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         m->openInputFile(fName, fileHandle);
  20         filename = fName;
  21         m->saveNextLabel = "";
  22 }
  23 /***********************************************************************/
  24
  25 InputData::~InputData(){
  26         fileHandle.close();
  27         m->saveNextLabel = "";
  28 }
  29
  30 /***********************************************************************/
  31
  32 InputData::InputData(string fName, string orderFileName, string f) : format(f){
  33         try {
  34                 m = MothurOut::getInstance();
  35                 ifstream ofHandle;
  36                 m->openInputFile(orderFileName, ofHandle);
  37                 string name;
  38
  39                 int count = 0;
  40
  41                 while(ofHandle){
  42                         ofHandle >> name;
  43                         orderMap[name] = count;
  44                         count++;
  45                         m->gobble(ofHandle);
  46                 }
  47                 ofHandle.close();
  48
  49                 m->openInputFile(fName, fileHandle);
  50                 m->saveNextLabel = "";
  51
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "InputData", "InputData");
  55                 exit(1);
  56         }
  57 }
  58 /***********************************************************************/
  59
  60 ListVector* InputData::getListVector(){
  61         try {
  62                 if(!fileHandle.eof()){
  63                         if(format == "list") {
  64                                 list = new ListVector(fileHandle);
  65                         }else{ list = NULL;  }
  66
  67                         m->gobble(fileHandle);
  68                         return list;
  69                 }
  70                 else{
  71                         return NULL;
  72                 }
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "InputData", "getListVector");
  76                 exit(1);
  77         }
  78 }
  79
  80 /***********************************************************************/
  81 ListVector* InputData::getListVector(string label){
  82         try {
  83                 ifstream in;
  84                 string  thisLabel;
  85                 m->openInputFile(filename, in);
  86         m->saveNextLabel = "";
  87
  88                 if(in){
  89
  90                         if (format == "list") {
  91
  92                                 while (in.eof() != true) {
  93
  94                                         list = new ListVector(in);
  95                                         thisLabel = list->getLabel();
  96
  97                                         //if you are at the last label
  98                                         if (thisLabel == label) {  break;  }
  99                                         //so you don't loose this memory
 100                                         else {  delete list;    }
 101                                         m->gobble(in);
 102                                 }
 103                         }else{ list = NULL;  }
 104
 105                         in.close();
 106                         return list;
 107                 }
 108                 else{
 109                         return NULL;
 110                 }
 111         }
 112         catch(exception& e) {
 113                 m->errorOut(e, "InputData", "getListVector");
 114                 exit(1);
 115         }
 116 }
 117 /***********************************************************************/
 118 ListVector* InputData::getListVector(string label, bool resetFP){
 119         try {
 120                 string  thisLabel;
 121                 fileHandle.clear();
 122                 fileHandle.seekg(0);
 123         m->saveNextLabel = "";
 124
 125                 if(fileHandle){
 126
 127                         if (format == "list") {
 128
 129                                 while (fileHandle.eof() != true) {
 130
 131                                         list = new ListVector(fileHandle); m->gobble(fileHandle);
 132                                         thisLabel = list->getLabel();
 133
 134                                         //if you are at the last label
 135                                         if (thisLabel == label) {  break;  }
 136                                         //so you don't loose this memory
 137                                         else {  delete list;    }
 138                                 }
 139                         }else{ list = NULL;  }
 140
 141                         return list;
 142                 }
 143                 else{
 144                         return NULL;
 145                 }
 146         }
 147         catch(exception& e) {
 148                 m->errorOut(e, "InputData", "getListVector");
 149                 exit(1);
 150         }
 151 }
 152
 153 /***********************************************************************/
 154
 155 SharedListVector* InputData::getSharedListVector(){
 156         try {
 157                 if(fileHandle){
 158                         if (format == "shared")  {
 159                                 SharedList = new SharedListVector(fileHandle);
 160                         }else{ SharedList = NULL;  }
 161
 162                         m->gobble(fileHandle);
 163                         return SharedList;
 164                 }
 165                 else{
 166                         return NULL;
 167                 }
 168         }
 169         catch(exception& e) {
 170                 m->errorOut(e, "InputData", "getSharedListVector");
 171                 exit(1);
 172         }
 173 }
 174 /***********************************************************************/
 175
 176 SharedListVector* InputData::getSharedListVector(string label){
 177         try {
 178                 ifstream in;
