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                  m = MothurOut::getInstance();
  16
  17                  initialSingle();
  18                  initialShared();
  19                  initialRarefaction();
  20                  initialSharedRarefact();
  21                  initialSummary();
  22                  initialSharedSummary();
  23                  initialVennSingle();
  24                  initialVennShared();
  25                  initialTreeGroups();
  26                  initialBoot();
  27                  initialDistance();
  28                  initialMatrix();
  29                  initialHeat();
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "ValidCalculator", "ValidCalculator");
  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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
  54                                 }
  55                                 m->mothurOutEndLine();
  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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
  66                                 }
  67                                 m->mothurOutEndLine();
  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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
  78                                 }
  79                                 m->mothurOutEndLine();
  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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
  90                                 }
  91                                 m->mothurOutEndLine();
  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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
 102                                 }
 103                                 m->mothurOutEndLine();
 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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
 113                                 }
 114                                 m->mothurOutEndLine();
 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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
 124                                 }
 125                                 m->mothurOutEndLine();
 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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
 135                                 }
 136                                 m->mothurOutEndLine();
 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                                 m->mothurOut(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                                         m->mothurOut(it->first + ", ");
 146                                 }
 147                                 m->mothurOutEndLine();
 148                                 return false; }
 149                 }else if (parameter == "matrix") {
 150                         //is it valid
 151                         if ((matrix.find(calculator)) != (matrix.end())) {
 152                                 return true;
 153                         }else {
 154                                 m->mothurOut(calculator +  " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ");
 155                                 for (it = matrix.begin(); it != matrix.end(); it++) {
 156                                         m->mothurOut(it->first + ", ");
 157                                 }
 158                                 m->mothurOutEndLine();
 159                                 return false; }
 160                 }else if (parameter == "heat") {
 161                         //is it valid
 162                         if ((heat.find(calculator)) != (heat.end())) {
 163                                 return true;
 164                         }else {
 165                                 m->mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
 166                                 for (it = heat.begin(); it != heat.end(); it++) {
 167                                         m->mothurOut(it->first + ", ");
 168                                 }
 169                                 m->mothurOutEndLine();
 170                                 return false; }
 171                 }else if (parameter == "boot") {
 172                         //is it valid
 173                         if ((boot.find(calculator)) != (boot.end())) {
 174                                 return true;
 175                         }else {
 176                                 m->mothurOut(calculator + " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ");
 177                                 for (it = boot.begin(); it != boot.end(); it++) {
 178                                         m->mothurOut(it->first + ", ");
 179                                 }
 180                                 m->mothurOutEndLine();
 181                                 return false; }
 182                 }else if (parameter == "distance") {
 183                         //is it valid
 184                         if ((distance.find(calculator)) != (distance.end())) {
 185                                 return true;
 186                         }else {
 187                                 m->mothurOut(calculator +  " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ");
 188                                 for (it = distance.begin(); it != distance.end(); it++) {
 189                                         m->mothurOut(it->first + ", ");
 190                                 }
 191                                 m->mothurOutEndLine();
 192                                 return false; }
 193                 //not a valid parameter
 194                 }else { return false; }
 195
 196         }
 197         catch(exception& e) {
 198                 m->errorOut(e, "ValidCalculator", "isValidCalculator");
 199                 exit(1);
 200         }
 201 }
 202
 203 /********************************************************************/
 204 void ValidCalculators::initialSingle() {
 205         try {
 206                 single["sobs"]          = "sobs";
 207                 single["chao"]              = "chao";
 208                 single["ace"]               = "ace";
 209                 single["jack"]              = "jack";
 210                 single["shannon"]           = "shannon";
 211                 single["npshannon"]     = "npshannon";
