inputdata.cpp

   1 /*
   2  *  inputdata.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 11/18/08.
   6  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "inputdata.h"
  11 #include "ordervector.hpp"
  12 #include "listvector.hpp"
  13 #include "rabundvector.hpp"
  14
  15 /***********************************************************************/
  16
  17 InputData::InputData(string fName, string f) : format(f){
  18         m = MothurOut::getInstance();
  19         globaldata = GlobalData::getInstance();
  20         m->openInputFile(fName, fileHandle);
  21         filename = fName;
  22
  23 }
  24
  25 /***********************************************************************/
  26
  27
  28 InputData::~InputData(){
  29         fileHandle.close();
  30         globaldata = GlobalData::getInstance();
  31         globaldata->saveNextLabel = "";
  32 //      delete output;
  33
  34 }
  35
  36 /***********************************************************************/
  37
  38 InputData::InputData(string fName, string orderFileName, string f) : format(f){
  39         try {
  40                 m = MothurOut::getInstance();
  41                 globaldata = GlobalData::getInstance();
  42                 ifstream ofHandle;
  43                 m->openInputFile(orderFileName, ofHandle);
  44                 string name;
  45
  46                 int count = 0;
  47
  48                 while(ofHandle){
  49                         ofHandle >> name;
  50                         orderMap[name] = count;
  51                         count++;
  52                         m->gobble(ofHandle);
  53                 }
  54                 ofHandle.close();
  55
  56                 m->openInputFile(fName, fileHandle);
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "InputData", "InputData");
  60                 exit(1);
  61         }
  62 }
  63 /***********************************************************************/
  64
  65 ListVector* InputData::getListVector(){
  66         try {
  67                 if(!fileHandle.eof()){
  68                         if(format == "list") {
  69                                 list = new ListVector(fileHandle);
  70                         }else{ list = NULL;  }
  71
  72                         m->gobble(fileHandle);
  73                         return list;
  74                 }
  75                 else{
  76                         return NULL;
  77                 }
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "InputData", "getListVector");
  81                 exit(1);
  82         }
  83 }
  84
  85 /***********************************************************************/
  86 ListVector* InputData::getListVector(string label){
  87         try {
  88                 ifstream in;
  89                 string  thisLabel;
  90                 m->openInputFile(filename, in);
  91
  92                 if(in){
  93
  94                         if (format == "list") {
  95
  96                                 while (in.eof() != true) {
  97
  98                                         list = new ListVector(in);
  99                                         thisLabel = list->getLabel();
 100
 101                                         //if you are at the last label
 102                                         if (thisLabel == label) {  break;  }
 103                                         //so you don't loose this memory
 104                                         else {  delete list;    }
 105                                         m->gobble(in);
 106                                 }
 107                         }else{ list = NULL;  }
 108
 109                         in.close();
 110                         return list;
 111                 }
 112                 else{
 113                         return NULL;
 114                 }
 115         }
 116         catch(exception& e) {
 117                 m->errorOut(e, "InputData", "getListVector");
 118                 exit(1);
 119         }
 120 }
 121 /***********************************************************************/
 122 ListVector* InputData::getListVector(string label, bool resetFP){
 123         try {
 124                 string  thisLabel;
 125                 fileHandle.clear();
 126                 fileHandle.seekg(0);
 127
 128                 if(fileHandle){
 129
 130                         if (format == "list") {
 131
 132                                 while (fileHandle.eof() != true) {
 133
 134                                         list = new ListVector(fileHandle); m->gobble(fileHandle);
 135                                         thisLabel = list->getLabel();
 136
 137                                         //if you are at the last label
 138                                         if (thisLabel == label) {  break;  }
 139                                         //so you don't loose this memory
 140                                         else {  delete list;    }
 141                                 }
 142                         }else{ list = NULL;  }
 143
 144                         return list;
 145                 }
 146                 else{
 147                         return NULL;
 148                 }
 149         }
 150         catch(exception& e) {
 151                 m->errorOut(e, "InputData", "getListVector");
 152                 exit(1);
 153         }
 154 }
 155
 156 /***********************************************************************/
 157
 158 SharedListVector* InputData::getSharedListVector(){
 159         try {
 160                 if(fileHandle){
 161                         if (format == "shared")  {
 162                                 SharedList = new SharedListVector(fileHandle);
 163                         }else{ SharedList = NULL;  }
 164
 165                         m->gobble(fileHandle);
 166                         return SharedList;
 167                 }
 168                 else{
 169                         return NULL;
 170                 }
 171         }
 172         catch(exception& e) {
 173                 m->errorOut(e, "InputData", "getSharedListVector");
 174                 exit(1);
 175         }
 176 }
 177 /***********************************************************************/
 178
 179 SharedListVector* InputData::getSharedListVector(string label){
 180         try {
 181                 ifstream in;