 179                 string  thisLabel;
 180                 m->openInputFile(filename, in);
 181
 182                 if(in){
 183
 184                         if (format == "shared")  {
 185
 186                                 while (in.eof() != true) {
 187
 188                                         SharedList = new SharedListVector(in);
 189                                         thisLabel = SharedList->getLabel();
 190
 191                                         //if you are at the last label
 192                                         if (thisLabel == label) {  break;  }
 193                                         //so you don't loose this memory
 194                                         else {  delete SharedList;      }
 195                                         m->gobble(in);
 196                                 }
 197
 198                         }else{ SharedList = NULL;  }
 199
 200                         in.close();
 201                         return SharedList;
 202
 203                 }else{
 204                         return NULL;
 205                 }
 206         }
 207         catch(exception& e) {
 208                 m->errorOut(e, "InputData", "getSharedListVector");
 209                 exit(1);
 210         }
 211 }
 212
 213
 214
 215 /***********************************************************************/
 216
 217 SharedOrderVector* InputData::getSharedOrderVector(){
 218         try {
 219                 if(fileHandle){
 220                         if (format == "sharedfile")  {
 221                                 SharedOrder = new SharedOrderVector(fileHandle);
 222                         }else{ SharedOrder = NULL;  }
 223
 224                         m->gobble(fileHandle);
 225                         return SharedOrder;
 226
 227                 }else{
 228                         return NULL;
 229                 }
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "InputData", "getSharedOrderVector");
 233                 exit(1);
 234         }
 235 }
 236
 237 /***********************************************************************/
 238
 239 SharedOrderVector* InputData::getSharedOrderVector(string label){
 240         try {
 241                 ifstream in;
 242                 string  thisLabel;
 243                 m->openInputFile(filename, in);
 244         m->saveNextLabel = "";
 245
 246                 if(in){
 247
 248                         if (format == "sharedfile")  {
 249
 250                                 while (in.eof() != true) {
 251
 252                                         SharedOrder = new SharedOrderVector(in);
 253                                         thisLabel = SharedOrder->getLabel();
 254
 255                                         //if you are at the last label
 256                                         if (thisLabel == label) {  break;  }
 257                                         //so you don't loose this memory
 258                                         else {  delete SharedOrder;     }
 259                                         m->gobble(in);
 260                                 }
 261
 262                         }else{ SharedOrder = NULL;  }
 263
 264                         in.close();
 265                         return SharedOrder;
 266
 267                 }else{
 268                         return NULL;
 269                 }
 270         }
 271         catch(exception& e) {
 272                 m->errorOut(e, "InputData", "getSharedOrderVector");
 273                 exit(1);
 274         }
 275 }
 276
 277
 278
 279 /***********************************************************************/
 280
 281 OrderVector* InputData::getOrderVector(){
 282         try {
 283                 if(fileHandle){
 284                         if((format == "list") || (format == "listorder")) {
 285                                 input = new ListVector(fileHandle);
 286                         }
 287                         else if (format == "shared")  {
 288                                 input = new SharedListVector(fileHandle);
 289                         }
 290                         else if(format == "rabund"){
 291                                 input = new RAbundVector(fileHandle);
 292                         }
 293                         else if(format == "order"){
 294                                 input = new OrderVector(fileHandle);
 295                         }
 296                         else if(format == "sabund"){
 297                                 input = new SAbundVector(fileHandle);
 298                         }
 299
 300                         m->gobble(fileHandle);
 301
 302                         output = new OrderVector();
 303                         *output = (input->getOrderVector());
 304
 305                         return output;
 306                 }
 307                 else{
 308                         return NULL;
 309                 }
 310         }
 311         catch(exception& e) {
 312                 m->errorOut(e, "InputData", "getOrderVector");
 313                 exit(1);
 314         }
 315 }
 316
 317 /***********************************************************************/
 318 OrderVector* InputData::getOrderVector(string label){
 319         try {
 320
 321                 ifstream in;
 322                 string  thisLabel;
 323                 m->openInputFile(filename, in);
 324
 325                 if(in){
 326                         if((format == "list") || (format == "listorder")) {
 327                 m->saveNextLabel = "";
 328                                 while (in.eof() != true) {
 329
 330                                         input = new ListVector(in);
 331                                         thisLabel = input->getLabel();
 332
 333                                         //if you are at the last label
 334                                         if (thisLabel == label) {  break;  }