 212                 single["shannoneven"]   = "shannoneven";
 213                 single["smithwilson"]   = "smithwilson";
 214                 single["heip"]                  = "heip";
 215                 single["simpson"]           = "simpson";
 216                 single["simpsoneven"]   = "simpsoneven";
 217                 single["invsimpson"]    = "invsimpson";
 218                 single["bergerparker"]  = "bergerparker";
 219                 single["bootstrap"]     = "bootstrap";
 220                 single["geometric"]     = "geometric";
 221                 single["logseries"]             = "logseries";
 222                 single["qstat"]         = "qstat";
 223                 single["bstick"]        = "bstick";
 224                 single["goodscoverage"] = "goodscoverage";
 225                 single["nseqs"]                 = "nseqs";
 226                 single["coverage"]              = "coverage";
 227                 single["efron"]         = "efron";
 228                 single["boneh"]         = "boneh";
 229                 single["solow"]         = "solow";
 230                 single["shen"]          = "shen";
 231                 single["default"]           = "default";
 232         }
 233         catch(exception& e) {
 234                 m->errorOut(e, "ValidCalculator", "initialSingle");
 235                 exit(1);
 236         }
 237 }
 238
 239 /********************************************************************/
 240 void ValidCalculators::initialShared() {
 241         try {
 242                 shared["sharedsobs"]                    = "sharedsobs";
 243                 shared["sharedchao"]                    = "sharedchao";
 244                 shared["sharedace"]                             = "sharedace";
 245                 shared["jabund"]                                = "jabund";
 246                 shared["sorabund"]                              = "sorabund";
 247                 shared["jclass"]                                = "jclass";
 248                 shared["sorclass"]                              = "sorclass";
 249                 shared["jest"]                                  = "jest";
 250                 shared["sorest"]                                = "sorest";
 251                 shared["thetayc"]                               = "thetayc";
 252                 shared["thetan"]                                = "thetan";
 253                 shared["kstest"]                                = "kstest";
 254                 shared["whittaker"]                         = "whittaker";
 255                 shared["sharednseqs"]                   = "sharednseqs";
 256                 shared["ochiai"]                                = "ochiai";
 257                 shared["anderberg"]                             = "anderberg";
 258                 shared["kulczynski"]                    = "kulczynski";
 259                 shared["kulczynskicody"]                = "kulczynskicody";
 260                 shared["lennon"]                                = "lennon";
 261                 shared["morisitahorn"]                  = "morisitahorn";
 262                 shared["braycurtis"]                    = "braycurtis";
 263                 shared["odum"]                                  = "odum";
 264                 shared["canberra"]                              = "canberra";
 265                 shared["structeuclidean"]               = "structeuclidean";
 266                 shared["structchord"]                   = "structchord";
 267                 shared["hellinger"]                             = "hellinger";
 268                 shared["manhattan"]                             = "manhattan";
 269                 shared["structpearson"]                 = "structpearson";
 270                 shared["soergel"]                               = "soergel";
 271                 shared["spearman"]                              = "spearman";
 272                 shared["structkulczynski"]              = "structkulczynski";
 273                 shared["structchi2"]                    = "structchi2";
 274                 shared["speciesprofile"]                = "speciesprofile";
 275                 shared["hamming"]                               = "hamming";
 276                 shared["gower"]                                 = "gower";
 277                 shared["memchi2"]                               = "memchi2";
 278                 shared["memchord"]                              = "memchord";
 279                 shared["memeuclidean"]                  = "memeuclidean";
 280                 shared["mempearson"]                    = "mempearson";
 281                 shared["default"]                   = "default";
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "ValidCalculator", "initialShared");
 285                 exit(1);
 286         }
 287 }
 288
 289 /********************************************************************/
 290 void ValidCalculators::initialRarefaction() {
 291         try {
 292                 rarefaction["sobs"]                     = "sobs";
 293                 rarefaction["chao"]                     = "chao";
 294                 rarefaction["ace"]                      = "ace";
 295                 rarefaction["jack"]                     = "jack";
 296                 rarefaction["shannon"]          = "shannon";
 297                 rarefaction["smithwilson"]      = "smithwilson";
 298                 rarefaction["heip"]                     = "heip";
 299                 rarefaction["npshannon"]        = "npshannon";
 300                 rarefaction["shannoneven"]      = "shannoneven";
 301                 rarefaction["simpson"]          = "simpson";
 302                 rarefaction["invsimpson"]       = "invsimpson";
 303                 rarefaction["simpsoneven"]      = "simpsoneven";
 304                 rarefaction["bootstrap"]        = "bootstrap";
 305                 rarefaction["nseqs"]            = "nseqs";
 306                 rarefaction["coverage"]         = "coverage";
 307                 rarefaction["default"]      = "default";
 308         }
 309         catch(exception& e) {
 310                 m->errorOut(e, "ValidCalculator", "initialRarefaction");
 311                 exit(1);
 312         }
 313 }
 314
 315 /********************************************************************/
