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                  initialMatrix();
  27         }
  28         catch(exception& e) {
  29                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32         catch(...) {
  33                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36 }
  37
  38 /********************************************************************/
  39
  40 ValidCalculators::~ValidCalculators() {}
  41
  42 /********************************************************************/
  43
  44 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  45         try {
  46                 //are you looking for a calculator for a single parameter
  47                 if (parameter == "single") {
  48                         //is it valid
  49                         if ((single.find(calculator)) != (single.end())) {
  50                                 return true;
  51                         }else {
  52                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  53                                 for (it = single.begin(); it != single.end(); it++) {
  54                                         cout << it->first << ", ";
  55                                 }
  56                                 cout << endl;
  57                                 return false; }
  58                 //are you looking for a calculator for a shared parameter
  59                 }else if (parameter == "shared") {
  60                         //is it valid
  61                         if ((shared.find(calculator)) != (shared.end())) {
  62                                 return true;
  63                         }else {
  64                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  65                                 for (it = shared.begin(); it != shared.end(); it++) {
  66                                         cout << it->first << ", ";
  67                                 }
  68                                 cout << endl;
  69                                 return false; }
  70                 //are you looking for a calculator for a rarefaction parameter
  71                 }else if (parameter == "rarefaction") {
  72                         //is it valid
  73                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  74                                 return true;
  75                         }else {
  76                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  77                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  78                                         cout << it->first << ", ";
  79                                 }
  80                                 cout << endl;
  81                                 return false; }
  82                 //are you looking for a calculator for a summary parameter
  83                 }else if (parameter == "summary") {
  84                         //is it valid
  85                         if ((summary.find(calculator)) != (summary.end())) {
  86                                 return true;
  87                         }else {
  88                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  89                                 for (it = summary.begin(); it != summary.end(); it++) {
  90                                         cout << it->first << ", ";
  91                                 }
  92                                 cout << endl;
  93                                 return false; }
  94                 //are you looking for a calculator for a sharedsummary parameter
  95                 }else if (parameter == "sharedsummary") {
  96                         //is it valid
  97                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  98                                 return true;
  99                         }else {
 100                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
 101                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 102                                         cout << it->first << ", ";
 103                                 }
 104                                 cout << endl;
 105                                 return false; }
 106                 }else if (parameter == "sharedrarefaction") {
 107                         //is it valid
 108                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 109                                 return true;
 110                         }else {
 111                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 112                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 113                                         cout << it->first << ", ";
 114                                 }
 115                                 cout << endl;
 116                                 return false; }
 117                 }else if (parameter == "vennsingle") {
 118                         //is it valid
 119                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 120                                 return true;
 121                         }else {
 122                                 cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
 123                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 124                                         cout << it->first << ", ";
 125                                 }
 126                                 cout << endl;
 127                                 return false; }
 128                 }else if (parameter == "vennshared") {
 129                         //is it valid
 130                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 131                                 return true;
 132                         }else {
 133                                 cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
 134                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 135                                         cout << it->first << ", ";
 136                                 }
 137                                 cout << endl;
 138                                 return false; }
 139                 }else if (parameter == "treegroup") {
 140                         //is it valid
 141                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 142                                 return true;
 143                         }else {
 144                                 cout << calculator << " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ";
 145                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 146                                         cout << it->first << ", ";
 147                                 }
 148                                 cout << endl;
 149                                 return false; }
 150                 }else if (parameter == "matrix") {
 151                         //is it valid
 152                         if ((matrix.find(calculator)) != (matrix.end())) {
 153                                 return true;
 154                         }else {
 155                                 cout << calculator << " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ";
 156                                 for (it = matrix.begin(); it != matrix.end(); it++) {
