sharedsabundvector.cpp

   1 /*
   2  *  sharedSharedSAbundVector.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 12/10/08.
   6  *  Copyright 2008 __MyCompanyName__. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedsabundvector.h"
  11 #include "sabundvector.hpp"
  12 #include "datavector.hpp"
  13 #include "utilities.hpp"
  14 #include <exception>
  15
  16 using namespace std;
  17
  18
  19 /***********************************************************************/
  20
  21 SharedSAbundVector::SharedSAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
  22
  23 /***********************************************************************/
  24
  25 SharedSAbundVector::SharedSAbundVector(int size) :      DataVector(), maxRank(0), numBins(0), numSeqs(0) {
  26                 individual newGuy;
  27                 //initialize data
  28                 for (int i=0; i< size; i++) {
  29                         newGuy.bin = i;
  30                         newGuy.abundance = 0;
  31                         data.push_back(newGuy);
  32                 }
  33         //      for(int i=0;i<data.size();i++){
  34         //              if(data[i].abundance != 0){     maxRank = i;    }
  35         //              numSeqs += i*data[i].abundance;
  36         //              numBins += data[i].abundance;
  37         //      }
  38
  39 };
  40
  41 /***********************************************************************
  42
  43 SharedSAbundVector::SharedSAbundVector(string id, vector<int> sav) : DataVector(id), data(sav) {
  44         try {
  45
  46                 for(int i=0;i<sav.size();i++){
  47                         if(data[i] != 0){       maxRank = i;    }
  48                         numSeqs += i*data[i];
  49                         numBins += data[i];
  50                 }
  51         }
  52         catch(exception& e) {
  53                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56         catch(...) {
  57                 cout << "An unknown error has occurred in the SharedSAbundVector class function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60 }
  61
  62 /***********************************************************************
  63
  64 SharedSAbundVector::SharedSAbundVector(ifstream& f): DataVector(), maxRank(0), numBins(0), numSeqs(0) {
  65         try {
  66                 int hold;
  67                 f >> label >> hold;
  68
  69                 data.assign(hold+1, 0);
  70                 int inputData;
  71
  72                 for(int i=1;i<=hold;i++){
  73                         f >> inputData;
  74                         set(i, inputData);
  75                 }
  76         }
  77         catch(exception& e) {
  78                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81         catch(...) {
  82                 cout << "An unknown error has occurred in the SharedSAbundVector class function SharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  83                 exit(1);
  84         }
  85 }
  86
  87 /***********************************************************************/
  88
  89 void SharedSAbundVector::set(int bin, int abundance, string groupName){
  90         try {
  91
  92                 int initSize = data[bin].abundance;
  93                 data[bin].abundance = abundance;
  94                 data[bin].group = groupName;
  95
  96                 if(bin != 0){
  97                         numBins += (abundance - initSize);
  98                 }
  99
 100                 numSeqs += bin * (abundance - initSize);
 101
 102                 if(bin > maxRank)       {       maxRank = bin;          }
 103         }
 104         catch(exception& e) {
 105                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108         catch(...) {
 109                 cout << "An unknown error has occurred in the SharedSAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112 }
 113
 114 /***********************************************************************/
 115
 116 individual SharedSAbundVector::get(int index){
 117         return data[index];
 118 }
 119 /***********************************************************************/
 120
 121 int SharedSAbundVector::getAbundance(int index){
 122         return data[index].abundance;
 123 }
 124
 125 /***********************************************************************/
 126
 127 void SharedSAbundVector::push_back(int abundance, int bin, string groupName){
 128         try {
 129                 individual newGuy;
 130                 newGuy.abundance = abundance;
 131                 newGuy.bin = bin;
 132                 newGuy.group = groupName;
 133
 134                 data.push_back(newGuy);
 135
 136                 maxRank++;
 137
 138                 numBins += abundance;
 139
 140                 numSeqs += (maxRank * abundance);
 141         }
 142         catch(exception& e) {
 143                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 144                 exit(1);
 145         }
 146         catch(...) {
 147                 cout << "An unknown error has occurred in the SharedSAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 148                 exit(1);
 149         }
 150 }
 151
 152 /***********************************************************************/
 153
 154 void SharedSAbundVector::resize(int size){
 155         data.resize(size);
 156 }
 157
 158 /***********************************************************************/
 159
 160 int SharedSAbundVector::size(){
 161         return data.size();
 162 }
 163
 164 /***********************************************************************/
 165 void SharedSAbundVector::print(ostream& output){
 166         try {
 167                 output << label << '\t' << maxRank << '\t';
 168
 169                 for(int i=1;i<=maxRank;i++){
 170                         output << data[i].abundance << '\t';
 171                 }
 172                 output << endl;
 173         }
 174         catch(exception& e) {
 175                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 176                 exit(1);
 177         }
 178         catch(...) {
 179                 cout << "An unknown error has occurred in the SharedSAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 180                 exit(1);
 181         }
 182 }
