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["simpson"]           = "simpson";
 213                 single["bergerparker"]  = "bergerparker";
 214                 single["bootstrap"]     = "bootstrap";
 215                 single["geometric"]     = "geometric";
 216                 single["logseries"]         = "logseries";
 217                 single["qstat"]         = "qstat";
 218                 single["bstick"]        = "bstick";
 219                 single["goodscoverage"] = "goodscoverage";
 220                 single["nseqs"]                 = "nseqs";
 221                 single["coverage"]              = "coverage";
 222                 single["efron"]         = "efron";
 223                 single["boneh"]         = "boneh";
 224                 single["solow"]         = "solow";
 225                 single["shen"]          = "shen";
 226                 single["default"]           = "default";
 227         }
 228         catch(exception& e) {
 229                 m->errorOut(e, "ValidCalculator", "initialSingle");
 230                 exit(1);
 231         }
 232 }
 233
 234 /********************************************************************/
 235 void ValidCalculators::initialShared() {
 236         try {
 237                 shared["sharedsobs"]                    = "sharedsobs";
 238                 shared["sharedchao"]                    = "sharedchao";
 239                 shared["sharedace"]                             = "sharedace";
 240                 shared["jabund"]                                = "jabund";
 241                 shared["sorabund"]                              = "sorabund";
 242                 shared["jclass"]                                = "jclass";
 243                 shared["sorclass"]                              = "sorclass";
 244                 shared["jest"]                                  = "jest";
 245                 shared["sorest"]                                = "sorest";
 246                 shared["thetayc"]                               = "thetayc";
 247                 shared["thetan"]                                = "thetan";
 248                 shared["kstest"]                                = "kstest";
 249                 shared["whittaker"]                         = "whittaker";
 250                 shared["sharednseqs"]                   = "sharednseqs";
 251                 shared["ochiai"]                                = "ochiai";
 252                 shared["anderberg"]                             = "anderberg";
 253                 shared["kulczynski"]                    = "kulczynski";
 254                 shared["kulczynskicody"]                = "kulczynskicody";
 255                 shared["lennon"]                                = "lennon";
 256                 shared["morisitahorn"]                  = "morisitahorn";
 257                 shared["braycurtis"]                    = "braycurtis";
 258                 shared["default"]                   = "default";
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "ValidCalculator", "initialShared");
 262                 exit(1);
 263         }
 264 }
 265
 266 /********************************************************************/
 267 void ValidCalculators::initialRarefaction() {
 268         try {
 269                 rarefaction["sobs"]                     = "sobs";
 270                 rarefaction["chao"]                     = "chao";
 271                 rarefaction["ace"]                      = "ace";
 272                 rarefaction["jack"]                     = "jack";
 273                 rarefaction["shannon"]          = "shannon";
 274                 rarefaction["npshannon"]        = "npshannon";
 275                 rarefaction["simpson"]          = "simpson";
 276                 rarefaction["bootstrap"]        = "bootstrap";
 277                 rarefaction["nseqs"]            = "nseqs";
 278                 rarefaction["coverage"]         = "coverage";
 279                 rarefaction["default"]      = "default";
 280         }
 281         catch(exception& e) {
 282                 m->errorOut(e, "ValidCalculator", "initialRarefaction");
 283                 exit(1);
 284         }
 285 }
 286
 287 /********************************************************************/
 288
 289 void ValidCalculators::initialSummary() {
 290         try {
 291                 summary["sobs"]                 = "sobs";
 292                 summary["chao"]                 = "chao";
 293                 summary["ace"]                  = "ace";
 294                 summary["jack"]                 = "jack";
 295                 summary["shannon"]              = "shannon";
 296                 summary["npshannon"]    = "npshannon";
 297                 summary["simpson"]              = "simpson";
 298                 summary["bergerparker"] = "bergerparker";
 299                 summary["geometric"]    = "geometric";
 300                 summary["bootstrap"]    = "bootstrap";
 301                 summary["logseries"]    = "logseries";
 302                 summary["qstat"]        = "qstat";
 303                 summary["bstick"]       = "bstick";
 304                 summary["nseqs"]                = "nseqs";
 305                 summary["goodscoverage"]= "goodscoverage";
 306                 summary["coverage"]             = "coverage";
 307                 summary["efron"]        = "efron";
 308                 summary["boneh"]        = "boneh";
 309                 summary["solow"]        = "solow";
 310                 summary["shen"]         = "shen";
 311                 summary["default"]          = "default";
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "ValidCalculator", "initialSummary");
 315                 exit(1);
 316         }
 317 }
 318
 319 /********************************************************************/
 320 void ValidCalculators::initialSharedSummary() {
 321         try {
 322                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 323                 sharedsummary["sharedchao"]                             = "sharedchao";
 324                 sharedsummary["sharedace"]                              = "sharedace";