 335                                         //so you don't loose this memory
 336                                         else {  delete input;   }
 337                                         m->gobble(in);
 338                                 }
 339                         }
 340                         else if (format == "shared")  {
 341                                 m->saveNextLabel = "";
 342                                 while (in.eof() != true) {
 343
 344                                         input = new SharedListVector(in);
 345                                         thisLabel = input->getLabel();
 346
 347                                         //if you are at the last label
 348                                         if (thisLabel == label) {  break;  }
 349                                         //so you don't loose this memory
 350                                         else {  delete input;   }
 351                                         m->gobble(in);
 352                                 }
 353
 354                         }
 355                         else if(format == "rabund"){
 356
 357                                 while (in.eof() != true) {
 358
 359                                         input = new RAbundVector(in);
 360                                         thisLabel = input->getLabel();
 361
 362                                         //if you are at the last label
 363                                         if (thisLabel == label) {  break;  }
 364                                         //so you don't loose this memory
 365                                         else {  delete input;   }
 366                                         m->gobble(in);
 367                                 }
 368
 369                         }
 370                         else if(format == "order"){
 371
 372                                 while (in.eof() != true) {
 373
 374                                         input = new OrderVector(in);
 375                                         thisLabel = input->getLabel();
 376
 377                                         //if you are at the last label
 378                                         if (thisLabel == label) {  break;  }
 379                                         //so you don't loose this memory
 380                                         else {  delete input;   }
 381                                         m->gobble(in);
 382                                 }
 383
 384                         }
 385                         else if(format == "sabund"){
 386
 387                                 while (in.eof() != true) {
 388
 389                                         input = new SAbundVector(in);
 390                                         thisLabel = input->getLabel();
 391
 392                                         //if you are at the last label
 393                                         if (thisLabel == label) {  break;  }
 394                                         //so you don't loose this memory
 395                                         else {  delete input;   }
 396                                         m->gobble(in);
 397
 398                                 }
 399
 400                         }
 401
 402                         in.close();
 403
 404                         output = new OrderVector();
 405                         *output = (input->getOrderVector());
 406
 407                         return output;
 408
 409                 }
 410                 else{
 411                         return NULL;
 412                 }
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "InputData", "getOrderVector");
 416                 exit(1);
 417         }
 418 }
 419
 420 /***********************************************************************/
 421 //this is used when you don't need the order vector
 422 vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
 423         try {
 424                 if(fileHandle){
 425                         if (format == "sharedfile")  {
 426                                 SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
 427                                 if (SharedRAbund != NULL) {
 428                                         return SharedRAbund->getSharedRAbundVectors();
 429                                 }
 430                         }else if (format == "shared") {
 431                                 SharedList = new SharedListVector(fileHandle);
 432
 433                                 if (SharedList != NULL) {
 434                                         return SharedList->getSharedRAbundVector();
 435                                 }
 436                         }
 437                         m->gobble(fileHandle);
 438                 }
 439
 440                 //this is created to signal to calling function that the input file is at eof
 441                 vector<SharedRAbundVector*> null;  null.push_back(NULL);
 442                 return null;
 443
 444         }
 445         catch(exception& e) {
 446                 m->errorOut(e, "InputData", "getSharedRAbundVectors");
 447                 exit(1);
 448         }
 449 }
 450 /***********************************************************************/
 451 vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
 452         try {
 453                 ifstream in;
 454                 string  thisLabel;
 455
 456                 m->openInputFile(filename, in);
 457                 m->saveNextLabel = "";
 458
 459                 if(in){
 460                         if (format == "sharedfile")  {
 461                                 while (in.eof() != true) {
 462
 463                                         SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
 464                                         if (SharedRAbund != NULL) {
