sharedlistvector.cpp

   1 /*
   2  *  sharedSharedListVector.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/22/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10
  11 using namespace std;
  12
  13
  14 #include "sabundvector.hpp"
  15 #include "rabundvector.hpp"
  16 #include "ordervector.hpp"
  17 #include "sharedlistvector.h"
  18 #include "sharedordervector.h"
  19 #include "sharedutilities.h"
  20
  21 /***********************************************************************/
  22
  23 SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){};
  24
  25 /***********************************************************************/
  26
  27 SharedListVector::SharedListVector(int n):      DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){};
  28
  29 /***********************************************************************/
  30 SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
  31         try {
  32                 globaldata = GlobalData::getInstance();
  33
  34                 //set up groupmap for later.
  35                 groupmap = new GroupMap(globaldata->getGroupFile());
  36                 groupmap->readMap();
  37
  38                 int hold;
  39                 string inputData;
  40                 f >> label >> hold;
  41
  42                 data.assign(hold, "");
  43
  44                 for(int i=0;i<hold;i++){
  45                         f >> inputData;
  46                         set(i, inputData);
  47                 }
  48
  49         }
  50         catch(exception& e) {
  51                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  52                 exit(1);
  53         }
  54         catch(...) {
  55                 cout << "An unknown error has occurred in the SharedListVector class function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58 }
  59
  60 /***********************************************************************/
  61 void SharedListVector::set(int binNumber, string seqNames){
  62         try {
  63                 int nNames_old = getNumNames(data[binNumber]);
  64                 data[binNumber] = seqNames;
  65                 int nNames_new = getNumNames(seqNames);
  66
  67                 if(nNames_old == 0)                     {       numBins++;                              }
  68                 if(nNames_new == 0)                     {       numBins--;                              }
  69                 if(nNames_new > maxRank)        {       maxRank = nNames_new;   }
  70
  71                 numSeqs += (nNames_new - nNames_old);
  72         }
  73         catch(exception& e) {
  74                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  75                 exit(1);
  76         }
  77         catch(...) {
  78                 cout << "An unknown error has occurred in the SharedListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81 }
  82
  83 /***********************************************************************/
  84
  85 string SharedListVector::get(int index){
  86         return data[index];
  87 }
  88
  89 /***********************************************************************/
  90
  91 void SharedListVector::push_back(string seqNames){
  92         try {
  93                 data.push_back(seqNames);
  94                 int nNames = getNumNames(seqNames);
  95
  96                 numBins++;
  97
  98                 if(nNames > maxRank)    {       maxRank = nNames;       }
  99
 100                 numSeqs += nNames;
 101         }
 102         catch(exception& e) {
 103                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 104                 exit(1);
 105         }
 106         catch(...) {
 107                 cout << "An unknown error has occurred in the SharedListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110 }
 111
 112 /***********************************************************************/
 113
 114 void SharedListVector::resize(int size){
 115         data.resize(size);
 116 }
 117
 118 /***********************************************************************/
 119
 120 int SharedListVector::size(){
 121         return data.size();
 122 }
 123 /***********************************************************************/
 124
 125 void SharedListVector::clear(){
 126         numBins = 0;
 127         maxRank = 0;
 128         numSeqs = 0;
 129         return data.clear();
 130
 131 }
 132
 133 /***********************************************************************/
 134
 135 void SharedListVector::print(ostream& output){
 136         try {
 137                 output << label << '\t' << numBins << '\t';
 138
 139                 for(int i=0;i<data.size();i++){
 140                         if(data[i] != ""){
 141                                 output << data[i] << '\t';
 142                         }
 143                 }
 144                 output << endl;
 145         }
 146         catch(exception& e) {
 147                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 148                 exit(1);
 149         }
 150         catch(...) {
 151                 cout << "An unknown error has occurred in the SharedListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 152                 exit(1);
 153         }
 154 }
 155
 156
 157 /***********************************************************************/
 158
 159 RAbundVector SharedListVector::getRAbundVector(){
 160         try {
 161                 RAbundVector rav;
 162
 163                 for(int i=0;i<data.size();i++){
 164                         int binSize = getNumNames(data[i]);
 165                         rav.push_back(binSize);
 166                 }
 167
 168         //  This was here before to output data in a nice format, but it screws up the name mapping steps
 169         //      sort(rav.rbegin(), rav.rend());
 170         //
 171         //      for(int i=data.size()-1;i>=0;i--){
 172         //              if(rav.get(i) == 0){    rav.pop_back(); }
 173         //              else{
 174         //                      break;
 175         //              }
 176         //      }
 177                 rav.setLabel(label);
 178
 179                 return rav;
 180         }
 181         catch(exception& e) {
 182                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 183                 exit(1);
 184         }
 185         catch(...) {
 186                 cout << "An unknown error has occurred in the SharedListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 187                 exit(1);
 188         }
 189 }
 190
 191 /***********************************************************************/
 192
 193 SAbundVector SharedListVector::getSAbundVector(){
 194         try {
 195                 SAbundVector sav(maxRank+1);
 196
 197                 for(int i=0;i<data.size();i++){
 198                         int binSize = getNumNames(data[i]);
 199                         sav.set(binSize, sav.get(binSize) + 1);
 200                 }
 201                 sav.set(0, 0);
 202                 sav.setLabel(label);
 203
 204                 return sav;
 205         }
 206         catch(exception& e) {
 207                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210         catch(...) {