 316
 317 void ValidCalculators::initialSummary() {
 318         try {
 319                 summary["sobs"]                 = "sobs";
 320                 summary["chao"]                 = "chao";
 321                 summary["ace"]                  = "ace";
 322                 summary["jack"]                 = "jack";
 323                 summary["shannon"]              = "shannon";
 324                 summary["heip"]                 = "heip";
 325                 summary["shannoneven"]  = "shannoneven";
 326                 summary["smithwilson"]  = "smithwilson";
 327                 summary["invsimpson"]   = "invsimpson";
 328                 summary["npshannon"]    = "npshannon";
 329                 summary["simpson"]              = "simpson";
 330                 summary["simpsoneven"]  = "simpsoneven";
 331                 summary["bergerparker"] = "bergerparker";
 332                 summary["geometric"]    = "geometric";
 333                 summary["bootstrap"]    = "bootstrap";
 334                 summary["logseries"]    = "logseries";
 335                 summary["qstat"]        = "qstat";
 336                 summary["bstick"]       = "bstick";
 337                 summary["nseqs"]                = "nseqs";
 338                 summary["goodscoverage"]= "goodscoverage";
 339                 summary["coverage"]             = "coverage";
 340                 summary["efron"]        = "efron";
 341                 summary["boneh"]        = "boneh";
 342                 summary["solow"]        = "solow";
 343                 summary["shen"]         = "shen";
 344                 summary["default"]          = "default";
 345         }
 346         catch(exception& e) {
 347                 m->errorOut(e, "ValidCalculator", "initialSummary");
 348                 exit(1);
 349         }
 350 }
 351
 352 /********************************************************************/
 353 void ValidCalculators::initialSharedSummary() {
 354         try {
 355                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 356                 sharedsummary["sharedchao"]                             = "sharedchao";
 357                 sharedsummary["sharedace"]                              = "sharedace";
 358                 sharedsummary["jabund"]                                 = "jabund";
 359                 sharedsummary["sorabund"]                               = "sorabund";
 360                 sharedsummary["jclass"]                                 = "jclass";
 361                 sharedsummary["sorclass"]                               = "sorclass";
 362                 sharedsummary["jest"]                                   = "jest";
 363                 sharedsummary["sorest"]                                 = "sorest";
 364                 sharedsummary["thetayc"]                                = "thetayc";
 365                 sharedsummary["thetan"]                                 = "thetan";
 366                 sharedsummary["kstest"]                                 = "kstest";
 367                 sharedsummary["whittaker"]                              = "whittaker";
 368                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 369                 sharedsummary["ochiai"]                                 = "ochiai";
 370                 sharedsummary["anderberg"]                              = "anderberg";
 371                 sharedsummary["kulczynski"]                             = "kulczynski";
 372                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 373                 sharedsummary["lennon"]                                 = "lennon";
 374                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 375                 sharedsummary["braycurtis"]                             = "braycurtis";
 376                 sharedsummary["odum"]                                   = "odum";
 377                 sharedsummary["canberra"]                               = "canberra";
 378                 sharedsummary["structeuclidean"]                = "structeuclidean";
 379                 sharedsummary["structchord"]                    = "structchord";
 380                 sharedsummary["hellinger"]                              = "hellinger";
 381                 sharedsummary["manhattan"]                              = "manhattan";
 382                 sharedsummary["structpearson"]                  = "structpearson";
 383                 sharedsummary["structkulczynski"]               = "structkulczynski";
 384                 sharedsummary["structchi2"]                             = "structchi2";
 385                 sharedsummary["soergel"]                                = "soergel";
 386                 sharedsummary["spearman"]                               = "spearman";
 387                 sharedsummary["speciesprofile"]                 = "speciesprofile";
 388                 sharedsummary["hamming"]                                = "hamming";
 389                 sharedsummary["gower"]                                  = "gower";
 390                 sharedsummary["memchi2"]                                = "memchi2";
 391                 sharedsummary["memchord"]                               = "memchord";
 392                 sharedsummary["memeuclidean"]                   = "memeuclidean";
 393                 sharedsummary["mempearson"]                             = "mempearson";
 394                 sharedsummary["default"]                                = "default";
 395         }
 396         catch(exception& e) {
 397                 m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 398                 exit(1);
 399         }
 400 }
 401
 402
 403 /********************************************************************/
 404
 405 void ValidCalculators::initialSharedRarefact() {
 406         try {
 407                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 408                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 409                 sharedrarefaction["default"]        = "default";
 410         }
 411         catch(exception& e) {
 412                 m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 413                 exit(1);
 414         }
 415 }
 416
 417
 418 /********************************************************************/