 465                                                 thisLabel = SharedRAbund->getLabel();
 466
 467                                                 //if you are at the last label
 468                                                 if (thisLabel == label) {  in.close(); return SharedRAbund->getSharedRAbundVectors();  }
 469                                                 else {
 470                                                         //so you don't loose this memory
 471                                                         vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
 472                                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 473                                                         delete SharedRAbund;
 474                                                 }
 475                                         }else{  break;  }
 476                                         m->gobble(in);
 477
 478                                 }
 479                         }else if (format == "shared") {
 480                                 while (in.eof() != true) {
 481
 482                                         SharedList = new SharedListVector(in);
 483
 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                 m->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                         m->gobble(fileHandle);
 631
 632                         sabund = new SAbundVector();
 633                         *sabund = (input->getSAbundVector());
 634
 635                         return sabund;
 636                 }
 637                 else{
 638                         return NULL;
 639                 }
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "InputData", "getSAbundVector");
 643                 exit(1);
 644         }
 645 }
 646 /***********************************************************************/
 647 SAbundVector* InputData::getSAbundVector(string label){
 648         try {
 649
 650                 ifstream in;
 651                 string  thisLabel;
 652                 m->openInputFile(filename, in);
 653
 654                 if(in){
 655                         if (format == "list") {
 656                 m->saveNextLabel = "";
 657                                 while (in.eof() != true) {
 658
 659                                         input = new ListVector(in);
 660                                         thisLabel = input->getLabel();
 661
 662                                         //if you are at the last label
 663                                         if (thisLabel == label) {  break;  }
 664                                         //so you don't loose this memory
 665                                         else {  delete input;   }
 666                                         m->gobble(in);
 667                                 }
 668                         }
 669                         else if (format == "shared")  {
 670                                 m->saveNextLabel = "";
 671                                 while (in.eof() != true) {
 672
 673                                         input = new SharedListVector(in);
 674                                         thisLabel = input->getLabel();
 675
 676                                         //if you are at the last label
 677                                         if (thisLabel == label) {  break;  }
 678                                         //so you don't loose this memory
 679                                         else {  delete input;   }
 680                                         m->gobble(in);
 681                                 }
 682
 683                         }
 684                         else if(format == "rabund"){
 685
 686                                 while (in.eof() != true) {
 687
 688                                         input = new RAbundVector(in);
 689                                         thisLabel = input->getLabel();
 690
 691                                         //if you are at the last label
 692                                         if (thisLabel == label) {  break;  }
 693                                         //so you don't loose this memory
 694                                         else {  delete input;   }
 695                                         m->gobble(in);
 696                                 }
 697
 698                         }
 699                         else if(format == "order"){
 700
 701                                 while (in.eof() != true) {
 702
 703                                         input = new OrderVector(in);
 704                                         thisLabel = input->getLabel();
 705
 706                                         //if you are at the last label
 707                                         if (thisLabel == label) {  break;  }
 708                                         //so you don't loose this memory
 709                                         else {  delete input;   }
 710                                         m->gobble(in);
 711                                 }
 712
 713                         }
 714                         else if(format == "sabund"){
 715
 716                                 while (in.eof() != true) {
 717
 718                                         input = new SAbundVector(in);
 719                                         thisLabel = input->getLabel();
 720
 721                                         //if you are at the last label
 722                                         if (thisLabel == label) {  break;  }
 723                                         //so you don't loose this memory
 724                                         else {  delete input;   }
 725                                         m->gobble(in);
 726
 727                                 }
 728
 729                         }
 730
 731                         in.close();
 732
 733                         sabund = new SAbundVector();
