sharedrabundfloatvector.cpp

   1 /*
   2  *  sharedrabundfloatvector.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 8/18/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedrabundfloatvector.h"
  11 #include "sharedutilities.h"
  12
  13 /***********************************************************************/
  14
  15 SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {}
  16 /***********************************************************************/
  17
  18 SharedRAbundFloatVector::~SharedRAbundFloatVector() {}
  19
  20 /***********************************************************************/
  21 SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(0.0), numBins(n), numSeqs(0.0) {
  22
  23                 individualFloat newGuy;
  24                 //initialize data
  25                 for (int i=0; i< n; i++) {
  26                         newGuy.bin = i;
  27                         newGuy.abundance = 0.0;
  28                         data.push_back(newGuy);
  29                 }
  30 }
  31 /***********************************************************************/
  32 //reads a shared file
  33 SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
  34         try {
  35
  36                 m->clearAllGroups();
  37                 vector<string> allGroups;
  38
  39                 int num, count;
  40                 float inputData;
  41                 count = 0;
  42                 string holdLabel, nextLabel, groupN;
  43                 individualFloat newguy;
  44
  45                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
  46                 lookup.clear();
  47
  48                 //are we at the beginning of the file??
  49                 if (m->saveNextLabel == "") {
  50                         f >> label;
  51
  52                         //is this a shared file that has headers
  53                         if (label == "label") {
  54                                 //gets "group"
  55                                 f >> label; m->gobble(f);
  56
  57                                 //gets "numOtus"
  58                                 f >> label; m->gobble(f);
  59
  60                                 //eat rest of line
  61                                 label = m->getline(f); m->gobble(f);
  62
  63                                 //parse labels to save
  64                                 istringstream iStringStream(label);
  65                                 m->binLabelsInFile.clear();
  66                                 while(!iStringStream.eof()){
  67                                         if (m->control_pressed) { break; }
  68                                         string temp;
  69                                         iStringStream >> temp;  m->gobble(iStringStream);
  70
  71                                         m->binLabelsInFile.push_back(temp);
  72                                 }
  73
  74                                 f >> label >> groupN >> num;
  75                         }else {
  76                 //read in first row since you know there is at least 1 group.
  77                 f >> groupN >> num;
  78
  79                 //make binlabels because we don't have any
  80                 string snumBins = toString(num);
  81                 m->binLabelsInFile.clear();
  82                 for (int i = 0; i < num; i++) {
  83                     //if there is a bin label use it otherwise make one
  84                     string binLabel = "Otu";
  85                     string sbinNumber = toString(i+1);
  86                     if (sbinNumber.length() < snumBins.length()) {
  87                         int diff = snumBins.length() - sbinNumber.length();
  88                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
  89                     }
  90                     binLabel += sbinNumber;
  91                     m->binLabelsInFile.push_back(binLabel);
  92                 }
  93             }
  94                 }else {
  95             label = m->saveNextLabel;
  96
  97             //read in first row since you know there is at least 1 group.
  98             f >> groupN >> num;
  99         }
 100
 101                 //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
 102                 m->currentBinLabels = m->binLabelsInFile;
 103
 104                 holdLabel = label;
 105
 106                 //add new vector to lookup
 107                 SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
 108                 lookup.push_back(temp);
 109                 lookup[0]->setLabel(label);
 110                 lookup[0]->setGroup(groupN);
 111
 112                 allGroups.push_back(groupN);
 113
 114                 //fill vector.  data = first sharedrabund in file
 115                 for(int i=0;i<num;i++){
 116                         f >> inputData;
 117
 118                         lookup[0]->push_back(inputData, groupN); //abundance, bin, group
 119                         push_back(inputData, groupN);
 120
 121                         if (inputData > maxRank) { maxRank = inputData; }
 122                 }
 123
 124                 m->gobble(f);
 125
 126                 if (f.eof() != true) { f >> nextLabel; }
 127
 128                 //read the rest of the groups info in
 129                 while ((nextLabel == holdLabel) && (f.eof() != true)) {
 130                         f >> groupN >> num;
 131
 132                         count++;
 133
 134                         allGroups.push_back(groupN);
 135
 136                         //add new vector to lookup
 137                         temp = new SharedRAbundFloatVector();
 138                         lookup.push_back(temp);
 139                         lookup[count]->setLabel(label);
 140                         lookup[count]->setGroup(groupN);
 141
 142                         //fill vector.