 419 void ValidCalculators::initialVennSingle() {
 420         try {
 421                 vennsingle["sobs"]              = "sobs";
 422                 vennsingle["chao"]                  = "chao";
 423                 vennsingle["ace"]                       = "ace";
 424                 vennsingle["jack"]                  = "jack";
 425                 vennsingle["default"]           = "default";
 426         }
 427         catch(exception& e) {
 428                 m->errorOut(e, "ValidCalculator", "initialVennSingle");
 429                 exit(1);
 430         }
 431 }
 432
 433 /********************************************************************/
 434 void ValidCalculators::initialVennShared() {
 435         try {
 436                 vennshared["sharedsobs"]        = "sharedsobs";
 437                 vennshared["sharedchao"]        = "sharedchao";
 438                 vennshared["sharedace"]         = "sharedace";
 439                 vennshared["default"]           = "default";
 440         }
 441         catch(exception& e) {
 442                 m->errorOut(e, "ValidCalculator", "initialVennShared");
 443                 exit(1);
 444         }
 445 }
 446
 447 /********************************************************************/
 448 void ValidCalculators::initialTreeGroups() {
 449         try {
 450                 treegroup["sharedsobs"]                         = "sharedsobs";
 451                 treegroup["sharedchao"]                         = "sharedchao";
 452                 treegroup["sharedace"]                          = "sharedace";
 453                 treegroup["jabund"]                                     = "jabund";
 454                 treegroup["sorabund"]                           = "sorabund";
 455                 treegroup["jclass"]                                     = "jclass";
 456                 treegroup["sorclass"]                           = "sorclass";
 457                 treegroup["jest"]                                       = "jest";
 458                 treegroup["sorest"]                                     = "sorest";
 459                 treegroup["thetayc"]                            = "thetayc";
 460                 treegroup["thetan"]                                     = "thetan";
 461                 treegroup["kstest"]                                     = "kstest";
 462                 treegroup["whittaker"]                          = "whittaker";
 463                 treegroup["sharednseqs"]                        = "sharednseqs";
 464                 treegroup["ochiai"]                                     = "ochiai";
 465                 treegroup["anderberg"]                          = "anderberg";
 466                 treegroup["kulczynski"]                         = "kulczynski";
 467                 treegroup["kulczynskicody"]                     = "kulczynskicody";
 468                 treegroup["lennon"]                                     = "lennon";
 469                 treegroup["morisitahorn"]                       = "morisitahorn";
 470                 treegroup["braycurtis"]                         = "braycurtis";
 471                 treegroup["odum"]                                       = "odum";
 472                 treegroup["canberra"]                           = "canberra";
 473                 treegroup["structeuclidean"]            = "structeuclidean";
 474                 treegroup["structchord"]                        = "structchord";
 475                 treegroup["hellinger"]                          = "hellinger";
 476                 treegroup["manhattan"]                          = "manhattan";
 477                 treegroup["structpearson"]                      = "structpearson";
 478                 treegroup["structkulczynski"]           = "structkulczynski";
 479                 treegroup["structchi2"]                         = "structchi2";
 480                 treegroup["soergel"]                            = "soergel";
 481                 treegroup["spearman"]                           = "spearman";
 482                 treegroup["speciesprofile"]                     = "speciesprofile";
 483                 treegroup["hamming"]                            = "hamming";
 484                 treegroup["gower"]                                      = "gower";
 485                 treegroup["memchi2"]                            = "memchi2";
 486                 treegroup["memchord"]                           = "memchord";
 487                 treegroup["memeuclidean"]                       = "memeuclidean";
 488                 treegroup["mempearson"]                         = "mempearson";
 489
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "ValidCalculator", "initialTreeGroups");
 493                 exit(1);
 494         }
 495 }
 496 /********************************************************************/
 497 void ValidCalculators::initialHeat() {
 498         try {
 499                 heat["jabund"]                          = "jabund";
 500                 heat["sorabund"]                        = "sorabund";
 501                 heat["jclass"]                          = "jclass";
 502                 heat["sorclass"]                        = "sorclass";
 503                 heat["jest"]                            = "jest";
 504                 heat["sorest"]                          = "sorest";
 505                 heat["thetayc"]                         = "thetayc";
 506                 heat["thetan"]                          = "thetan";
 507                 heat["morisitahorn"]            = "morisitahorn";
 508                 heat["braycurtis"]                      = "braycurtis";
 509         }
 510         catch(exception& e) {
 511                 m->errorOut(e, "ValidCalculator", "initialHeat");
 512                 exit(1);
 513         }
 514 }
 515
 516 /********************************************************************/
 517 void ValidCalculators::initialMatrix() {
 518         try {
 519                 matrix["sharedsobs"]                            = "sharedsobs";
 520                 matrix["sharedchao"]                            = "sharedchao";
 521                 matrix["sharedace"]                             = "sharedace";
 522                 matrix["jabund"]                                        = "jabund";