 734                         *sabund = (input->getSAbundVector());
 735
 736                         return sabund;
 737
 738                 }
 739                 else{
 740                         return NULL;
 741                 }
 742         }
 743         catch(exception& e) {
 744                 m->errorOut(e, "InputData", "getSAbundVector");
 745                 exit(1);
 746         }
 747 }
 748
 749 /***********************************************************************/
 750 RAbundVector* InputData::getRAbundVector(){
 751         try {
 752                 if(fileHandle){
 753                         if (format == "list") {
 754                                 input = new ListVector(fileHandle);
 755                         }
 756                         else if (format == "shared")  {
 757                                 input = new SharedListVector(fileHandle);
 758                         }
 759                         else if(format == "rabund"){
 760                                 input = new RAbundVector(fileHandle);
 761                         }
 762                         else if(format == "order"){
 763                                 input = new OrderVector(fileHandle);
 764                         }
 765                         else if(format == "sabund"){
 766                                 input = new SAbundVector(fileHandle);
 767                         }
 768
 769                         m->gobble(fileHandle);
 770
 771                         rabund = new RAbundVector();
 772                         *rabund = (input->getRAbundVector());
 773
 774                         return rabund;
 775                 }
 776                 else{
 777                         return NULL;
 778                 }
 779         }
 780         catch(exception& e) {
 781                 m->errorOut(e, "InputData", "getRAbundVector");
 782                 exit(1);
 783         }
 784 }
 785 /***********************************************************************/
 786 RAbundVector* InputData::getRAbundVector(string label){
 787         try {
 788
 789                 ifstream in;
 790                 string  thisLabel;
 791                 m->openInputFile(filename, in);
 792
 793                 if(in){
 794                         if (format == "list") {
 795                 m->saveNextLabel = "";
 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                 m->saveNextLabel = "";
 811
 812                                 while (in.eof() != true) {
 813
 814                                         input = new SharedListVector(in);
 815                                         thisLabel = input->getLabel();
 816
 817                                         //if you are at the last label
 818                                         if (thisLabel == label) {  break;  }
 819                                         //so you don't loose this memory
 820                                         else {  delete input;   }
 821                                         m->gobble(in);
 822                                 }
 823
 824                         }
 825                         else if(format == "rabund"){
 826
 827                                 while (in.eof() != true) {
 828
 829                                         input = new RAbundVector(in);
 830                                         thisLabel = input->getLabel();
 831
 832                                         //if you are at the last label
 833                                         if (thisLabel == label) {  break;  }
 834                                         //so you don't loose this memory
 835                                         else {  delete input;   }
 836                                         m->gobble(in);
 837                                 }
 838
 839                         }
 840                         else if(format == "order"){
 841
 842                                 while (in.eof() != true) {
 843
 844                                         input = new OrderVector(in);
 845                                         thisLabel = input->getLabel();
 846
 847                                         //if you are at the last label
 848                                         if (thisLabel == label) {  break;  }
 849                                         //so you don't loose this memory
 850                                         else {  delete input;   }
 851                                         m->gobble(in);
 852                                 }
 853
 854                         }
 855                         else if(format == "sabund"){
 856
 857                                 while (in.eof() != true) {
 858
 859                                         input = new SAbundVector(in);
 860                                         thisLabel = input->getLabel();
 861
 862                                         //if you are at the last label
 863                                         if (thisLabel == label) {  break;  }
 864                                         //so you don't loose this memory
 865                                         else {  delete input;   }
 866                                         m->gobble(in);
 867
 868                                 }
 869
 870                         }
 871
 872
 873                         in.close();
 874
 875                         rabund = new RAbundVector();
 876                         *rabund = (input->getRAbundVector());
 877
 878                         return rabund;
 879                 }
 880                 else{
 881                         return NULL;
 882                 }
 883         }
 884         catch(exception& e) {
 885                 m->errorOut(e, "InputData", "getRAbundVector");
 886                 exit(1);
 887         }
 888 }
 889
 890 /***********************************************************************/
 891
 892
 893