 182                 string  thisLabel;
 183                 m->openInputFile(filename, in);
 184
 185                 if(in){
 186
 187                         if (format == "shared")  {
 188
 189                                 while (in.eof() != true) {
 190
 191                                         SharedList = new SharedListVector(in);
 192                                         thisLabel = SharedList->getLabel();
 193
 194                                         //if you are at the last label
 195                                         if (thisLabel == label) {  break;  }
 196                                         //so you don't loose this memory
 197                                         else {  delete SharedList;      }
 198                                         m->gobble(in);
 199                                 }
 200
 201                         }else{ SharedList = NULL;  }
 202
 203                         in.close();
 204                         return SharedList;
 205
 206                 }else{
 207                         return NULL;
 208                 }
 209         }
 210         catch(exception& e) {
 211                 m->errorOut(e, "InputData", "getSharedListVector");
 212                 exit(1);
 213         }
 214 }
 215
 216
 217
 218 /***********************************************************************/
 219
 220 SharedOrderVector* InputData::getSharedOrderVector(){
 221         try {
 222                 if(fileHandle){
 223                         if (format == "sharedfile")  {
 224                                 SharedOrder = new SharedOrderVector(fileHandle);
 225                         }else{ SharedOrder = NULL;  }
 226
 227                         m->gobble(fileHandle);
 228                         return SharedOrder;
 229
 230                 }else{
 231                         return NULL;
 232                 }
 233         }
 234         catch(exception& e) {
 235                 m->errorOut(e, "InputData", "getSharedOrderVector");
 236                 exit(1);
 237         }
 238 }
 239
 240 /***********************************************************************/
 241
 242 SharedOrderVector* InputData::getSharedOrderVector(string label){
 243         try {
 244                 ifstream in;
 245                 string  thisLabel;
 246                 m->openInputFile(filename, in);
 247
 248                 if(in){
 249
 250                         if (format == "sharedfile")  {
 251
 252                                 while (in.eof() != true) {
 253
 254                                         SharedOrder = new SharedOrderVector(in);
 255                                         thisLabel = SharedOrder->getLabel();
 256
 257                                         //if you are at the last label
 258                                         if (thisLabel == label) {  break;  }
 259                                         //so you don't loose this memory
 260                                         else {  delete SharedOrder;     }
 261                                         m->gobble(in);
 262                                 }
 263
 264                         }else{ SharedOrder = NULL;  }
 265
 266                         in.close();
 267                         return SharedOrder;
 268
 269                 }else{
 270                         return NULL;
 271                 }
 272         }
 273         catch(exception& e) {
 274                 m->errorOut(e, "InputData", "getSharedOrderVector");
 275                 exit(1);
 276         }
 277 }
 278
 279
 280
 281 /***********************************************************************/
 282
 283 OrderVector* InputData::getOrderVector(){
 284         try {
 285                 if(fileHandle){
 286                         if((format == "list") || (format == "listorder")) {
 287                                 input = new ListVector(fileHandle);
 288                         }
 289                         else if (format == "shared")  {
 290                                 input = new SharedListVector(fileHandle);
 291                         }
 292                         else if(format == "rabund"){
 293                                 input = new RAbundVector(fileHandle);
 294                         }
 295                         else if(format == "order"){
 296                                 input = new OrderVector(fileHandle);
 297                         }
 298                         else if(format == "sabund"){
 299                                 input = new SAbundVector(fileHandle);
 300                         }
 301
 302                         m->gobble(fileHandle);
 303
 304                         output = new OrderVector();
 305                         *output = (input->getOrderVector());
 306
 307                         return output;
 308                 }
 309                 else{
 310                         return NULL;
 311                 }
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "InputData", "getOrderVector");
 315                 exit(1);
 316         }
 317 }
 318
 319 /***********************************************************************/
 320 OrderVector* InputData::getOrderVector(string label){
 321         try {
 322
 323                 ifstream in;
 324                 string  thisLabel;
 325                 m->openInputFile(filename, in);
 326
 327                 if(in){
 328                         if((format == "list") || (format == "listorder")) {
 329
 330                                 while (in.eof() != true) {
 331
 332                                         input = new ListVector(in);
 333                                         thisLabel = input->getLabel();
 334
 335                                         //if you are at the last label
 336                                         if (thisLabel == label) {  break;  }
 337                                         //so you don't loose this memory
 338                                         else {  delete input;   }
 339                                         m->gobble(in);
 340                                 }
 341                         }
 342                         else if (format == "shared")  {
 343
 344                                 while (in.eof() != true) {
 345
 346                                         input = new SharedListVector(in);
 347                                         thisLabel = input->getLabel();
