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         for (int i = 0; i < allGroups.size(); i++) { cout << allGroups[i] << endl; }
 156
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
 160                 exit(1);
 161         }
 162 }
 163
 164 /***********************************************************************/
 165
 166 void SharedRAbundFloatVector::set(int binNumber, float newBinSize, string groupname){
 167         try {
 168                 float oldBinSize = data[binNumber].abundance;
 169                 data[binNumber].abundance = newBinSize;
 170                 data[binNumber].group = groupname;
 171
 172                 if(newBinSize > maxRank)        {       newBinSize = newBinSize;        }
 173
 174                 numSeqs += (newBinSize - oldBinSize);
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "SharedRAbundFloatVector", "set");
 178                 exit(1);
 179         }
 180 }
 181 /***********************************************************************/
 182
 183 void SharedRAbundFloatVector::clear(){
 184         numBins = 0;
 185         maxRank = 0;
 186         numSeqs = 0;
 187         data.clear();
 188         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 189         lookup.clear();
 190 }
 191 /***********************************************************************/
 192 float SharedRAbundFloatVector::getAbundance(int index){
 193         return data[index].abundance;
 194 }
 195 /***********************************************************************/
 196 individualFloat SharedRAbundFloatVector::get(int index){
 197         return data[index];
 198 }
 199 /***********************************************************************/
 200 void SharedRAbundFloatVector::push_back(float binSize, string groupName){
 201         try {
 202                 individualFloat newGuy;
 203                 newGuy.abundance = binSize;
 204                 newGuy.group = groupName;
 205                 newGuy.bin = data.size();
 206
 207                 data.push_back(newGuy);
 208                 numBins++;
 209
 210                 if(binSize > maxRank){  maxRank = binSize;      }
 211
 212                 numSeqs += binSize;
 213         }
 214         catch(exception& e) {
 215                 m->errorOut(e, "SharedRAbundFloatVector", "push_back");
 216                 exit(1);
 217         }
 218 }
 219 /***********************************************************************/
 220 void SharedRAbundFloatVector::insert(float binSize, int otu, string groupName){
 221         try {
 222                 individualFloat newGuy;
 223                 newGuy.abundance = binSize;
 224                 newGuy.group = groupName;
 225                 newGuy.bin = otu;
 226
 227                 data.insert(data.begin()+otu, newGuy);
 228                 numBins++;
 229
 230                 if(binSize > maxRank){  maxRank = binSize;      }
 231
 232                 numSeqs += binSize;
 233         }
 234         catch(exception& e) {
 235                 m->errorOut(e, "SharedRAbundFloatVector", "insert");
 236                 exit(1);
 237         }
 238 }
 239
 240 /***********************************************************************/
 241 void SharedRAbundFloatVector::push_front(float binSize, int otu, string groupName){
 242         try {
 243                 individualFloat newGuy;
 244                 newGuy.abundance = binSize;
 245                 newGuy.group = groupName;
 246                 newGuy.bin = otu;
 247
 248                 data.insert(data.begin(), newGuy);
 249                 numBins++;
 250
 251                 if(binSize > maxRank){  maxRank = binSize;      }
 252
 253                 numSeqs += binSize;
 254         }
 255         catch(exception& e) {
 256                 m->errorOut(e, "SharedRAbundFloatVector", "push_front");
 257                 exit(1);
 258         }
 259 }
 260 /**********************************************************************/
 261 void SharedRAbundFloatVector::pop_back(){
 262         numSeqs -= data[data.size()-1].abundance;
 263         numBins--;
 264         data.pop_back();
 265 }
 266 /***********************************************************************/
 267 void SharedRAbundFloatVector::resize(int size){
 268         data.resize(size);
 269 }
 270 /**********************************************************************/
 271 int SharedRAbundFloatVector::size(){
 272         return data.size();
 273 }
 274 /***********************************************************************/
 275 void SharedRAbundFloatVector::printHeaders(ostream& output){
 276         try {
 277                 string snumBins = toString(numBins);
 278                 output << "label\tGroup\tnumOtus\t";
 279                 if (m->sharedHeaderMode == "tax") {
 280                         for (int i = 0; i < numBins; i++) {
 281
 282                                 //if there is a bin label use it otherwise make one
 283                                 string binLabel = "PhyloType";