 183 /***********************************************************************/
 184 string SharedSAbundVector::getGroup(){
 185         return group;
 186 }
 187
 188 /***********************************************************************/
 189
 190 void SharedSAbundVector::setGroup(string groupName){
 191         group = groupName;
 192 }
 193
 194 /**********************************************************************/
 195 int SharedSAbundVector::getNumBins(){
 196         return numBins;
 197 }
 198
 199 /***********************************************************************/
 200
 201 int SharedSAbundVector::getNumSeqs(){
 202         return numSeqs;
 203 }
 204
 205 /***********************************************************************/
 206
 207 int SharedSAbundVector::getMaxRank(){
 208         return maxRank;
 209 }
 210 /***********************************************************************/
 211 RAbundVector SharedSAbundVector::getRAbundVector(){
 212         try {
 213                 RAbundVector rav;
 214
 215                 for(int i=1;i<=data.size();i++){
 216                         for(int j=0;j<data[i].abundance;j++){
 217                                 rav.push_back(i);
 218                         }
 219                 }
 220                 sort(rav.rbegin(), rav.rend());
 221
 222                 rav.setLabel(label);
 223                 return rav;
 224         }
 225         catch(exception& e) {
 226                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 227                 exit(1);
 228         }
 229         catch(...) {
 230                 cout << "An unknown error has occurred in the SharedSAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 231                 exit(1);
 232         }
 233 }
 234 /***********************************************************************/
 235 SAbundVector SharedSAbundVector::getSAbundVector(){
 236         try {
 237                 RAbundVector rav;
 238                 SAbundVector sav;
 239
 240                 rav = getRAbundVector();
 241                 sav = rav.getSAbundVector();
 242                 return sav;
 243
 244         }
 245         catch(exception& e) {
 246                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 247                 exit(1);
 248         }
 249         catch(...) {
 250                 cout << "An unknown error has occurred in the SharedSAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 251                 exit(1);
 252         }
 253 }
 254
 255 /***********************************************************************/
 256
 257 bool compareMembers (individual member, individual member2){
 258
 259   if(member.abundance < member2.abundance){
 260     return true;   }
 261   else{
 262         return false;
 263   }
 264 }
 265
 266 /***********************************************************************/
 267 SharedRAbundVector SharedSAbundVector::getSharedRAbundVector(){
 268         try {
 269                 SharedRAbundVector rav;
 270
 271                 int binNumber = 0;
 272                 for(int i=1;i<=data.size();i++){
 273                         for(int j=0;j<data[i].abundance;j++){
 274                                 rav.push_back(i, binNumber, data[i].group);
 275                                 binNumber++;
 276                         }
 277                 }
 278                 sort(rav.rbegin(), rav.rend(), compareMembers);
 279
 280                 rav.setLabel(label);
 281                 rav.setGroup(group);
 282
 283                 return rav;
 284         }
 285         catch(exception& e) {
 286                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSharedVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 287                 exit(1);
 288         }
 289         catch(...) {
 290                 cout << "An unknown error has occurred in the SharedSAbundVector class function getSharedVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 291                 exit(1);
 292         }
 293 }
 294
 295
 296 /***********************************************************************/
 297
 298 SharedSAbundVector SharedSAbundVector::getSharedSAbundVector(){
 299         return *this;
 300 }
 301
 302 /***********************************************************************/
 303 SharedOrderVector SharedSAbundVector::getSharedOrderVector() {
 304         try {
 305                 SharedRAbundVector rav;
 306                 SharedOrderVector ov;
 307
 308                 rav = this->getSharedRAbundVector();
 309                 ov = rav.getSharedOrderVector();
 310
 311                 return ov;
 312         }
 313         catch(exception& e) {
 314                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 315                 exit(1);
 316         }
 317         catch(...) {
 318                 cout << "An unknown error has occurred in the SharedSAbundVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 319                 exit(1);
 320         }
 321 }
 322 /***********************************************************************/
 323 OrderVector SharedSAbundVector::getOrderVector(map<string,int>* hold = NULL){
 324         try {
 325                 OrderVector ov;
 326
 327                 int binIndex = 0;
 328
 329                 for(int i=1;i<data.size();i++){
 330                         for(int j=0;j<data[i].abundance;j++){
 331                                 for(int k=0;k<i;k++){
 332                                         ov.push_back(binIndex);
 333                                 }
 334                                 binIndex++;
 335                         }
 336                 }
 337
 338                 random_shuffle(ov.begin(), ov.end());
 339
 340                 ov.setLabel(label);
 341                 ov.getNumBins();
 342                 return ov;
 343         }
 344         catch(exception& e) {
 345                 cout << "Standard Error: " << e.what() << " has occurred in the SharedSAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 346                 exit(1);
 347         }
 348         catch(...) {
 349                 cout << "An unknown error has occurred in the SharedSAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 350                 exit(1);
 351         }
 352 }
 353
 354 /***********************************************************************/
 355