 143                         for(int i=0;i<num;i++){
 144                                 f >> inputData;
 145                                 lookup[count]->push_back(inputData, groupN); //abundance, bin, group
 146                         }
 147
 148                         m->gobble(f);
 149
 150                         if (f.eof() != true) { f >> nextLabel; }
 151                 }
 152
 153                 m->saveNextLabel = nextLabel;
 154                 m->setAllGroups(allGroups);
 155         }
 156         catch(exception& e) {
 157                 m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
 158                 exit(1);
 159         }
 160 }
 161
 162 /***********************************************************************/
 163
 164 void SharedRAbundFloatVector::set(int binNumber, float newBinSize, string groupname){
 165         try {
 166                 float oldBinSize = data[binNumber].abundance;
 167                 data[binNumber].abundance = newBinSize;
 168                 data[binNumber].group = groupname;
 169
 170                 if(newBinSize > maxRank)        {       newBinSize = newBinSize;        }
 171
 172                 numSeqs += (newBinSize - oldBinSize);
 173         }
 174         catch(exception& e) {
 175                 m->errorOut(e, "SharedRAbundFloatVector", "set");
 176                 exit(1);
 177         }
 178 }
 179 /***********************************************************************/
 180
 181 void SharedRAbundFloatVector::clear(){
 182         numBins = 0;
 183         maxRank = 0;
 184         numSeqs = 0;
 185         data.clear();
 186         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 187         lookup.clear();
 188 }
 189 /***********************************************************************/
 190 float SharedRAbundFloatVector::getAbundance(int index){
 191         return data[index].abundance;
 192 }
 193 /***********************************************************************/
 194 individualFloat SharedRAbundFloatVector::get(int index){
 195         return data[index];
 196 }
 197 /***********************************************************************/
 198 void SharedRAbundFloatVector::push_back(float binSize, string groupName){
 199         try {
 200                 individualFloat newGuy;
 201                 newGuy.abundance = binSize;
 202                 newGuy.group = groupName;
 203                 newGuy.bin = data.size();
 204
 205                 data.push_back(newGuy);
 206                 numBins++;
 207
 208                 if(binSize > maxRank){  maxRank = binSize;      }
 209
 210                 numSeqs += binSize;
 211         }
 212         catch(exception& e) {
 213                 m->errorOut(e, "SharedRAbundFloatVector", "push_back");
 214                 exit(1);
 215         }
 216 }
 217 /***********************************************************************/
 218 void SharedRAbundFloatVector::insert(float binSize, int otu, string groupName){
 219         try {
 220                 individualFloat newGuy;
 221                 newGuy.abundance = binSize;
 222                 newGuy.group = groupName;
 223                 newGuy.bin = otu;
 224
 225                 data.insert(data.begin()+otu, newGuy);
 226                 numBins++;
 227
 228                 if(binSize > maxRank){  maxRank = binSize;      }
 229
 230                 numSeqs += binSize;
 231         }
 232         catch(exception& e) {
 233                 m->errorOut(e, "SharedRAbundFloatVector", "insert");
 234                 exit(1);
 235         }
 236 }
 237
 238 /***********************************************************************/
 239 void SharedRAbundFloatVector::push_front(float binSize, int otu, string groupName){
 240         try {
 241                 individualFloat newGuy;
 242                 newGuy.abundance = binSize;
 243                 newGuy.group = groupName;
 244                 newGuy.bin = otu;
 245
 246                 data.insert(data.begin(), newGuy);
 247                 numBins++;
 248
 249                 if(binSize > maxRank){  maxRank = binSize;      }
 250
 251                 numSeqs += binSize;
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "SharedRAbundFloatVector", "push_front");
 255                 exit(1);
 256         }
 257 }
 258 /**********************************************************************/
 259 void SharedRAbundFloatVector::pop_back(){
 260         numSeqs -= data[data.size()-1].abundance;
 261         numBins--;
 262         data.pop_back();
 263 }
 264 /***********************************************************************/
 265 void SharedRAbundFloatVector::resize(int size){
 266         data.resize(size);
 267 }
 268 /**********************************************************************/
 269 int SharedRAbundFloatVector::size(){
 270         return data.size();
 271 }
 272 /***********************************************************************/
 273 void SharedRAbundFloatVector::printHeaders(ostream& output){
 274         try {
 275                 string snumBins = toString(numBins);
 276                 output << "label\tGroup\tnumOtus\t";