 348
 349                                         //if you are at the last label
 350                                         if (thisLabel == label) {  break;  }
 351                                         //so you don't loose this memory
 352                                         else {  delete input;   }
 353                                         m->gobble(in);
 354                                 }
 355
 356                         }
 357                         else if(format == "rabund"){
 358
 359                                 while (in.eof() != true) {
 360
 361                                         input = new RAbundVector(in);
 362                                         thisLabel = input->getLabel();
 363
 364                                         //if you are at the last label
 365                                         if (thisLabel == label) {  break;  }
 366                                         //so you don't loose this memory
 367                                         else {  delete input;   }
 368                                         m->gobble(in);
 369                                 }
 370
 371                         }
 372                         else if(format == "order"){
 373
 374                                 while (in.eof() != true) {
 375
 376                                         input = new OrderVector(in);
 377                                         thisLabel = input->getLabel();
 378
 379                                         //if you are at the last label
 380                                         if (thisLabel == label) {  break;  }
 381                                         //so you don't loose this memory
 382                                         else {  delete input;   }
 383                                         m->gobble(in);
 384                                 }
 385
 386                         }
 387                         else if(format == "sabund"){
 388
 389                                 while (in.eof() != true) {
 390
 391                                         input = new SAbundVector(in);
 392                                         thisLabel = input->getLabel();
 393
 394                                         //if you are at the last label
 395                                         if (thisLabel == label) {  break;  }
 396                                         //so you don't loose this memory
 397                                         else {  delete input;   }
 398                                         m->gobble(in);
 399
 400                                 }
 401
 402                         }
 403
 404                         in.close();
 405
 406                         output = new OrderVector();
 407                         *output = (input->getOrderVector());
 408
 409                         return output;
 410
 411                 }
 412                 else{
 413                         return NULL;
 414                 }
 415         }
 416         catch(exception& e) {
 417                 m->errorOut(e, "InputData", "getOrderVector");
 418                 exit(1);
 419         }
 420 }
 421
 422 /***********************************************************************/
 423 //this is used when you don't need the order vector
 424 vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
 425         try {
 426                 if(fileHandle){
 427                         if (format == "sharedfile")  {
 428                                 SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
 429                                 if (SharedRAbund != NULL) {
 430                                         return SharedRAbund->getSharedRAbundVectors();
 431                                 }
 432                         }else if (format == "shared") {
 433                                 SharedList = new SharedListVector(fileHandle);
 434                                 if (SharedList != NULL) {
 435                                         return SharedList->getSharedRAbundVector();
 436                                 }
 437                         }
 438                         m->gobble(fileHandle);
 439                 }
 440
 441                 //this is created to signal to calling function that the input file is at eof
 442                 vector<SharedRAbundVector*> null;  null.push_back(NULL);
 443                 return null;
 444
 445         }
 446         catch(exception& e) {
 447                 m->errorOut(e, "InputData", "getSharedRAbundVectors");
 448                 exit(1);
 449         }
 450 }
 451 /***********************************************************************/
 452 vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
 453         try {
 454                 ifstream in;
 455                 string  thisLabel;
 456
 457                 m->openInputFile(filename, in);
 458                 globaldata->saveNextLabel = "";
 459
 460                 if(in){
 461                         if (format == "sharedfile")  {
 462                                 while (in.eof() != true) {
 463
 464                                         SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
 465                                         if (SharedRAbund != NULL) {
 466                                                 thisLabel = SharedRAbund->getLabel();
 467
 468                                                 //if you are at the last label
 469                                                 if (thisLabel == label) {  in.close(); return SharedRAbund->getSharedRAbundVectors();  }
 470                                                 else {
 471                                                         //so you don't loose this memory
 472                                                         vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
 473                                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 474                                                         delete SharedRAbund;
 475                                                 }
 476                                         }else{  break;  }
 477                                         m->gobble(in);
 478
 479                                 }
 480                         }else if (format == "shared") {
 481                                 while (in.eof() != true) {
 482