 157                                         cout << it->first << ", ";
 158                                 }
 159                                 cout << endl;
 160                                 return false; }
 161                 }else if (parameter == "boot") {
 162                         //is it valid
 163                         if ((boot.find(calculator)) != (boot.end())) {
 164                                 return true;
 165                         }else {
 166                                 cout << calculator << " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ";
 167                                 for (it = boot.begin(); it != boot.end(); it++) {
 168                                         cout << it->first << ", ";
 169                                 }
 170                                 cout << endl;
 171                                 return false; }
 172                 }else if (parameter == "distance") {
 173                         //is it valid
 174                         if ((distance.find(calculator)) != (distance.end())) {
 175                                 return true;
 176                         }else {
 177                                 cout << calculator << " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ";
 178                                 for (it = distance.begin(); it != distance.end(); it++) {
 179                                         cout << it->first << ", ";
 180                                 }
 181                                 cout << endl;
 182                                 return false; }
 183                 //not a valid parameter
 184                 }else { return false; }
 185
 186         }
 187         catch(exception& e) {
 188                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 189                 exit(1);
 190         }
 191         catch(...) {
 192                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 193                 exit(1);
 194         }
 195 }
 196
 197 /********************************************************************/
 198 void ValidCalculators::initialSingle() {
 199         try {
 200                 single["sobs"]          = "sobs";
 201                 single["chao"]              = "chao";
 202                 single["ace"]               = "ace";
 203                 single["jack"]              = "jack";
 204                 single["shannon"]           = "shannon";
 205                 single["npshannon"]     = "npshannon";
 206                 single["simpson"]           = "simpson";
 207                 single["bergerparker"]  = "bergerparker";
 208                 single["bootstrap"]     = "bootstrap";
 209                 single["geometric"]     = "geometric";
 210                 single["logseries"]         = "logseries";
 211                 single["qstat"]         = "qstat";
 212                 single["bstick"]        = "bstick";
 213                 single["goodscoverage"] = "goodscoverage";
 214                 single["nseqs"]                 = "nseqs";
 215                 single["coverage"]              = "coverage";
 216                 single["efron"]         = "efron";
 217                 single["boneh"]         = "boneh";
 218                 single["solow"]         = "solow";
 219                 single["shen"]          = "shen";
 220                 single["default"]           = "default";
 221         }
 222         catch(exception& e) {
 223                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 224                 exit(1);
 225         }
 226         catch(...) {
 227                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 228                 exit(1);
 229         }
 230 }
 231
 232 /********************************************************************/
 233 void ValidCalculators::initialShared() {
 234         try {
 235                 shared["sharedsobs"]                    = "sharedsobs";
 236                 shared["sharedchao"]                    = "sharedchao";
 237                 shared["sharedace"]                             = "sharedace";
 238                 shared["jabund"]                                = "jabund";
 239                 shared["sorabund"]                              = "sorabund";
 240                 shared["jclass"]                                = "jclass";
 241                 shared["sorclass"]                              = "sorclass";
 242                 shared["jest"]                                  = "jest";
 243                 shared["sorest"]                                = "sorest";
 244                 shared["thetayc"]                               = "thetayc";
 245                 shared["thetan"]                                = "thetan";
 246                 shared["kstest"]                                = "kstest";
 247                 shared["whittaker"]                         = "whittaker";
 248                 shared["sharednseqs"]                   = "sharednseqs";
 249                 shared["ochiai"]                                = "ochiai";
 250                 shared["anderberg"]                             = "anderberg";
 251                 shared["kulczynski"]                    = "kulczynski";
 252                 shared["kulczynskicody"]                = "kulczynskicody";
 253                 shared["lennon"]                                = "lennon";
 254                 shared["morisitahorn"]                  = "morisitahorn";
 255                 shared["braycurtis"]                    = "braycurtis";
 256                 shared["default"]                   = "default";
 257         }
 258         catch(exception& e) {
 259                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 260                 exit(1);
 261         }
 262         catch(...) {
 263                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 264                 exit(1);
 265         }
 266 }
 267
 268 /********************************************************************/
 269 void ValidCalculators::initialRarefaction() {
 270         try {
 271                 rarefaction["sobs"]                     = "sobs";
 272                 rarefaction["chao"]                     = "chao";
 273                 rarefaction["ace"]                      = "ace";
 274                 rarefaction["jack"]                     = "jack";
 275                 rarefaction["shannon"]          = "shannon";
 276                 rarefaction["npshannon"]        = "npshannon";
 277                 rarefaction["simpson"]          = "simpson";
 278                 rarefaction["bootstrap"]        = "bootstrap";
 279                 rarefaction["nseqs"]            = "nseqs";
 280                 rarefaction["coverage"]         = "coverage";
 281                 rarefaction["default"]      = "default";
 282         }
 283         catch(exception& e) {
 284                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 285                 exit(1);
 286         }
 287         catch(...) {
 288                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 289                 exit(1);
 290         }
 291 }
 292
 293 /********************************************************************/
