treegroup") {
 138                         //is it valid
 139                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 140                                 return true;
 141                         }else {
 142                                 cout << calculator << " is not a valid estimator for the tree.shared command in shared mode and will be disregarded. Valid estimators are ";
 143                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 144                                         cout << it->first << ", ";
 145                                 }
 146                                 cout << endl;
 147                                 return false; }
 148                 }else if (parameter == "boot") {
 149                         //is it valid
 150                         if ((boot.find(calculator)) != (boot.end())) {
 151                                 return true;
 152                         }else {
 153                                 cout << calculator << " is not a valid estimator for the bootstrap.shared command in shared mode and will be disregarded. Valid estimators are ";
 154                                 for (it = boot.begin(); it != boot.end(); it++) {
 155                                         cout << it->first << ", ";
 156                                 }
 157                                 cout << endl;
 158                                 return false; }
 159                 //not a valid parameter
 160                 }else { return false; }
 161
 162         }
 163         catch(exception& e) {
 164                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 165                 exit(1);
 166         }
 167         catch(...) {
 168                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 169                 exit(1);
 170         }
 171 }
 172
 173 /********************************************************************/
 174 void ValidCalculators::initialSingle() {
 175         try {
 176                 single["sobs"]          = "sobs";
 177                 single["chao"]              = "chao";
 178                 single["ace"]               = "ace";
 179                 single["jack"]              = "jack";
 180                 single["shannon"]           = "shannon";
 181                 single["npshannon"]     = "npshannon";
 182                 single["simpson"]           = "simpson";
 183                 single["bergerparker"]  = "bergerparker";
 184                 single["bootstrap"]     = "bootstrap";
 185                 single["geometric"]     = "geometric";
 186                 single["logseries"]         = "logseries";
 187                 single["qstat"]         = "qstat";
 188                 single["bstick"]        = "bstick";
 189                 single["nseqs"]                 = "nseqs";
 190                 single["coverage"]              = "coverage";
 191
 192                 single["default"]           = "default";
 193         }
 194         catch(exception& e) {
 195                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 196                 exit(1);
 197         }
 198         catch(...) {
 199                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202 }
 203
 204 /********************************************************************/
 205 void ValidCalculators::initialShared() {
 206         try {
 207                 shared["sharedsobs"]                    = "sharedsobs";
 208                 shared["sharedchao"]                    = "sharedchao";
 209                 shared["sharedace"]                             = "sharedace";
 210                 shared["jabund"]                                = "jabund";
 211                 shared["sorensonabund"]                 = "sorensonabund";
 212                 shared["jclass"]                                = "jclass";
 213                 shared["sorclass"]                              = "sorclass";
 214                 shared["jest"]                                  = "jest";
 215                 shared["sorest"]                                = "sorest";
 216                 shared["thetayc"]                               = "thetayc";
 217                 shared["thetan"]                                = "thetan";
 218                 shared["kstest"]                                = "kstest";
 219                 shared["bdiversity"]                    = "bdiversity";
 220                 shared["sharednseqs"]                   = "sharednseqs";
 221                 shared["ochiai"]                                = "ochiai";
 222                 shared["anderberg"]                             = "anderberg";
 223                 shared["kulczynski"]                    = "kulczynski";
 224                 shared["kulczynskicody"]                = "kulczynskicody";
 225                 shared["lennon"]                                = "lennon";
 226                 shared["morisitahorn"]                  = "morisitahorn";
 227                 shared["braycurtis"]                    = "braycurtis";
 228                 shared["default"]                   = "default";
 229         }
 230         catch(exception& e) {
 231                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 232                 exit(1);
 233         }
 234         catch(...) {
 235                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 236                 exit(1);
 237         }
 238 }
 239
 240 /********************************************************************/
 241 void ValidCalculators::initialRarefaction() {
 242         try {
 243                 rarefaction["sobs"]                     = "sobs";
 244                 rarefaction["chao"]                     = "chao";
 245                 rarefaction["ace"]                      = "ace";
 246                 rarefaction["jack"]                     = "jack";
 247                 rarefaction["shannon"]          = "shannon";
 248                 rarefaction["npshannon"]        = "npshannon";
 249                 rarefaction["simpson"]          = "simpson";
 250                 rarefaction["bootstrap"]        = "bootstrap";