 483                                         SharedList = new SharedListVector(in);
 484                                         if (SharedList != NULL) {
 485                                                 thisLabel = SharedList->getLabel();
 486                                                 //if you are at the last label
 487                                                 if (thisLabel == label) {  in.close(); return SharedList->getSharedRAbundVector();  }
 488                                                 else {
 489                                                         //so you don't loose this memory
 490                                                         delete SharedList;
 491                                                 }
 492                                         }else{  break;  }
 493                                         m->gobble(in);
 494
 495                                 }
 496
 497                         }
 498                 }
 499
 500                 //this is created to signal to calling function that the input file is at eof
 501                 vector<SharedRAbundVector*> null;  null.push_back(NULL);
 502                 in.close();
 503                 return null;
 504
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "InputData", "getSharedRAbundVectors");
 508                 exit(1);
 509         }
 510 }
 511
 512 /***********************************************************************/
 513 //this is used when you don't need the order vector
 514 vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(){
 515         try {
 516                 if(fileHandle){
 517                         if (format == "relabund")  {
 518                                 SharedRAbundFloatVector* SharedRelAbund = new SharedRAbundFloatVector(fileHandle);
 519                                 if (SharedRelAbund != NULL) {
 520                                         return SharedRelAbund->getSharedRAbundFloatVectors();
 521                                 }
 522                         }else if (format == "sharedfile")  {
 523                                 SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
 524                                 if (SharedRAbund != NULL) {
 525                                         vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
 526                                         vector<SharedRAbundFloatVector*> lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup);
 527                                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
 528                                         return lookupFloat;
 529                                 }
 530
 531                         }
 532                         m->gobble(fileHandle);
 533                 }
 534
 535                 //this is created to signal to calling function that the input file is at eof
 536                 vector<SharedRAbundFloatVector*> null;  null.push_back(NULL);
 537                 return null;
 538
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "InputData", "getSharedRAbundFloatVectors");
 542                 exit(1);
 543         }
 544 }
 545 /***********************************************************************/
 546 vector<SharedRAbundFloatVector*> InputData::getSharedRAbundFloatVectors(string label){
 547         try {
 548                 ifstream in;
 549                 string  thisLabel;
 550
 551                 m->openInputFile(filename, in);
 552                 globaldata->saveNextLabel = "";
 553
 554                 if(in){
 555                         if (format == "relabund")  {
 556                                 while (in.eof() != true) {
 557
 558                                         SharedRAbundFloatVector* SharedRelAbund = new SharedRAbundFloatVector(in);
 559                                         if (SharedRelAbund != NULL) {
 560                                                 thisLabel = SharedRelAbund->getLabel();
 561                                                 //if you are at the last label
 562                                                 if (thisLabel == label) {  in.close(); return SharedRelAbund->getSharedRAbundFloatVectors();  }
 563                                                 else {
 564                                                         //so you don't loose this memory
 565                                                         vector<SharedRAbundFloatVector*> lookup = SharedRelAbund->getSharedRAbundFloatVectors();
 566                                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 567                                                         delete SharedRelAbund;
 568                                                 }
 569                                         }else{  break;  }
 570                                         m->gobble(in);
 571                                 }
 572                         }else if (format == "sharedfile")  {
 573                                 while (in.eof() != true) {
 574
 575                                         SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
 576                                         if (SharedRAbund != NULL) {
 577                                                 thisLabel = SharedRAbund->getLabel();
 578
 579                                                 //if you are at the last label
 580                                                 if (thisLabel == label) {
 581                                                         in.close();
 582                                                         vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
 583                                                         vector<SharedRAbundFloatVector*> lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup);
 584                                                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
 585                                                         return lookupFloat;
 586                                                 }else {
 587                                                         //so you don't loose this memory
 588                                                         vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
 589                                                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
