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["default"]                   = "default";
 264         }
 265         catch(exception& e) {
 266                 m->errorOut(e, "ValidCalculator", "initialShared");
 267                 exit(1);
 268         }
 269 }
 270
 271 /********************************************************************/
 272 void ValidCalculators::initialRarefaction() {
 273         try {
 274                 rarefaction["sobs"]                     = "sobs";
 275                 rarefaction["chao"]                     = "chao";
 276                 rarefaction["ace"]                      = "ace";
 277                 rarefaction["jack"]                     = "jack";
 278                 rarefaction["shannon"]          = "shannon";
 279                 rarefaction["smithwilson"]      = "smithwilson";
 280                 rarefaction["heip"]                     = "heip";
 281                 rarefaction["npshannon"]        = "npshannon";
 282                 rarefaction["shannoneven"]      = "shannoneven";
 283                 rarefaction["simpson"]          = "simpson";
 284                 rarefaction["invsimpson"]       = "invsimpson";
 285                 rarefaction["simpsoneven"]      = "simpsoneven";
 286                 rarefaction["bootstrap"]        = "bootstrap";
 287                 rarefaction["nseqs"]            = "nseqs";
 288                 rarefaction["coverage"]         = "coverage";
 289                 rarefaction["default"]      = "default";
 290         }
 291         catch(exception& e) {
 292                 m->errorOut(e, "ValidCalculator", "initialRarefaction");
 293                 exit(1);
 294         }
 295 }
 296
 297 /********************************************************************/
 298
 299 void ValidCalculators::initialSummary() {
 300         try {
 301                 summary["sobs"]                 = "sobs";
 302                 summary["chao"]                 = "chao";
 303                 summary["ace"]                  = "ace";
 304                 summary["jack"]                 = "jack";
 305                 summary["shannon"]              = "shannon";
 306                 summary["heip"]                 = "heip";
 307                 summary["shannoneven"]  = "shannoneven";
 308                 summary["smithwilson"]  = "smithwilson";
 309                 summary["invsimpson"]   = "invsimpson";
 310                 summary["npshannon"]    = "npshannon";
 311                 summary["simpson"]              = "simpson";
 312                 summary["simpsoneven"]  = "simpsoneven";
 313                 summary["bergerparker"] = "bergerparker";
 314                 summary["geometric"]    = "geometric";
 315                 summary["bootstrap"]    = "bootstrap";
 316                 summary["logseries"]    = "logseries";
 317                 summary["qstat"]        = "qstat";
 318                 summary["bstick"]       = "bstick";
 319                 summary["nseqs"]                = "nseqs";
 320                 summary["goodscoverage"]= "goodscoverage";
 321                 summary["coverage"]             = "coverage";
 322                 summary["efron"]        = "efron";
 323                 summary["boneh"]        = "boneh";
 324                 summary["solow"]        = "solow";
 325                 summary["shen"]         = "shen";
 326                 summary["default"]          = "default";
 327         }
 328         catch(exception& e) {
 329                 m->errorOut(e, "ValidCalculator", "initialSummary");
 330                 exit(1);
 331         }
 332 }
 333
 334 /********************************************************************/
 335 void ValidCalculators::initialSharedSummary() {
 336         try {
 337                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 338                 sharedsummary["sharedchao"]                             = "sharedchao";
 339                 sharedsummary["sharedace"]                              = "sharedace";
 340                 sharedsummary["jabund"]                                 = "jabund";
 341                 sharedsummary["sorabund"]                       = "sorabund";
 342                 sharedsummary["jclass"]                                 = "jclass";
 343                 sharedsummary["sorclass"]                               = "sorclass";
 344                 sharedsummary["jest"]                                   = "jest";
 345                 sharedsummary["sorest"]                                 = "sorest";
 346                 sharedsummary["thetayc"]                                = "thetayc";
 347                 sharedsummary["thetan"]                                 = "thetan";
 348                 sharedsummary["kstest"]                                 = "kstest";
 349                 sharedsummary["whittaker"]                              = "whittaker";
 350                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 351                 sharedsummary["ochiai"]                                 = "ochiai";
 352                 sharedsummary["anderberg"]                              = "anderberg";
 353                 sharedsummary["kulczynski"]                             = "kulczynski";
 354                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 355                 sharedsummary["lennon"]                                 = "lennon";
 356                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 357                 sharedsummary["braycurtis"]                             = "braycurtis";