 277                 if (m->sharedHeaderMode == "tax") {
 278                         for (int i = 0; i < numBins; i++) {
 279
 280                                 //if there is a bin label use it otherwise make one
 281                                 string binLabel = "PhyloType";
 282                                 string sbinNumber = toString(i+1);
 283                                 if (sbinNumber.length() < snumBins.length()) {
 284                                         int diff = snumBins.length() - sbinNumber.length();
 285                                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 286                                 }
 287                                 binLabel += sbinNumber;
 288                                 if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 289
 290                                 output << binLabel << '\t';
 291                         }
 292                         output << endl;
 293                 }else {
 294                         for (int i = 0; i < numBins; i++) {
 295                                 //if there is a bin label use it otherwise make one
 296                                 string binLabel = "Otu";
 297                                 string sbinNumber = toString(i+1);
 298                                 if (sbinNumber.length() < snumBins.length()) {
 299                                         int diff = snumBins.length() - sbinNumber.length();
 300                                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 301                                 }
 302                                 binLabel += sbinNumber;
 303                                 if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 304
 305                                 output << binLabel << '\t';
 306                         }
 307
 308                         output << endl;
 309                 }
 310
 311                 m->printedHeaders = true;
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "SharedRAbundVector", "printHeaders");
 315                 exit(1);
 316         }
 317 }
 318 /***********************************************************************/
 319 void SharedRAbundFloatVector::print(ostream& output){
 320         try {
 321                 output << numBins << '\t';
 322
 323                 for(int i=0;i<data.size();i++){         output << data[i].abundance << '\t';            }
 324                 output << endl;
 325         }
 326         catch(exception& e) {
 327                 m->errorOut(e, "SharedRAbundFloatVector", "print");
 328                 exit(1);
 329         }
 330 }
 331 /***********************************************************************/
 332 string SharedRAbundFloatVector::getGroup(){
 333         return group;
 334 }
 335 /***********************************************************************/
 336 void SharedRAbundFloatVector::setGroup(string groupName){
 337         group = groupName;
 338 }
 339 /***********************************************************************/
 340 int SharedRAbundFloatVector::getGroupIndex()  { return index; }
 341 /***********************************************************************/
 342 void SharedRAbundFloatVector::setGroupIndex(int vIndex) { index = vIndex; }
 343 /***********************************************************************/
 344 int SharedRAbundFloatVector::getNumBins(){      return numBins; }
 345 /***********************************************************************/
 346 float SharedRAbundFloatVector::getNumSeqs(){    return numSeqs; }
 347 /***********************************************************************/
 348 float SharedRAbundFloatVector::getMaxRank(){    return maxRank; }
 349 /***********************************************************************/
 350 SharedRAbundFloatVector SharedRAbundFloatVector::getSharedRAbundFloatVector(){
 351         return *this;
 352 }
 353 /***********************************************************************
 354 SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
 355         try {
 356                 SharedRAbundVector rav(numBins);
 357                 rav.setLabel(label);
 358                 rav.setGroup(group);
 359
 360                 for (int i = 0; i < data.size(); i++) {
 361
 362                         rav.push_back(data[i].abundance);
 363                 }
 364
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "SharedRAbundFloatVector", "getSharedRAbundVector");
 368                 exit(1);
 369         }
 370 }
 371 ***********************************************************************/
 372 vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
 373         try {
 374                 SharedUtil* util;
 375                 util = new SharedUtil();
 376
 377                 vector<string> Groups = m->getGroups();
 378                 vector<string> allGroups = m->getAllGroups();
 379                 util->setGroups(Groups, allGroups);
 380                 m->setGroups(Groups);
 381
 382                 bool remove = false;
 383                 for (int i = 0; i < lookup.size(); i++) {
 384                         //if this sharedrabund is not from a group the user wants then delete it.