 590                                                         delete SharedRAbund;
 591                                                 }
 592                                         }else{  break;  }
 593                                         m->gobble(in);
 594                                 }
 595                         }
 596                 }
 597
 598
 599                 //this is created to signal to calling function that the input file is at eof
 600                 vector<SharedRAbundFloatVector*> null;  null.push_back(NULL);
 601                 in.close();
 602                 return null;
 603
 604         }
 605         catch(exception& e) {
 606                 m->errorOut(e, "InputData", "getSharedRAbundFloatVectors");
 607                 exit(1);
 608         }
 609 }
 610 /***********************************************************************/
 611
 612 SAbundVector* InputData::getSAbundVector(){
 613         try {
 614                 if(fileHandle){
 615                         if (format == "list") {
 616                                 input = new ListVector(fileHandle);
 617                         }
 618                         else if (format == "shared")  {
 619                                 input = new SharedListVector(fileHandle);
 620                         }
 621                         else if(format == "rabund"){
 622                                 input = new RAbundVector(fileHandle);
 623                         }
 624                         else if(format == "order"){
 625                                 input = new OrderVector(fileHandle);
 626                         }
 627                         else if(format == "sabund"){
 628                                 input = new SAbundVector(fileHandle);
 629                         }
 630
 631                         m->gobble(fileHandle);
 632
 633                         sabund = new SAbundVector();
 634                         *sabund = (input->getSAbundVector());
 635
 636                         return sabund;
 637                 }
 638                 else{
 639                         return NULL;
 640                 }
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "InputData", "getSAbundVector");
 644                 exit(1);
 645         }
 646 }
 647 /***********************************************************************/
 648 SAbundVector* InputData::getSAbundVector(string label){
 649         try {
 650
 651                 ifstream in;
 652                 string  thisLabel;
 653                 m->openInputFile(filename, in);
 654
 655                 if(in){
 656                         if (format == "list") {
 657
 658                                 while (in.eof() != true) {
 659
 660                                         input = new ListVector(in);
 661                                         thisLabel = input->getLabel();
 662
 663                                         //if you are at the last label
 664                                         if (thisLabel == label) {  break;  }
 665                                         //so you don't loose this memory
 666                                         else {  delete input;   }
 667                                         m->gobble(in);
 668                                 }
 669                         }
 670                         else if (format == "shared")  {
 671
 672                                 while (in.eof() != true) {
 673
 674                                         input = new SharedListVector(in);
 675                                         thisLabel = input->getLabel();
 676
 677                                         //if you are at the last label
 678                                         if (thisLabel == label) {  break;  }
 679                                         //so you don't loose this memory
 680                                         else {  delete input;   }
 681                                         m->gobble(in);
 682                                 }
 683
 684                         }
 685                         else if(format == "rabund"){
 686
 687                                 while (in.eof() != true) {
 688
 689                                         input = new RAbundVector(in);
 690                                         thisLabel = input->getLabel();
 691
 692                                         //if you are at the last label
 693                                         if (thisLabel == label) {  break;  }
 694                                         //so you don't loose this memory
 695                                         else {  delete input;   }
 696                                         m->gobble(in);
 697                                 }
 698
 699                         }
 700                         else if(format == "order"){
 701
 702                                 while (in.eof() != true) {
 703
 704                                         input = new OrderVector(in);
 705                                         thisLabel = input->getLabel();
 706
 707                                         //if you are at the last label
 708                                         if (thisLabel == label) {  break;  }
 709                                         //so you don't loose this memory
 710                                         else {  delete input;   }
 711                                         m->gobble(in);
 712                                 }
 713
 714                         }
 715                         else if(format == "sabund"){
 716
 717                                 while (in.eof() != true) {
 718
 719                                         input = new SAbundVector(in);
 720                                         thisLabel = input->getLabel();
 721
 722                                         //if you are at the last label
 723                                         if (thisLabel == label) {  break;  }
 724                                         //so you don't loose this memory
 725                                         else {  delete input;   }
 726                                         m->gobble(in);
 727
 728                                 }
 729
 730                         }
 731
 732                         in.close();
 733
 734                         sabund = new SAbundVector();
 735                         *sabund = (input->getSAbundVector());
 736
