sharedrabundvector.cpp

   1 /*
   2  *  sharedvector.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 12/5/08.
   6  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedrabundvector.h"
  11 #include "sabundvector.hpp"
  12 #include "ordervector.hpp"
  13 #include "sharedutilities.h"
  14
  15
  16 /***********************************************************************/
  17
  18 SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();}
  19 /***********************************************************************/
  20
  21 SharedRAbundVector::~SharedRAbundVector() {
  22         //for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  23
  24 }
  25
  26 /***********************************************************************/
  27
  28 SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) {
  29                 globaldata = GlobalData::getInstance();
  30                 individual newGuy;
  31                 //initialize data
  32                 for (int i=0; i< n; i++) {
  33                         newGuy.bin = i;
  34                         newGuy.abundance = 0;
  35                         data.push_back(newGuy);
  36                 }
  37 }
  38
  39 /***********************************************************************
  40
  41 SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : DataVector(id), data(rav) {
  42         try {
  43                 numBins = 0;
  44                 maxRank = 0;
  45                 numSeqs = 0;
  46
  47                 for(int i=0;i<data.size();i++){
  48                         if(data[i].abundance != 0)              {       numBins = i+1;          }
  49                         if(data[i].abundance > maxRank) {       maxRank = data[i].abundance;    }
  50                         numSeqs += data[i].abundance;
  51                 }
  52         }
  53         catch(exception& e) {
  54                 errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
  55                 exit(1);
  56         }
  57 }
  58
  59
  60 /***********************************************************************/
  61 //reads a shared file
  62 SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
  63         try {
  64                 globaldata = GlobalData::getInstance();
  65
  66                 if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
  67
  68                 int num, inputData, count;
  69                 count = 0;
  70                 string holdLabel, nextLabel, groupN;
  71                 individual newguy;
  72
  73                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  74                 lookup.clear();
  75
  76                 //read in first row since you know there is at least 1 group.
  77                 f >> label >> groupN >> num;
  78                 holdLabel = label;
  79
  80                 //add new vector to lookup
  81                 SharedRAbundVector* temp = new SharedRAbundVector();
  82                 lookup.push_back(temp);
  83                 lookup[0]->setLabel(label);
  84                 lookup[0]->setGroup(groupN);
  85
  86                 if (globaldata->gGroupmap == NULL) {
  87                         //save group in groupmap
  88                         groupmap->namesOfGroups.push_back(groupN);
  89                         groupmap->groupIndex[groupN] = 0;
  90                 }
  91
  92                 //fill vector.  data = first sharedrabund in file
  93                 for(int i=0;i<num;i++){
  94                         f >> inputData;
  95
  96                         lookup[0]->push_back(inputData, i, groupN); //abundance, bin, group
  97                         push_back(inputData, i, groupN);
  98                         numSeqs += inputData;
  99                         numBins++;
 100                         if (inputData > maxRank) { maxRank = inputData; }
 101
 102                 }
 103
 104                 if (f.eof() != true) { f >> nextLabel; }
 105
 106                 //read the rest of the groups info in
 107                 while ((nextLabel == holdLabel) && (f.eof() != true)) {
 108                         f >> groupN >> num;
 109                         count++;
 110
 111                         if (globaldata->gGroupmap == NULL) {
 112                                 //save group in groupmap
 113                                 groupmap->namesOfGroups.push_back(groupN);
 114                                 groupmap->groupIndex[groupN] = count;
 115                         }
 116
 117                         //add new vector to lookup
 118                         temp = new SharedRAbundVector();
 119                         lookup.push_back(temp);
 120                         lookup[count]->setLabel(label);
 121                         lookup[count]->setGroup(groupN);
 122
 123                         //fill vector.