 523                 matrix["sorabund"]                              = "sorabund";
 524                 matrix["jclass"]                                        = "jclass";
 525                 matrix["sorclass"]                              = "sorclass";
 526                 matrix["jest"]                                  = "jest";
 527                 matrix["sorest"]                                        = "sorest";
 528                 matrix["thetayc"]                               = "thetayc";
 529                 matrix["thetan"]                                        = "thetan";
 530                 matrix["kstest"]                                        = "kstest";
 531                 matrix["whittaker"]                             = "whittaker";
 532                 matrix["sharednseqs"]                   = "sharednseqs";
 533                 matrix["ochiai"]                                        = "ochiai";
 534                 matrix["anderberg"]                             = "anderberg";
 535                 matrix["kulczynski"]                            = "kulczynski";
 536                 matrix["kulczynskicody"]                        = "kulczynskicody";
 537                 matrix["lennon"]                                        = "lennon";
 538                 matrix["morisitahorn"]                  = "morisitahorn";
 539                 matrix["braycurtis"]                            = "braycurtis";
 540                 matrix["odum"]                                  = "odum";
 541                 matrix["canberra"]                              = "canberra";
 542                 matrix["structeuclidean"]               = "structeuclidean";
 543                 matrix["structchord"]                   = "structchord";
 544                 matrix["hellinger"]                             = "hellinger";
 545                 matrix["manhattan"]                             = "manhattan";
 546                 matrix["structpearson"]                 = "structpearson";
 547                 matrix["structkulczynski"]              = "structkulczynski";
 548                 matrix["structchi2"]                            = "structchi2";
 549                 matrix["soergel"]                               = "soergel";
 550                 matrix["spearman"]                              = "spearman";
 551                 matrix["speciesprofile"]                        = "speciesprofile";
 552                 matrix["hamming"]                               = "hamming";
 553                 matrix["gower"]                                 = "gower";
 554                 matrix["memchi2"]                               = "memchi2";
 555                 matrix["memchord"]                              = "memchord";
 556                 matrix["memeuclidean"]                  = "memeuclidean";
 557                 matrix["mempearson"]                            = "mempearson";
 558
 559         }
 560         catch(exception& e) {
 561                 m->errorOut(e, "ValidCalculator", "initialMatrix");
 562                 exit(1);
 563         }
 564 }
 565
 566 /********************************************************************/
 567 void ValidCalculators::initialBoot() {
 568         try {
 569                 boot["jabund"]                          = "jabund";
 570                 boot["sorabund"]                        = "sorabund";
 571                 boot["jclass"]                          = "jclass";
 572                 boot["sorclass"]                        = "orclass";
 573                 boot["jest"]                            = "jest";
 574                 boot["sorest"]                          = "sorest";
 575                 boot["thetayc"]                         = "thetayc";
 576                 boot["thetan"]                          = "thetan";
 577                 boot["morisitahorn"]            = "morisitahorn";
 578                 boot["braycurtis"]                      = "braycurtis";
 579         }
 580         catch(exception& e) {
 581                 m->errorOut(e, "ValidCalculator", "initialBoot");
 582                 exit(1);
 583         }
 584 }
 585 /********************************************************************/
 586 void ValidCalculators::initialDistance() {
 587         try {
 588                 distance["nogaps"]              = "nogaps";
 589                 distance["eachgap"]             = "eachgap";
 590                 distance["onegap"]              = "onegap";
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "ValidCalculator", "initialDistance");
 594                 exit(1);
 595         }
 596 }
 597
 598 /********************************************************************/
 599 void ValidCalculators::printCalc(string parameter, ostream& out) {
 600         try{
 601                 out << "The available estimators for calc are ";
 602                 //are you looking for a calculator for a single parameter
 603                 if (parameter == "single") {
 604                         for (it = single.begin(); it != single.end(); it++) {
 605                                 out << it->first << ", ";
 606                         }
 607                 //are you looking for a calculator for a shared parameter
 608                 }else if (parameter == "shared") {
 609                         for (it = shared.begin(); it != shared.end(); it++) {
 610                                 out << it->first << ", ";
 611                         }
 612                 //are you looking for a calculator for a rarefaction parameter
 613                 }else if (parameter == "rarefaction") {
 614                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 615                                 out << it->first << ", ";
 616                         }
 617                 //are you looking for a calculator for a summary parameter
 618                 }else if (parameter == "summary") {
 619                         for (it = summary.begin(); it != summary.end(); it++) {
 620                                 out << it->first << ", ";
 621                         }
 622                 //are you looking for a calculator for a sharedsummary parameter
 623                 }else if (parameter == "sharedsummary") {