 251                 rarefaction["nseqs"]            = "nseqs";
 252                 rarefaction["coverage"]         = "coverage";
 253                 rarefaction["default"]      = "default";
 254         }
 255         catch(exception& e) {
 256                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 257                 exit(1);
 258         }
 259         catch(...) {
 260                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 261                 exit(1);
 262         }
 263 }
 264
 265 /********************************************************************/
 266
 267 void ValidCalculators::initialSummary() {
 268         try {
 269                 summary["sobs"]                 = "sobs";
 270                 summary["chao"]                 = "chao";
 271                 summary["ace"]                  = "ace";
 272                 summary["jack"]                 = "jack";
 273                 summary["shannon"]              = "shannon";
 274                 summary["npshannon"]    = "npshannon";
 275                 summary["simpson"]              = "simpson";
 276                 summary["bergerparker"] = "bergerparker";
 277                 summary["geometric"]    = "geometric";
 278                 summary["bootstrap"]    = "bootstrap";
 279                 summary["logsd"]        = "logsd";
 280                 summary["qstat"]        = "qstat";
 281                 summary["bstick"]       = "bstick";
 282                 summary["nseqs"]                = "nseqs";
 283                 summary["coverage"]             = "coverage";
 284                 summary["default"]          = "default";
 285         }
 286         catch(exception& e) {
 287                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 288                 exit(1);
 289         }
 290         catch(...) {
 291                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 292                 exit(1);
 293         }
 294 }
 295
 296 /********************************************************************/
 297 void ValidCalculators::initialSharedSummary() {
 298         try {
 299                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 300                 sharedsummary["sharedchao"]                             = "sharedchao";
 301                 sharedsummary["sharedace"]                              = "sharedace";
 302                 sharedsummary["jabund"]                                 = "jabund";
 303                 sharedsummary["sorensonabund"]                  = "sorensonabund";
 304                 sharedsummary["jclass"]                                 = "jclass";
 305                 sharedsummary["sorclass"]                               = "sorclass";
 306                 sharedsummary["jest"]                                   = "jest";
 307                 sharedsummary["sorest"]                                 = "sorest";
 308                 sharedsummary["thetayc"]                                = "thetayc";
 309                 sharedsummary["thetan"]                                 = "thetan";
 310                 sharedsummary["kstest"]                                 = "kstest";
 311                 sharedsummary["bdiversity"]                             = "bdiversity";
 312                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 313                 sharedsummary["ochiai"]                                 = "ochiai";
 314                 sharedsummary["anderberg"]                              = "anderberg";
 315                 sharedsummary["kulczynski"]                             = "kulczynski";
 316                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 317                 sharedsummary["lennon"]                                 = "lennon";
 318                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 319                 sharedsummary["braycurtis"]                             = "braycurtis";
 320                 sharedsummary["default"]                                = "default";
 321         }
 322         catch(exception& e) {
 323                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 324                 exit(1);
 325         }
 326         catch(...) {
 327                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 328                 exit(1);
 329         }
 330 }
 331
 332
 333 /********************************************************************/
 334
 335 void ValidCalculators::initialSharedRarefact() {
 336         try {
 337                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 338                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 339                 sharedrarefaction["default"]        = "default";
 340         }
 341         catch(exception& e) {
 342                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. 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 initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 347                 exit(1);
 348         }
 349 }
 350
 351
 352 /********************************************************************/
 353 void ValidCalculators::initialVennSingle() {
 354         try {
 355                 vennsingle["sobs"]              = "sobs";
 356                 vennsingle["chao"]                  = "chao";
 357                 vennsingle["ace"]                       = "ace";
 358                 vennsingle["jack"]                  = "jack";
 359                 vennsingle["default"]           = "default";
 360         }
 361         catch(exception& e) {
 362                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 363                 exit(1);
 364         }
 365         catch(...) {
 366                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 367                 exit(1);
 368         }
 369 }
 370
 371 /********************************************************************/
 372 void ValidCalculators::initialVennShared() {
 373         try {
 374                 vennshared["sharedsobs"]        = "sharedsobs";
 375                 vennshared["sharedchao"]        = "sharedchao";
 376                 vennshared["sharedace"]         = "sharedace";