 124                         for(int i=0;i<num;i++){
 125                                 f >> inputData;
 126                                 lookup[count]->push_back(inputData, i, groupN); //abundance, bin, group
 127                         }
 128
 129
 130                         if (f.eof() != true) { f >> nextLabel; }
 131                 }
 132
 133                 //put file pointer back since you are now at a new distance label
 134                 for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
 135
 136                 if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap;  }
 137
 138         }
 139         catch(exception& e) {
 140                 errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
 141                 exit(1);
 142         }
 143 }
 144
 145 /***********************************************************************/
 146
 147 void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
 148         try {
 149                 int oldBinSize = data[binNumber].abundance;
 150                 data[binNumber].abundance = newBinSize;
 151                 data[binNumber].group = groupname;
 152
 153                 if(newBinSize > maxRank)        {       maxRank = newBinSize;   }
 154
 155                 numSeqs += (newBinSize - oldBinSize);
 156         }
 157         catch(exception& e) {
 158                 errorOut(e, "SharedRAbundVector", "set");
 159                 exit(1);
 160         }
 161 }
 162 /***********************************************************************/
 163
 164 void SharedRAbundVector::setData(vector <individual> newData){
 165         data = newData;
 166 }
 167
 168 /***********************************************************************/
 169
 170 int SharedRAbundVector::getAbundance(int index){
 171         return data[index].abundance;
 172
 173 }
 174 /***********************************************************************/
 175
 176 int SharedRAbundVector::numNZ(){
 177         int sum = 0;
 178         for(int i = 1; i < numBins; i++)
 179                 if(data[i].abundance > 0)
 180                         sum++;
 181         return sum;
 182 }
 183 /***********************************************************************/
 184
 185 void SharedRAbundVector::sortD(){
 186         struct individual indObj;
 187         sort(data.begin()+1, data.end(), indObj);
 188 }
 189 /***********************************************************************/
 190
 191 individual SharedRAbundVector::get(int index){
 192         return data[index];
 193
 194 }
 195 /***********************************************************************/
 196
 197 vector <individual> SharedRAbundVector::getData(){
 198         return data;
 199 }
 200 /***********************************************************************/
 201
 202 void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
 203         try {
 204                 individual newGuy;
 205                 newGuy.abundance = binSize;
 206                 newGuy.group = groupName;
 207                 newGuy.bin = otu;
 208
 209                 data.push_back(newGuy);
 210                 numBins++;
 211
 212                 if(binSize > maxRank){
 213                         maxRank = binSize;
 214                 }
 215
 216                 numSeqs += binSize;
 217         }
 218         catch(exception& e) {
 219                 errorOut(e, "SharedRAbundVector", "push_back");
 220                 exit(1);
 221         }
 222 }
 223
 224 /***********************************************************************/
 225
 226 void SharedRAbundVector::insert(int binSize, int otu, string groupName){
 227         try {
 228                 individual newGuy;
 229                 newGuy.abundance = binSize;
 230                 newGuy.group = groupName;
 231                 newGuy.bin = otu;
 232
 233                 data.insert(data.begin()+otu, newGuy);
 234                 numBins++;
 235
 236                 if(binSize > maxRank){
 237                         maxRank = binSize;
 238                 }
 239
 240                 numSeqs += binSize;
 241         }
 242         catch(exception& e) {
 243                 errorOut(e, "SharedRAbundVector", "insert");
 244                 exit(1);
 245         }
 246 }
 247
 248 /***********************************************************************/
 249
 250 void SharedRAbundVector::push_front(int binSize, int otu, string groupName){
 251         try {
 252                 individual newGuy;
 253                 newGuy.abundance = binSize;
 254                 newGuy.group = groupName;
 255                 newGuy.bin = otu;
 256
 257                 data.insert(data.begin(), newGuy);
 258                 numBins++;
 259
 260                 if(binSize > maxRank){
 261                         maxRank = binSize;
 262                 }
 263
 264                 numSeqs += binSize;
 265         }
 266         catch(exception& e) {
 267                 errorOut(e, "SharedRAbundVector", "push_front");
 268                 exit(1);
 269         }
 270 }
 271
 272 /***********************************************************************/
 273 void SharedRAbundVector::pop_back(){
 274         numSeqs -= data[data.size()-1].abundance;
 275         numBins--;
 276         return data.pop_back();
 277 }
 278
 279 /***********************************************************************/
 280
 281
 282 vector<individual>::reverse_iterator SharedRAbundVector::rbegin(){
 283         return data.rbegin();
 284 }
 285
 286 /***********************************************************************/
 287
 288 vector<individual>::reverse_iterator SharedRAbundVector::rend(){
 289         return data.rend();
 290 }
 291
 292 /***********************************************************************/
 293 void SharedRAbundVector::resize(int size){
 294
 295         data.resize(size);
 296 }
 297
 298 /***********************************************************************/
 299
 300 int SharedRAbundVector::size(){
 301         return data.size();
 302 }
 303
 304 /***********************************************************************/
 305 void SharedRAbundVector::print(ostream& output){
 306         try {
 307                 output << numBins << '\t';
 308
 309                 for(int i=0;i<data.size();i++){         output << data[i].abundance << '\t';            }
 310                 output << endl;
 311         }
 312         catch(exception& e) {
 313                 errorOut(e, "SharedRAbundVector", "print");
 314                 exit(1);
 315         }
 316 }
 317 /***********************************************************************/
 318 string SharedRAbundVector::getGroup(){
 319         return group;
 320 }
 321
 322 /***********************************************************************/
 323
 324 void SharedRAbundVector::setGroup(string groupName){
 325         group = groupName;
 326 }
 327 /***********************************************************************/
 328 int SharedRAbundVector::getGroupIndex()  { return index; }
 329 /***********************************************************************/
 330 void SharedRAbundVector::setGroupIndex(int vIndex)      { index = vIndex; }
 331 /***********************************************************************/
 332 int SharedRAbundVector::getNumBins(){
 333         return numBins;
 334 }
 335
 336 /***********************************************************************/
 337
 338 int SharedRAbundVector::getNumSeqs(){
 339         return numSeqs;
 340 }
 341
 342 /***********************************************************************/
 343
 344 int SharedRAbundVector::getMaxRank(){
 345         return maxRank;
 346 }
 347 /***********************************************************************/
 348
 349 SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){
 350         return *this;
 351 }
 352 /***********************************************************************/
 353 vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 354         try {
 355                 SharedUtil* util;
 356                 util = new SharedUtil();
 357
 358                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
 359
 360                 for (int i = 0; i < lookup.size(); i++) {
 361                         //if this sharedrabund is not from a group the user wants then delete it.