 325                 sharedsummary["jabund"]                                 = "jabund";
 326                 sharedsummary["sorabund"]                       = "sorabund";
 327                 sharedsummary["jclass"]                                 = "jclass";
 328                 sharedsummary["sorclass"]                               = "sorclass";
 329                 sharedsummary["jest"]                                   = "jest";
 330                 sharedsummary["sorest"]                                 = "sorest";
 331                 sharedsummary["thetayc"]                                = "thetayc";
 332                 sharedsummary["thetan"]                                 = "thetan";
 333                 sharedsummary["kstest"]                                 = "kstest";
 334                 sharedsummary["whittaker"]                              = "whittaker";
 335                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 336                 sharedsummary["ochiai"]                                 = "ochiai";
 337                 sharedsummary["anderberg"]                              = "anderberg";
 338                 sharedsummary["kulczynski"]                             = "kulczynski";
 339                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 340                 sharedsummary["lennon"]                                 = "lennon";
 341                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 342                 sharedsummary["braycurtis"]                             = "braycurtis";
 343                 sharedsummary["default"]                                = "default";
 344         }
 345         catch(exception& e) {
 346                 m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 347                 exit(1);
 348         }
 349 }
 350
 351
 352 /********************************************************************/
 353
 354 void ValidCalculators::initialSharedRarefact() {
 355         try {
 356                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 357                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 358                 sharedrarefaction["default"]        = "default";
 359         }
 360         catch(exception& e) {
 361                 m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 362                 exit(1);
 363         }
 364 }
 365
 366
 367 /********************************************************************/
 368 void ValidCalculators::initialVennSingle() {
 369         try {
 370                 vennsingle["sobs"]              = "sobs";
 371                 vennsingle["chao"]                  = "chao";
 372                 vennsingle["ace"]                       = "ace";
 373                 vennsingle["jack"]                  = "jack";
 374                 vennsingle["default"]           = "default";
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "ValidCalculator", "initialVennSingle");
 378                 exit(1);
 379         }
 380 }
 381
 382 /********************************************************************/
 383 void ValidCalculators::initialVennShared() {
 384         try {
 385                 vennshared["sharedsobs"]        = "sharedsobs";
 386                 vennshared["sharedchao"]        = "sharedchao";
 387                 vennshared["sharedace"]         = "sharedace";
 388                 vennshared["default"]           = "default";
 389         }
 390         catch(exception& e) {
 391                 m->errorOut(e, "ValidCalculator", "initialVennShared");
 392                 exit(1);
 393         }
 394 }
 395
 396 /********************************************************************/
 397 void ValidCalculators::initialTreeGroups() {
 398         try {
 399                 treegroup["jabund"]                                     = "jabund";
 400                 treegroup["sorabund"]                           = "sorabund";
 401                 treegroup["jclass"]                                     = "jclass";
 402                 treegroup["sorclass"]                           = "sorclass";
 403                 treegroup["jest"]                                       = "jest";
 404                 treegroup["sorest"]                                     = "sorest";
 405                 treegroup["thetayc"]                            = "thetayc";
 406                 treegroup["thetan"]                                     = "thetan";
 407                 treegroup["morisitahorn"]                       = "morisitahorn";
 408                 treegroup["braycurtis"]                         = "braycurtis";
 409         }
 410         catch(exception& e) {
 411                 m->errorOut(e, "ValidCalculator", "initialTreeGroups");
 412                 exit(1);
 413         }
 414 }
 415 /********************************************************************/
 416 void ValidCalculators::initialHeat() {
 417         try {
 418                 heat["jabund"]                          = "jabund";
 419                 heat["sorabund"]                        = "sorabund";
 420                 heat["jclass"]                          = "jclass";
 421                 heat["sorclass"]                        = "sorclass";
 422                 heat["jest"]                            = "jest";
 423                 heat["sorest"]                          = "sorest";
 424                 heat["thetayc"]                         = "thetayc";
 425                 heat["thetan"]                          = "thetan";
 426                 heat["morisitahorn"]            = "morisitahorn";
 427                 heat["braycurtis"]                      = "braycurtis";
 428         }
 429         catch(exception& e) {
 430                 m->errorOut(e, "ValidCalculator", "initialHeat");
 431                 exit(1);
 432         }
 433 }
 434
 435 /********************************************************************/
 436 void ValidCalculators::initialMatrix() {
 437         try {
 438                 matrix["jabund"]                                = "jabund";
 439                 matrix["sorabund"]                              = "sorabund";
 440                 matrix["jclass"]                                = "jclass";