 377                 vennshared["default"]           = "default";
 378         }
 379         catch(exception& e) {
 380                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 381                 exit(1);
 382         }
 383         catch(...) {
 384                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 385                 exit(1);
 386         }
 387 }
 388
 389 /********************************************************************/
 390 void ValidCalculators::initialTreeGroups() {
 391         try {
 392                 treegroup["jabund"]                                     = "jabund";
 393                 treegroup["sorensonabund"]                      = "sorensonabund";
 394                 treegroup["jclass"]                                     = "jclass";
 395                 treegroup["sorclass"]                           = "sorclass";
 396                 treegroup["jest"]                                       = "jest";
 397                 treegroup["sorest"]                                     = "sorest";
 398                 treegroup["thetayc"]                            = "thetayc";
 399                 treegroup["thetan"]                                     = "thetan";
 400                 treegroup["morisitahorn"]                       = "morisitahorn";
 401         }
 402         catch(exception& e) {
 403                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 404                 exit(1);
 405         }
 406         catch(...) {
 407                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 408                 exit(1);
 409         }
 410 }
 411 /********************************************************************/
 412 void ValidCalculators::initialBoot() {
 413         try {
 414                 boot["jabund"]                          = "jabund";
 415                 boot["sorensonabund"]           = "sorensonabund";
 416                 boot["jclass"]                          = "jclass";
 417                 boot["sorclass"]                        = "orclass";
 418                 boot["jest"]                            = "jest";
 419                 boot["sorest"]                          = "sorest";
 420                 boot["thetayc"]                         = "thetayc";
 421                 boot["thetan"]                          = "thetan";
 422                 boot["morisitahorn"]            = "morisitahorn";
 423         }
 424         catch(exception& e) {
 425                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. 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 initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 430                 exit(1);
 431         }
 432 }
 433
 434 /********************************************************************/
 435 void ValidCalculators::printCalc(string parameter, ostream& out) {
 436         try{
 437                 out << "The available estimators for calc are ";
 438                 //are you looking for a calculator for a single parameter
 439                 if (parameter == "single") {
 440                         for (it = single.begin(); it != single.end(); it++) {
 441                                 out << it->first << ", ";
 442                         }
 443                 //are you looking for a calculator for a shared parameter
 444                 }else if (parameter == "shared") {
 445                         for (it = shared.begin(); it != shared.end(); it++) {
 446                                 out << it->first << ", ";
 447                         }
 448                 //are you looking for a calculator for a rarefaction parameter
 449                 }else if (parameter == "rarefaction") {
 450                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 451                                 out << it->first << ", ";
 452                         }
 453                 //are you looking for a calculator for a summary parameter
 454                 }else if (parameter == "summary") {
 455                         for (it = summary.begin(); it != summary.end(); it++) {
 456                                 out << it->first << ", ";
 457                         }
 458                 //are you looking for a calculator for a sharedsummary parameter
 459                 }else if (parameter == "sharedsummary") {
 460                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 461                                 out << it->first << ", ";
 462                         }
 463                 }else if (parameter == "sharedrarefaction") {
 464                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 465                                 out << it->first << ", ";
 466                         }
 467                 }else if (parameter == "vennsingle") {
 468                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 469                                 out << it->first << ", ";
 470                         }
 471                 }else if (parameter == "vennshared") {
 472                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 473                                 out << it->first << ", ";
 474                         }
 475                 }else if (parameter == "treegroup") {
 476                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 477                                 out << it->first << ", ";
 478                         }
 479                 }else if (parameter == "boot") {
 480                         for (it = boot.begin(); it != boot.end(); it++) {
 481                                 out << it->first << ", ";
 482                         }
 483                 }
 484                 out << endl;
 485         }
 486         catch(exception& e) {
 487                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 488                 exit(1);
 489         }
 490         catch(...) {
 491                 cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 492                 exit(1);
 493         }
 494
 495 }
 496 /********************************************************************/
 497