 362                         if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) {
 363                                 delete lookup[i];
 364                                 lookup.erase(lookup.begin()+i);
 365                                 i--;
 366                         }
 367                 }
 368
 369                 delete util;
 370
 371                 return lookup;
 372         }
 373         catch(exception& e) {
 374                 errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
 375                 exit(1);
 376         }
 377 }
 378 /***********************************************************************/
 379
 380 RAbundVector SharedRAbundVector::getRAbundVector() {
 381         try {
 382                 RAbundVector rav(data.size());
 383
 384                 for (int i = 0; i < data.size(); i++) {
 385                         rav.set(i, data[i].abundance);
 386                 }
 387
 388                 return rav;
 389         }
 390         catch(exception& e) {
 391                 errorOut(e, "SharedRAbundVector", "getRAbundVector");
 392                 exit(1);
 393         }
 394 }
 395 /***********************************************************************/
 396
 397 RAbundVector SharedRAbundVector::getRAbundVector2() {
 398         try {
 399                 RAbundVector rav;
 400                 for(int i = 0; i < numBins; i++)
 401                         if(data[i].abundance != 0)
 402                                 rav.push_back(data[i].abundance-1);
 403                 return rav;
 404         }
 405         catch(exception& e) {
 406                 errorOut(e, "SharedRAbundVector", "getRAbundVector2");
 407                 exit(1);
 408         }
 409 }
 410 /***********************************************************************/
 411
 412 SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
 413         try {
 414                 SharedSAbundVector sav(maxRank+1);
 415
 416                 for(int i=0;i<data.size();i++){
 417                         int abund = data[i].abundance;
 418                         sav.set(abund, sav.getAbundance(abund) + 1, group);
 419                 }
 420
 421                 sav.set(0, 0, group);
 422                 sav.setLabel(label);
 423                 sav.setGroup(group);
 424
 425                 return sav;
 426         }
 427         catch(exception& e) {
 428                 errorOut(e, "SharedRAbundVector", "getSharedSAbundVector");
 429                 exit(1);
 430         }
 431 }
 432 /***********************************************************************/
 433
 434 SAbundVector SharedRAbundVector::getSAbundVector() {
 435         try {
 436                 SAbundVector sav(maxRank+1);
 437
 438                 for(int i=0;i<data.size();i++){
 439                         int abund = data[i].abundance;
 440                         sav.set(abund, sav.get(abund) + 1);
 441                 }
 442                 sav.set(0, 0);
 443                 sav.setLabel(label);
 444                 return sav;
 445         }
 446         catch(exception& e) {
 447                 errorOut(e, "SharedRAbundVector", "getSAbundVector");
 448                 exit(1);
 449         }
 450 }
 451
 452 /***********************************************************************/
 453
 454 SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
 455         try {
 456                 SharedOrderVector ov;
 457
 458                 for(int i=0;i<data.size();i++){
 459                         for(int j=0;j<data[i].abundance;j++){
 460                                 ov.push_back(data[i].bin, data[i].abundance, data[i].group);
 461                         }
 462                 }
 463                 random_shuffle(ov.begin(), ov.end());
 464
 465                 ov.setLabel(label);
 466                 ov.updateStats();
 467
 468                 return ov;
 469         }
 470         catch(exception& e) {
 471                 errorOut(e, "SharedRAbundVector", "getSharedOrderVector");
 472                 exit(1);
 473         }
 474 }
 475 /***********************************************************************/
 476
 477 OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = NULL) {
 478         try {
 479                 OrderVector ov;
 480
 481                 for(int i=0;i<data.size();i++){
 482                         for(int j=0;j<data[i].abundance;j++){
 483                                 ov.push_back(i);
 484                         }
 485                 }
 486                 random_shuffle(ov.begin(), ov.end());
 487
 488                 ov.setLabel(label);
 489                 return ov;
 490         }
 491         catch(exception& e) {
 492                 errorOut(e, "SharedRAbundVector", "getOrderVector");
 493                 exit(1);
 494         }
 495 }
 496
 497 /***********************************************************************/
 498