 737                         return sabund;
 738
 739                 }
 740                 else{
 741                         return NULL;
 742                 }
 743         }
 744         catch(exception& e) {
 745                 m->errorOut(e, "InputData", "getSAbundVector");
 746                 exit(1);
 747         }
 748 }
 749
 750 /***********************************************************************/
 751 RAbundVector* InputData::getRAbundVector(){
 752         try {
 753                 if(fileHandle){
 754                         if (format == "list") {
 755                                 input = new ListVector(fileHandle);
 756                         }
 757                         else if (format == "shared")  {
 758                                 input = new SharedListVector(fileHandle);
 759                         }
 760                         else if(format == "rabund"){
 761                                 input = new RAbundVector(fileHandle);
 762                         }
 763                         else if(format == "order"){
 764                                 input = new OrderVector(fileHandle);
 765                         }
 766                         else if(format == "sabund"){
 767                                 input = new SAbundVector(fileHandle);
 768                         }
 769
 770                         m->gobble(fileHandle);
 771
 772                         rabund = new RAbundVector();
 773                         *rabund = (input->getRAbundVector());
 774
 775                         return rabund;
 776                 }
 777                 else{
 778                         return NULL;
 779                 }
 780         }
 781         catch(exception& e) {
 782                 m->errorOut(e, "InputData", "getRAbundVector");
 783                 exit(1);
 784         }
 785 }
 786 /***********************************************************************/
 787 RAbundVector* InputData::getRAbundVector(string label){
 788         try {
 789
 790                 ifstream in;
 791                 string  thisLabel;
 792                 m->openInputFile(filename, in);
 793
 794                 if(in){
 795                         if (format == "list") {
 796
 797                                 while (in.eof() != true) {
 798
 799                                         input = new ListVector(in);
 800                                         thisLabel = input->getLabel();
 801
 802                                         //if you are at the last label
 803                                         if (thisLabel == label) {  break;  }
 804                                         //so you don't loose this memory
 805                                         else {  delete input;   }
 806                                         m->gobble(in);
 807                                 }
 808                         }
 809                         else if (format == "shared")  {
 810
 811                                 while (in.eof() != true) {
 812
 813                                         input = new SharedListVector(in);
 814                                         thisLabel = input->getLabel();
 815
 816                                         //if you are at the last label
 817                                         if (thisLabel == label) {  break;  }
 818                                         //so you don't loose this memory
 819                                         else {  delete input;   }
 820                                         m->gobble(in);
 821                                 }
 822
 823                         }
 824                         else if(format == "rabund"){
 825
 826                                 while (in.eof() != true) {
 827
 828                                         input = new RAbundVector(in);
 829                                         thisLabel = input->getLabel();
 830
 831                                         //if you are at the last label
 832                                         if (thisLabel == label) {  break;  }
 833                                         //so you don't loose this memory
 834                                         else {  delete input;   }
 835                                         m->gobble(in);
 836                                 }
 837
 838                         }
 839                         else if(format == "order"){
 840
 841                                 while (in.eof() != true) {
 842
 843                                         input = new OrderVector(in);
 844                                         thisLabel = input->getLabel();
 845
 846                                         //if you are at the last label
 847                                         if (thisLabel == label) {  break;  }
 848                                         //so you don't loose this memory
 849                                         else {  delete input;   }
 850                                         m->gobble(in);
 851                                 }
 852
 853                         }
 854                         else if(format == "sabund"){
 855
 856                                 while (in.eof() != true) {
 857
 858                                         input = new SAbundVector(in);
 859                                         thisLabel = input->getLabel();
 860
 861                                         //if you are at the last label
 862                                         if (thisLabel == label) {  break;  }
 863                                         //so you don't loose this memory
 864                                         else {  delete input;   }
 865                                         m->gobble(in);
 866
 867                                 }
 868
 869                         }
 870
 871                         in.close();
 872
 873                         rabund = new RAbundVector();
 874                         *rabund = (input->getRAbundVector());
 875
 876                         return rabund;
 877                 }
 878                 else{
 879                         return NULL;
 880                 }
 881         }
 882         catch(exception& e) {
 883                 m->errorOut(e, "InputData", "getRAbundVector");
 884                 exit(1);
 885         }
 886 }
 887
 888 /***********************************************************************/
 889
 890
 891