 294
 295 void ValidCalculators::initialSummary() {
 296         try {
 297                 summary["sobs"]                 = "sobs";
 298                 summary["chao"]                 = "chao";
 299                 summary["ace"]                  = "ace";
 300                 summary["jack"]                 = "jack";
 301                 summary["shannon"]              = "shannon";
 302                 summary["npshannon"]    = "npshannon";
 303                 summary["simpson"]              = "simpson";
 304                 summary["bergerparker"] = "bergerparker";
 305                 summary["geometric"]    = "geometric";
 306                 summary["bootstrap"]    = "bootstrap";
 307                 summary["logseries"]    = "logseries";
 308                 summary["qstat"]        = "qstat";
 309                 summary["bstick"]       = "bstick";
 310                 summary["nseqs"]                = "nseqs";
 311                 summary["goodscoverage"]= "goodscoverage";
 312                 summary["coverage"]             = "coverage";
 313                 summary["efron"]        = "efron";
 314                 summary["boneh"]        = "boneh";
 315                 summary["solow"]        = "solow";
 316                 summary["shen"]         = "shen";
 317                 summary["default"]          = "default";
 318         }
 319         catch(exception& e) {
 320                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 321                 exit(1);
 322         }
 323         catch(...) {
 324                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 325                 exit(1);
 326         }
 327 }
 328
 329 /********************************************************************/
 330 void ValidCalculators::initialSharedSummary() {
 331         try {
 332                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 333                 sharedsummary["sharedchao"]                             = "sharedchao";
 334                 sharedsummary["sharedace"]                              = "sharedace";
 335                 sharedsummary["jabund"]                                 = "jabund";
 336                 sharedsummary["sorabund"]                       = "sorabund";
 337                 sharedsummary["jclass"]                                 = "jclass";
 338                 sharedsummary["sorclass"]                               = "sorclass";
 339                 sharedsummary["jest"]                                   = "jest";
 340                 sharedsummary["sorest"]                                 = "sorest";
 341                 sharedsummary["thetayc"]                                = "thetayc";
 342                 sharedsummary["thetan"]                                 = "thetan";
 343                 sharedsummary["kstest"]                                 = "kstest";
 344                 sharedsummary["whittaker"]                              = "whittaker";
 345                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 346                 sharedsummary["ochiai"]                                 = "ochiai";
 347                 sharedsummary["anderberg"]                              = "anderberg";
 348                 sharedsummary["kulczynski"]                             = "kulczynski";
 349                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 350                 sharedsummary["lennon"]                                 = "lennon";
 351                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 352                 sharedsummary["braycurtis"]                             = "braycurtis";
 353                 sharedsummary["default"]                                = "default";
 354         }
 355         catch(exception& e) {
 356                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 357                 exit(1);
 358         }
 359         catch(...) {
 360                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 361                 exit(1);
 362         }
 363 }
 364
 365
 366 /********************************************************************/
 367
 368 void ValidCalculators::initialSharedRarefact() {
 369         try {
 370                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 371                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 372                 sharedrarefaction["default"]        = "default";
 373         }
 374         catch(exception& e) {
 375                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. 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 initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 380                 exit(1);
 381         }
 382 }
 383
 384
 385 /********************************************************************/
 386 void ValidCalculators::initialVennSingle() {
 387         try {
 388                 vennsingle["sobs"]              = "sobs";
 389                 vennsingle["chao"]                  = "chao";
 390                 vennsingle["ace"]                       = "ace";
 391                 vennsingle["jack"]                  = "jack";
 392                 vennsingle["default"]           = "default";
 393         }
 394         catch(exception& e) {
 395                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 396                 exit(1);
 397         }
 398         catch(...) {
 399                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 400                 exit(1);
 401         }
 402 }
 403
 404 /********************************************************************/
 405 void ValidCalculators::initialVennShared() {
 406         try {
 407                 vennshared["sharedsobs"]        = "sharedsobs";
 408                 vennshared["sharedchao"]        = "sharedchao";
 409                 vennshared["sharedace"]         = "sharedace";
 410                 vennshared["default"]           = "default";
 411         }
 412         catch(exception& e) {
 413                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 414                 exit(1);
 415         }
 416         catch(...) {
 417                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 418                 exit(1);
 419         }
 420 }
 421
 422 /********************************************************************/
 423 void ValidCalculators::initialTreeGroups() {
 424         try {
 425                 treegroup["jabund"]                                     = "jabund";
 426                 treegroup["sorabund"]                           = "sorabund";
 427                 treegroup["jclass"]                                     = "jclass";
 428                 treegroup["sorclass"]                           = "sorclass";
 429                 treegroup["jest"]                                       = "jest";
 430                 treegroup["sorest"]                                     = "sorest";
 431                 treegroup["thetayc"]                            = "thetayc";
 432                 treegroup["thetan"]                                     = "thetan";
 433                 treegroup["morisitahorn"]                       = "morisitahorn";