 358                 sharedsummary["default"]                                = "default";
 359         }
 360         catch(exception& e) {
 361                 m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 362                 exit(1);
 363         }
 364 }
 365
 366
 367 /********************************************************************/
 368
 369 void ValidCalculators::initialSharedRarefact() {
 370         try {
 371                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 372                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 373                 sharedrarefaction["default"]        = "default";
 374         }
 375         catch(exception& e) {
 376                 m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 377                 exit(1);
 378         }
 379 }
 380
 381
 382 /********************************************************************/
 383 void ValidCalculators::initialVennSingle() {
 384         try {
 385                 vennsingle["sobs"]              = "sobs";
 386                 vennsingle["chao"]                  = "chao";
 387                 vennsingle["ace"]                       = "ace";
 388                 vennsingle["jack"]                  = "jack";
 389                 vennsingle["default"]           = "default";
 390         }
 391         catch(exception& e) {
 392                 m->errorOut(e, "ValidCalculator", "initialVennSingle");
 393                 exit(1);
 394         }
 395 }
 396
 397 /********************************************************************/
 398 void ValidCalculators::initialVennShared() {
 399         try {
 400                 vennshared["sharedsobs"]        = "sharedsobs";
 401                 vennshared["sharedchao"]        = "sharedchao";
 402                 vennshared["sharedace"]         = "sharedace";
 403                 vennshared["default"]           = "default";
 404         }
 405         catch(exception& e) {
 406                 m->errorOut(e, "ValidCalculator", "initialVennShared");
 407                 exit(1);
 408         }
 409 }
 410
 411 /********************************************************************/
 412 void ValidCalculators::initialTreeGroups() {
 413         try {
 414                 treegroup["jabund"]                                     = "jabund";
 415                 treegroup["sorabund"]                           = "sorabund";
 416                 treegroup["jclass"]                                     = "jclass";
 417                 treegroup["sorclass"]                           = "sorclass";
 418                 treegroup["jest"]                                       = "jest";
 419                 treegroup["sorest"]                                     = "sorest";
 420                 treegroup["thetayc"]                            = "thetayc";
 421                 treegroup["thetan"]                                     = "thetan";
 422                 treegroup["morisitahorn"]                       = "morisitahorn";
 423                 treegroup["braycurtis"]                         = "braycurtis";
 424         }
 425         catch(exception& e) {
 426                 m->errorOut(e, "ValidCalculator", "initialTreeGroups");
 427                 exit(1);
 428         }
 429 }
 430 /********************************************************************/
 431 void ValidCalculators::initialHeat() {
 432         try {
 433                 heat["jabund"]                          = "jabund";
 434                 heat["sorabund"]                        = "sorabund";
 435                 heat["jclass"]                          = "jclass";
 436                 heat["sorclass"]                        = "sorclass";
 437                 heat["jest"]                            = "jest";
 438                 heat["sorest"]                          = "sorest";
 439                 heat["thetayc"]                         = "thetayc";
 440                 heat["thetan"]                          = "thetan";
 441                 heat["morisitahorn"]            = "morisitahorn";
 442                 heat["braycurtis"]                      = "braycurtis";
 443         }
 444         catch(exception& e) {
 445                 m->errorOut(e, "ValidCalculator", "initialHeat");
 446                 exit(1);
 447         }
 448 }
 449
 450 /********************************************************************/
 451 void ValidCalculators::initialMatrix() {
 452         try {
 453                 matrix["jabund"]                                = "jabund";
 454                 matrix["sorabund"]                              = "sorabund";
 455                 matrix["jclass"]                                = "jclass";
 456                 matrix["sorclass"]                              = "sorclass";
 457                 matrix["jest"]                                  = "jest";
 458                 matrix["sorest"]                                = "sorest";
 459                 matrix["thetayc"]                               = "thetayc";
 460                 matrix["thetan"]                                = "thetan";
 461                 matrix["morisitahorn"]                  = "morisitahorn";
 462                 matrix["braycurtis"]                    = "braycurtis";
 463         }
 464         catch(exception& e) {
 465                 m->errorOut(e, "ValidCalculator", "initialMatrix");
 466                 exit(1);
 467         }
 468 }