 284                                 string sbinNumber = toString(i+1);
 285                                 if (sbinNumber.length() < snumBins.length()) {
 286                                         int diff = snumBins.length() - sbinNumber.length();
 287                                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 288                                 }
 289                                 binLabel += sbinNumber;
 290                                 if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 291
 292                                 output << binLabel << '\t';
 293                         }
 294                         output << endl;
 295                 }else {
 296                         for (int i = 0; i < numBins; i++) {
 297                                 //if there is a bin label use it otherwise make one
 298                                 string binLabel = "Otu";
 299                                 string sbinNumber = toString(i+1);
 300                                 if (sbinNumber.length() < snumBins.length()) {
 301                                         int diff = snumBins.length() - sbinNumber.length();
 302                                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 303                                 }
 304                                 binLabel += sbinNumber;
 305                                 if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 306
 307                                 output << binLabel << '\t';
 308                         }
 309
 310                         output << endl;
 311                 }
 312
 313                 m->printedHeaders = true;
 314         }
 315         catch(exception& e) {
 316                 m->errorOut(e, "SharedRAbundVector", "printHeaders");
 317                 exit(1);
 318         }
 319 }
 320 /***********************************************************************/
 321 void SharedRAbundFloatVector::print(ostream& output){
 322         try {
 323                 output << numBins << '\t';
 324
 325                 for(int i=0;i<data.size();i++){         output << data[i].abundance << '\t';            }
 326                 output << endl;
 327         }
 328         catch(exception& e) {
 329                 m->errorOut(e, "SharedRAbundFloatVector", "print");
 330                 exit(1);
 331         }
 332 }
 333 /***********************************************************************/
 334 string SharedRAbundFloatVector::getGroup(){
 335         return group;
 336 }
 337 /***********************************************************************/
 338 void SharedRAbundFloatVector::setGroup(string groupName){
 339         group = groupName;
 340 }
 341 /***********************************************************************/
 342 int SharedRAbundFloatVector::getGroupIndex()  { return index; }
 343 /***********************************************************************/
 344 void SharedRAbundFloatVector::setGroupIndex(int vIndex) { index = vIndex; }
 345 /***********************************************************************/
 346 int SharedRAbundFloatVector::getNumBins(){      return numBins; }
 347 /***********************************************************************/
 348 float SharedRAbundFloatVector::getNumSeqs(){    return numSeqs; }
 349 /***********************************************************************/
 350 float SharedRAbundFloatVector::getMaxRank(){    return maxRank; }
 351 /***********************************************************************/
 352 SharedRAbundFloatVector SharedRAbundFloatVector::getSharedRAbundFloatVector(){
 353         return *this;
 354 }
 355 /***********************************************************************
 356 SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
 357         try {
 358                 SharedRAbundVector rav(numBins);
 359                 rav.setLabel(label);
 360                 rav.setGroup(group);
 361
 362                 for (int i = 0; i < data.size(); i++) {
 363
 364                         rav.push_back(data[i].abundance);
 365                 }
 366
 367         }
 368         catch(exception& e) {
 369                 m->errorOut(e, "SharedRAbundFloatVector", "getSharedRAbundVector");
 370                 exit(1);
 371         }
 372 }
 373 ***********************************************************************/
 374 vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
 375         try {
 376                 SharedUtil* util;
 377                 util = new SharedUtil();
 378
 379                 vector<string> Groups = m->getGroups();
 380                 vector<string> allGroups = m->getAllGroups();
 381                 util->setGroups(Groups, allGroups);
 382                 m->setGroups(Groups);
 383
 384                 bool remove = false;
 385                 for (int i = 0; i < lookup.size(); i++) {
 386                         //if this sharedrabund is not from a group the user wants then delete it.