 441                 matrix["sorclass"]                              = "sorclass";
 442                 matrix["jest"]                                  = "jest";
 443                 matrix["sorest"]                                = "sorest";
 444                 matrix["thetayc"]                               = "thetayc";
 445                 matrix["thetan"]                                = "thetan";
 446                 matrix["morisitahorn"]                  = "morisitahorn";
 447                 matrix["braycurtis"]                    = "braycurtis";
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "ValidCalculator", "initialMatrix");
 451                 exit(1);
 452         }
 453 }
 454
 455 /********************************************************************/
 456 void ValidCalculators::initialBoot() {
 457         try {
 458                 boot["jabund"]                          = "jabund";
 459                 boot["sorabund"]                        = "sorabund";
 460                 boot["jclass"]                          = "jclass";
 461                 boot["sorclass"]                        = "orclass";
 462                 boot["jest"]                            = "jest";
 463                 boot["sorest"]                          = "sorest";
 464                 boot["thetayc"]                         = "thetayc";
 465                 boot["thetan"]                          = "thetan";
 466                 boot["morisitahorn"]            = "morisitahorn";
 467                 boot["braycurtis"]                      = "braycurtis";
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "ValidCalculator", "initialBoot");
 471                 exit(1);
 472         }
 473 }
 474 /********************************************************************/
 475 void ValidCalculators::initialDistance() {
 476         try {
 477                 distance["nogaps"]              = "nogaps";
 478                 distance["eachgap"]             = "eachgap";
 479                 distance["onegap"]              = "onegap";
 480         }
 481         catch(exception& e) {
 482                 m->errorOut(e, "ValidCalculator", "initialDistance");
 483                 exit(1);
 484         }
 485 }
 486
 487 /********************************************************************/
 488 void ValidCalculators::printCalc(string parameter, ostream& out) {
 489         try{
 490                 out << "The available estimators for calc are ";
 491                 //are you looking for a calculator for a single parameter
 492                 if (parameter == "single") {
 493                         for (it = single.begin(); it != single.end(); it++) {
 494                                 out << it->first << ", ";
 495                         }
 496                 //are you looking for a calculator for a shared parameter
 497                 }else if (parameter == "shared") {
 498                         for (it = shared.begin(); it != shared.end(); it++) {
 499                                 out << it->first << ", ";
 500                         }
 501                 //are you looking for a calculator for a rarefaction parameter
 502                 }else if (parameter == "rarefaction") {
 503                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 504                                 out << it->first << ", ";
 505                         }
 506                 //are you looking for a calculator for a summary parameter
 507                 }else if (parameter == "summary") {
 508                         for (it = summary.begin(); it != summary.end(); it++) {
 509                                 out << it->first << ", ";
 510                         }
 511                 //are you looking for a calculator for a sharedsummary parameter
 512                 }else if (parameter == "sharedsummary") {
 513                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 514                                 out << it->first << ", ";
 515                         }
 516                 }else if (parameter == "sharedrarefaction") {
 517                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 518                                 out << it->first << ", ";
 519                         }
 520                 }else if (parameter == "vennsingle") {
 521                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 522                                 out << it->first << ", ";
 523                         }
 524                 }else if (parameter == "vennshared") {
 525                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 526                                 out << it->first << ", ";
 527                         }
 528                 }else if (parameter == "treegroup") {
 529                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 530                                 out << it->first << ", ";
 531                         }
 532                 }else if (parameter == "matrix") {
 533                         for (it = matrix.begin(); it != matrix.end(); it++) {
 534                                 out << it->first << ", ";
 535                         }
 536                 }else if (parameter == "heat") {
 537                         for (it = heat.begin(); it != heat.end(); it++) {
 538                                 out << it->first << ", ";
 539                         }
 540                 }else if (parameter == "boot") {
 541                         for (it = boot.begin(); it != boot.end(); it++) {
 542                                 out << it->first << ", ";
 543                         }
 544                 }else if (parameter == "distance") {
 545                         for (it = distance.begin(); it != distance.end(); it++) {
 546                                 out << it->first << ", ";
 547                         }
 548                 }
 549
 550                 out << endl;
 551         }
 552         catch(exception& e) {
 553                 m->errorOut(e, "ValidCalculator", "printCalc");
 554                 exit(1);
 555         }
 556 }
 557 /********************************************************************/
 558