 434                 treegroup["braycurtis"]                         = "braycurtis";
 435         }
 436         catch(exception& e) {
 437                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 438                 exit(1);
 439         }
 440         catch(...) {
 441                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 442                 exit(1);
 443         }
 444 }
 445 /********************************************************************/
 446 void ValidCalculators::initialMatrix() {
 447         try {
 448                 matrix["jabund"]                                = "jabund";
 449                 matrix["sorabund"]                              = "sorabund";
 450                 matrix["jclass"]                                = "jclass";
 451                 matrix["sorclass"]                              = "sorclass";
 452                 matrix["jest"]                                  = "jest";
 453                 matrix["sorest"]                                = "sorest";
 454                 matrix["thetayc"]                               = "thetayc";
 455                 matrix["thetan"]                                = "thetan";
 456                 matrix["morisitahorn"]                  = "morisitahorn";
 457                 matrix["braycurtis"]                    = "braycurtis";
 458         }
 459         catch(exception& e) {
 460                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 461                 exit(1);
 462         }
 463         catch(...) {
 464                 cout << "An unknown error has occurred in the ValidCalculator class function initialMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 465                 exit(1);
 466         }
 467 }
 468
 469 /********************************************************************/
 470 void ValidCalculators::initialBoot() {
 471         try {
 472                 boot["jabund"]                          = "jabund";
 473                 boot["sorabund"]                        = "sorabund";
 474                 boot["jclass"]                          = "jclass";
 475                 boot["sorclass"]                        = "orclass";
 476                 boot["jest"]                            = "jest";
 477                 boot["sorest"]                          = "sorest";
 478                 boot["thetayc"]                         = "thetayc";
 479                 boot["thetan"]                          = "thetan";
 480                 boot["morisitahorn"]            = "morisitahorn";
 481                 boot["braycurtis"]                      = "braycurtis";
 482         }
 483         catch(exception& e) {
 484                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 485                 exit(1);
 486         }
 487         catch(...) {
 488                 cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 489                 exit(1);
 490         }
 491 }
 492 /********************************************************************/
 493 void ValidCalculators::initialDistance() {
 494         try {
 495                 distance["nogaps"]              = "nogaps";
 496                 distance["eachgap"]             = "eachgap";
 497                 distance["onegap"]              = "onegap";
 498         }
 499         catch(exception& e) {
 500                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 501                 exit(1);
 502         }
 503         catch(...) {
 504                 cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 505                 exit(1);
 506         }
 507 }
 508
 509 /********************************************************************/
 510 void ValidCalculators::printCalc(string parameter, ostream& out) {
 511         try{
 512                 out << "The available estimators for calc are ";
 513                 //are you looking for a calculator for a single parameter
 514                 if (parameter == "single") {
 515                         for (it = single.begin(); it != single.end(); it++) {
 516                                 out << it->first << ", ";
 517                         }
 518                 //are you looking for a calculator for a shared parameter
 519                 }else if (parameter == "shared") {
 520                         for (it = shared.begin(); it != shared.end(); it++) {
 521                                 out << it->first << ", ";
 522                         }
 523                 //are you looking for a calculator for a rarefaction parameter
 524                 }else if (parameter == "rarefaction") {
 525                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 526                                 out << it->first << ", ";
 527                         }
 528                 //are you looking for a calculator for a summary parameter
 529                 }else if (parameter == "summary") {
 530                         for (it = summary.begin(); it != summary.end(); it++) {
 531                                 out << it->first << ", ";
 532                         }
 533                 //are you looking for a calculator for a sharedsummary parameter
 534                 }else if (parameter == "sharedsummary") {
 535                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 536                                 out << it->first << ", ";
 537                         }
 538                 }else if (parameter == "sharedrarefaction") {
 539                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 540                                 out << it->first << ", ";
 541                         }
 542                 }else if (parameter == "vennsingle") {
 543                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 544                                 out << it->first << ", ";
 545                         }
 546                 }else if (parameter == "vennshared") {
 547                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 548                                 out << it->first << ", ";
 549                         }
 550                 }else if (parameter == "treegroup") {
 551                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 552                                 out << it->first << ", ";
 553                         }
 554                 }else if (parameter == "boot") {
 555                         for (it = boot.begin(); it != boot.end(); it++) {
 556                                 out << it->first << ", ";
 557                         }
 558                 }else if (parameter == "distance") {
 559                         for (it = distance.begin(); it != distance.end(); it++) {
 560                                 out << it->first << ", ";
 561                         }
 562                 }
 563
 564                 out << endl;
 565         }
 566         catch(exception& e) {
 567                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 568                 exit(1);
 569         }
 570         catch(...) {
 571                 cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 572                 exit(1);
 573         }
 574
 575 }
 576 /********************************************************************/
 577