 387                         if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) {
 388                                 delete lookup[i]; lookup[i] = NULL;
 389                                 lookup.erase(lookup.begin()+i);
 390                                 i--;
 391                                 remove = true;
 392                         }
 393                 }
 394
 395                 delete util;
 396
 397                 if (remove) { eliminateZeroOTUS(lookup); }
 398
 399                 return lookup;
 400         }
 401         catch(exception& e) {
 402                 m->errorOut(e, "SharedRAbundFloatVector", "getSharedRAbundFloatVectors");
 403                 exit(1);
 404         }
 405 }
 406 /***********************************************************************/
 407
 408 RAbundVector SharedRAbundFloatVector::getRAbundVector() {
 409         try {
 410                 RAbundVector rav(numBins);
 411
 412                 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 413
 414                 rav.setLabel(label);
 415                 return rav;
 416         }
 417         catch(exception& e) {
 418                 m->errorOut(e, "SharedRAbundFloatVector", "getRAbundVector");
 419                 exit(1);
 420         }
 421 }
 422 /***********************************************************************
 423
 424 SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
 425         try {
 426                 SharedSAbundVector sav(maxRank+1);
 427
 428                 for(int i=0;i<data.size();i++){
 429                         int abund = data[i].abundance;
 430                         sav.set(abund, sav.getAbundance(abund) + 1, group);
 431                 }
 432
 433                 sav.set(0, 0, group);
 434                 sav.setLabel(label);
 435                 sav.setGroup(group);
 436
 437                 return sav;
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector");
 441                 exit(1);
 442         }
 443 }
 444 ***********************************************************************/
 445
 446 SAbundVector SharedRAbundFloatVector::getSAbundVector() {
 447         try {
 448                 SAbundVector sav(ceil(maxRank)+1);
 449
 450                 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 451
 452                 sav.set(0, 0);
 453                 sav.setLabel(label);
 454                 return sav;
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "SharedRAbundFloatVector", "getSAbundVector");
 458                 exit(1);
 459         }
 460 }
 461
 462 /***********************************************************************
 463
 464 SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
 465         try {
 466                 SharedOrderVector ov;
 467
 468                 for(int i=0;i<data.size();i++){
 469                         int round = ceil(data[i].abundance);
 470                         for(int j=0;j<round;j++){
 471                                 ov.push_back(data[i].bin, round, data[i].group);
 472                         }
 473                 }
 474                 random_shuffle(ov.begin(), ov.end());
 475
 476                 ov.setLabel(label);
 477                 ov.updateStats();
 478
 479                 return ov;
 480         }
 481         catch(exception& e) {
 482                 m->errorOut(e, "SharedRAbundFloatVector", "getSharedOrderVector");
 483                 exit(1);
 484         }
 485 }
 486 ***********************************************************************/
 487 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 488 OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
 489         try {
 490                 OrderVector ov;
 491
 492                 for(int i=0;i<data.size();i++){
 493                         int round = ceil(data[i].abundance);
 494                         for(int j=0;j<round;j++){
 495                                 ov.push_back(i);
 496                         }
 497                 }
 498                 random_shuffle(ov.begin(), ov.end());
 499
 500                 ov.setLabel(label);
 501                 return ov;
 502         }
 503         catch(exception& e) {
 504                 m->errorOut(e, "SharedRAbundFloatVector", "getOrderVector");
 505                 exit(1);
 506         }
 507 }
 508 //**********************************************************************************************************************
 509 int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
 510         try {
 511
 512                 vector<SharedRAbundFloatVector*> newLookup;
 513                 for (int i = 0; i < thislookup.size(); i++) {
 514                         SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
 515                         temp->setLabel(thislookup[i]->getLabel());
 516                         temp->setGroup(thislookup[i]->getGroup());
 517                         newLookup.push_back(temp);
 518                 }
 519
 520                 //for each bin
 521                 vector<string> newBinLabels;
 522                 string snumBins = toString(thislookup[0]->getNumBins());
 523                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 524                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 525
 526                         //look at each sharedRabund and make sure they are not all zero
 527                         bool allZero = true;
 528                         for (int j = 0; j < thislookup.size(); j++) {
 529                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 530                         }
 531
 532                         //if they are not all zero add this bin
 533                         if (!allZero) {
 534                                 for (int j = 0; j < thislookup.size(); j++) {
 535                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 536                                 }
 537                                 //if there is a bin label use it otherwise make one
 538                                 string binLabel = "Otu";
 539                                 string sbinNumber = toString(i+1);
 540                                 if (sbinNumber.length() < snumBins.length()) {
 541                                         int diff = snumBins.length() - sbinNumber.length();
 542                                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
 543                                 }
 544                                 binLabel += sbinNumber;
 545                                 if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
 546
 547                                 newBinLabels.push_back(binLabel);
 548                         }
 549                 }
 550
 551                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 552
 553                 thislookup = newLookup;
 554                 m->currentBinLabels = newBinLabels;
 555
 556                 return 0;
 557
 558         }
 559         catch(exception& e) {
 560                 m->errorOut(e, "SharedRAbundFloatVector", "eliminateZeroOTUS");
 561                 exit(1);
 562         }
 563 }
 564 /***********************************************************************/
 565