 624                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 625                                 out << it->first << ", ";
 626                         }
 627                 }else if (parameter == "sharedrarefaction") {
 628                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 629                                 out << it->first << ", ";
 630                         }
 631                 }else if (parameter == "vennsingle") {
 632                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 633                                 out << it->first << ", ";
 634                         }
 635                 }else if (parameter == "vennshared") {
 636                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 637                                 out << it->first << ", ";
 638                         }
 639                 }else if (parameter == "treegroup") {
 640                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 641                                 out << it->first << ", ";
 642                         }
 643                 }else if (parameter == "matrix") {
 644                         for (it = matrix.begin(); it != matrix.end(); it++) {
 645                                 out << it->first << ", ";
 646                         }
 647                 }else if (parameter == "heat") {
 648                         for (it = heat.begin(); it != heat.end(); it++) {
 649                                 out << it->first << ", ";
 650                         }
 651                 }else if (parameter == "boot") {
 652                         for (it = boot.begin(); it != boot.end(); it++) {
 653                                 out << it->first << ", ";
 654                         }
 655                 }else if (parameter == "distance") {
 656                         for (it = distance.begin(); it != distance.end(); it++) {
 657                                 out << it->first << ", ";
 658                         }
 659                 }
 660
 661                 out << endl;
 662         }
 663         catch(exception& e) {
 664                 m->errorOut(e, "ValidCalculator", "printCalc");
 665                 exit(1);
 666         }
 667 }
 668 /********************************************************************/
 669 string ValidCalculators::printCalc(string parameter) {
 670         try{
 671                 string output = "The available estimators for calc are ";
 672                 //are you looking for a calculator for a single parameter
 673                 if (parameter == "single") {
 674                         for (it = single.begin(); it != single.end(); it++) {
 675                                 output += it->first + ", ";
 676                         }
 677                         //are you looking for a calculator for a shared parameter
 678                 }else if (parameter == "shared") {
 679                         for (it = shared.begin(); it != shared.end(); it++) {
 680                                 output += it->first + ", ";
 681                         }
 682                         //are you looking for a calculator for a rarefaction parameter
 683                 }else if (parameter == "rarefaction") {
 684                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 685                                 output += it->first + ", ";
 686                         }
 687                         //are you looking for a calculator for a summary parameter
 688                 }else if (parameter == "summary") {
 689                         for (it = summary.begin(); it != summary.end(); it++) {
 690                                 output += it->first + ", ";
 691                         }
 692                         //are you looking for a calculator for a sharedsummary parameter
 693                 }else if (parameter == "sharedsummary") {
 694                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 695                                 output += it->first + ", ";
 696                         }
 697                 }else if (parameter == "sharedrarefaction") {
 698                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 699                                 output += it->first + ", ";
 700                         }
 701                 }else if (parameter == "vennsingle") {
 702                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 703                                 output += it->first + ", ";
 704                         }
 705                 }else if (parameter == "vennshared") {
 706                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 707                                 output += it->first + ", ";
 708                         }
 709                 }else if (parameter == "treegroup") {
 710                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 711                                 output += it->first + ", ";
 712                         }
 713                 }else if (parameter == "matrix") {
 714                         for (it = matrix.begin(); it != matrix.end(); it++) {
 715                                 output += it->first + ", ";
 716                         }
 717                 }else if (parameter == "heat") {
 718                         for (it = heat.begin(); it != heat.end(); it++) {
 719                                 output += it->first + ", ";
 720                         }
 721                 }else if (parameter == "boot") {
 722                         for (it = boot.begin(); it != boot.end(); it++) {
 723                                 output += it->first + ", ";
 724                         }
 725                 }else if (parameter == "distance") {
 726                         for (it = distance.begin(); it != distance.end(); it++) {
 727                                 output += it->first + ", ";
 728                         }
 729                 }
 730
 731                 //rip off comma
 732                 output = output.substr(0, output.length()-1);
 733                 output += "\n";
 734
 735                 return output;
 736         }
 737         catch(exception& e) {
 738                 m->errorOut(e, "ValidCalculator", "printCalc");
 739                 exit(1);
 740         }
 741 }
 742 /********************************************************************/
 743
 744