 469
 470 /********************************************************************/
 471 void ValidCalculators::initialBoot() {
 472         try {
 473                 boot["jabund"]                          = "jabund";
 474                 boot["sorabund"]                        = "sorabund";
 475                 boot["jclass"]                          = "jclass";
 476                 boot["sorclass"]                        = "orclass";
 477                 boot["jest"]                            = "jest";
 478                 boot["sorest"]                          = "sorest";
 479                 boot["thetayc"]                         = "thetayc";
 480                 boot["thetan"]                          = "thetan";
 481                 boot["morisitahorn"]            = "morisitahorn";
 482                 boot["braycurtis"]                      = "braycurtis";
 483         }
 484         catch(exception& e) {
 485                 m->errorOut(e, "ValidCalculator", "initialBoot");
 486                 exit(1);
 487         }
 488 }
 489 /********************************************************************/
 490 void ValidCalculators::initialDistance() {
 491         try {
 492                 distance["nogaps"]              = "nogaps";
 493                 distance["eachgap"]             = "eachgap";
 494                 distance["onegap"]              = "onegap";
 495         }
 496         catch(exception& e) {
 497                 m->errorOut(e, "ValidCalculator", "initialDistance");
 498                 exit(1);
 499         }
 500 }
 501
 502 /********************************************************************/
 503 void ValidCalculators::printCalc(string parameter, ostream& out) {
 504         try{
 505                 out << "The available estimators for calc are ";
 506                 //are you looking for a calculator for a single parameter
 507                 if (parameter == "single") {
 508                         for (it = single.begin(); it != single.end(); it++) {
 509                                 out << it->first << ", ";
 510                         }
 511                 //are you looking for a calculator for a shared parameter
 512                 }else if (parameter == "shared") {
 513                         for (it = shared.begin(); it != shared.end(); it++) {
 514                                 out << it->first << ", ";
 515                         }
 516                 //are you looking for a calculator for a rarefaction parameter
 517                 }else if (parameter == "rarefaction") {
 518                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 519                                 out << it->first << ", ";
 520                         }
 521                 //are you looking for a calculator for a summary parameter
 522                 }else if (parameter == "summary") {
 523                         for (it = summary.begin(); it != summary.end(); it++) {
 524                                 out << it->first << ", ";
 525                         }
 526                 //are you looking for a calculator for a sharedsummary parameter
 527                 }else if (parameter == "sharedsummary") {
 528                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 529                                 out << it->first << ", ";
 530                         }
 531                 }else if (parameter == "sharedrarefaction") {
 532                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 533                                 out << it->first << ", ";
 534                         }
 535                 }else if (parameter == "vennsingle") {
 536                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 537                                 out << it->first << ", ";
 538                         }
 539                 }else if (parameter == "vennshared") {
 540                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 541                                 out << it->first << ", ";
 542                         }
 543                 }else if (parameter == "treegroup") {
 544                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 545                                 out << it->first << ", ";
 546                         }
 547                 }else if (parameter == "matrix") {
 548                         for (it = matrix.begin(); it != matrix.end(); it++) {
 549                                 out << it->first << ", ";
 550                         }
 551                 }else if (parameter == "heat") {
 552                         for (it = heat.begin(); it != heat.end(); it++) {
 553                                 out << it->first << ", ";
 554                         }
 555                 }else if (parameter == "boot") {
 556                         for (it = boot.begin(); it != boot.end(); it++) {
 557                                 out << it->first << ", ";
 558                         }
 559                 }else if (parameter == "distance") {
 560                         for (it = distance.begin(); it != distance.end(); it++) {
 561                                 out << it->first << ", ";
 562                         }
 563                 }
 564
 565                 out << endl;
 566         }
 567         catch(exception& e) {
 568                 m->errorOut(e, "ValidCalculator", "printCalc");
 569                 exit(1);
 570         }
 571 }
 572 /********************************************************************/
 573