 385                         if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) {
 386                                 delete lookup[i]; lookup[i] = NULL;
 387                                 lookup.erase(lookup.begin()+i);
 388                                 i--;
 389                                 remove = true;
 390                         }
 391                 }
 392
 393                 delete util;
 394
 395                 if (remove) { eliminateZeroOTUS(lookup); }
 396
 397                 return lookup;
 398         }
 399         catch(exception& e) {
 400                 m->errorOut(e, "SharedRAbundFloatVector", "getSharedRAbundFloatVectors");
 401                 exit(1);
 402         }
 403 }
 404 /***********************************************************************/
 405
 406 RAbundVector SharedRAbundFloatVector::getRAbundVector() {
 407         try {
 408                 RAbundVector rav(numBins);
 409
 410                 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 411
 412                 rav.setLabel(label);
 413                 return rav;
 414         }
 415         catch(exception& e) {
 416                 m->errorOut(e, "SharedRAbundFloatVector", "getRAbundVector");
 417                 exit(1);
 418         }
 419 }
 420 /***********************************************************************
 421
 422 SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
 423         try {
 424                 SharedSAbundVector sav(maxRank+1);
 425
 426                 for(int i=0;i<data.size();i++){
 427                         int abund = data[i].abundance;
 428                         sav.set(abund, sav.getAbundance(abund) + 1, group);
 429                 }
 430
 431                 sav.set(0, 0, group);
 432                 sav.setLabel(label);
 433                 sav.setGroup(group);
 434
 435                 return sav;
 436         }
 437         catch(exception& e) {
 438                 m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector");
 439                 exit(1);
 440         }
 441 }
 442 ***********************************************************************/
 443
 444 SAbundVector SharedRAbundFloatVector::getSAbundVector() {
 445         try {
 446                 SAbundVector sav(ceil(maxRank)+1);
 447
 448                 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 449
 450                 sav.set(0, 0);
 451                 sav.setLabel(label);
 452                 return sav;
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "SharedRAbundFloatVector", "getSAbundVector");
 456                 exit(1);
 457         }
 458 }
 459
 460 /***********************************************************************
 461
 462 SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
 463         try {
 464                 SharedOrderVector ov;
 465
 466                 for(int i=0;i<data.size();i++){
 467                         int round = ceil(data[i].abundance);
 468                         for(int j=0;j<round;j++){
 469                                 ov.push_back(data[i].bin, round, data[i].group);
 470                         }
 471                 }
 472                 random_shuffle(ov.begin(), ov.end());
 473
 474                 ov.setLabel(label);
 475                 ov.updateStats();
 476
 477                 return ov;
 478         }
 479         catch(exception& e) {
 480                 m->errorOut(e, "SharedRAbundFloatVector", "getSharedOrderVector");
 481                 exit(1);
 482         }
 483 }
 484 ***********************************************************************/
 485 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 486 OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
 487         try {
 488                 OrderVector ov;
 489
 490                 for(int i=0;i<data.size();i++){
 491                         int round = ceil(data[i].abundance);
 492                         for(int j=0;j<round;j++){
 493                                 ov.push_back(i);
 494                         }
 495                 }
 496                 random_shuffle(ov.begin(), ov.end());
 497
 498                 ov.setLabel(label);
 499                 return ov;
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "SharedRAbundFloatVector", "getOrderVector");
 503                 exit(1);
 504         }
 505 }
 506 //**********************************************************************************************************************
 507 int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
 508         try {
 509
 510                 vector<SharedRAbundFloatVector*> newLookup;
 511                 for (int i = 0; i < thislookup.size(); i++) {
 512                         SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
 513                         temp->setLabel(thislookup[i]->getLabel());
 514                         temp->setGroup(thislookup[i]->getGroup());
 515                         newLookup.push_back(temp);
 516                 }
 517
 518                 //for each bin
 519                 vector<string> newBinLabels;
 520                 string snumBins = toString(thislookup[0]->getNumBins());
 521                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 522                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 523
 524                         //look at each sharedRabund and make sure they are not all zero
 525                         bool allZero = true;
 526                         for (int j = 0; j < thislookup.size(); j++) {
 527                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 528                         }
 529
 530                         //if they are not all zero add this bin
 531                         if (!allZero) {
 532                                 for (int j = 0; j < thislookup.size(); j++) {
 533                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 534                                 }
 535                                 //if there is a bin label use it otherwise make one
 536                                 string binLabel = "Otu";
 537                                 string sbinNumber = toString(i+1);
 538                                 if (sbinNumber.length() < snumBins.length()) {
 539                                         int diff = snumBins.length() - sbinNumber.length();
 540                                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 541                                 }
 542                                 binLabel += sbinNumber;
 543                                 if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 544
 545                                 newBinLabels.push_back(binLabel);
 546                         }
 547                 }
 548
 549                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 550
 551                 thislookup = newLookup;
 552                 m->currentBinLabels = newBinLabels;
 553
 554                 return 0;
 555
 556         }
 557         catch(exception& e) {
 558                 m->errorOut(e, "SharedRAbundFloatVector", "eliminateZeroOTUS");
 559                 exit(1);
 560         }
 561 }
 562 /***********************************************************************/
 563