 211                 cout << "An unknown error has occurred in the SharedListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214 }
 215
 216 /***********************************************************************/
 217 SharedOrderVector* SharedListVector::getSharedOrderVector(){
 218         try {
 219                 string groupName, names, name;
 220
 221                 SharedOrderVector* order = new SharedOrderVector();
 222                 order->setLabel(label);
 223
 224                 for(int i=0;i<numBins;i++){
 225                         int binSize = getNumNames(get(i));      //find number of individual in given bin
 226                         names = get(i);
 227                         while (names.find_first_of(',') != -1) {
 228                                 name = names.substr(0,names.find_first_of(','));
 229                                 names = names.substr(names.find_first_of(',')+1, names.length());
 230                                 groupName = groupmap->getGroup(name);
 231                                 order->push_back(i, binSize, groupName);  //i represents what bin you are in
 232                         }
 233                         //get last name
 234                         groupName = groupmap->getGroup(names);
 235                         order->push_back(i, binSize, groupName);
 236                 }
 237                 random_shuffle(order->begin(), order->end());
 238                 return order;
 239         }
 240         catch(exception& e) {
 241                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 242                 exit(1);
 243         }
 244         catch(...) {
 245                 cout << "An unknown error has occurred in the SharedListVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 246                 exit(1);
 247         }
 248
 249 }
 250 /***********************************************************************/
 251 SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) {
 252         try {
 253                 SharedRAbundVector rav(data.size());
 254                 string group, names, name;
 255
 256                 for(int i=0;i<numBins;i++){
 257                         names = get(i);
 258                         while (names.find_first_of(',') != -1) {
 259                                 name = names.substr(0,names.find_first_of(','));
 260                                 names = names.substr(names.find_first_of(',')+1, names.length());
 261                                 group = groupmap->getGroup(name);
 262                                 if (group == groupName) { //this name is in the group you want the vector for.
 263                                         rav.set(i, rav.getAbundance(i) + 1, group);  //i represents what bin you are in
 264                                 }
 265                         }
 266
 267                         //get last name
 268                         groupName = groupmap->getGroup(names);
 269                         if (group == groupName) { //this name is in the group you want the vector for.
 270                                         rav.set(i, rav.getAbundance(i) + 1, group);  //i represents what bin you are in
 271                         }
 272                 }
 273
 274                 rav.setLabel(label);
 275                 rav.setGroup(groupName);
 276                 return rav;
 277
 278         }
 279         catch(exception& e) {
 280                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 281                 exit(1);
 282         }
 283         catch(...) {
 284                 cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 285                 exit(1);
 286         }
 287 }
 288 /***********************************************************************/
 289 vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 290         try {
 291                 SharedUtil* util;
 292                 util = new SharedUtil();
 293                 vector<SharedRAbundVector*> lookup;
 294
 295                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
 296                 util->getSharedVectors(globaldata->Groups, lookup, this->getSharedOrderVector());
 297
 298                 return lookup;
 299         }
 300         catch(exception& e) {
 301                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 302                 exit(1);
 303         }
 304         catch(...) {
 305                 cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 306                 exit(1);
 307         }
 308
 309 }
 310
 311 /***********************************************************************/
 312 SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) {
 313         try {
 314                 SharedSAbundVector sav;
 315                 SharedRAbundVector rav;
 316
 317                 rav = this->getSharedRAbundVector(groupName);
 318                 sav = rav.getSharedSAbundVector();
 319
 320                 return sav;
 321         }
 322         catch(exception& e) {
 323                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 324                 exit(1);
 325         }
 326         catch(...) {
 327                 cout << "An unknown error has occurred in the SharedListVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 328                 exit(1);
 329         }
 330 }
 331 /***********************************************************************/
 332
 333 OrderVector SharedListVector::getOrderVector(map<string,int>* orderMap = NULL){
 334
 335         try {
 336                 if(orderMap == NULL){
 337                         OrderVector ov;
 338
 339                         for(int i=0;i<data.size();i++){
 340                                 int binSize = getNumNames(data[i]);
 341                                 for(int j=0;j<binSize;j++){
 342                                         ov.push_back(i);
 343                                 }
 344                         }
 345                         random_shuffle(ov.begin(), ov.end());
 346                         ov.setLabel(label);
 347                         ov.getNumBins();
 348
 349                         return ov;
 350
 351                 }
 352                 else{
 353                         OrderVector ov(numSeqs);
 354
 355                         for(int i=0;i<data.size();i++){
 356                                 string listOTU = data[i];
 357                                 int length = listOTU.size();
 358
 359                                 string seqName="";
 360
 361                                 for(int j=0;j<length;j++){
 362
 363                                         if(listOTU[j] != ','){
 364                                                 seqName += listOTU[j];
 365                                         }
 366                                         else{
 367                                                 if(orderMap->count(seqName) == 0){
 368                                                         cerr << seqName << " not found, check *.names file\n";
 369                                                         exit(1);
 370                                                 }
 371
 372                                                 ov.set((*orderMap)[seqName], i);
 373                                                 seqName = "";
 374                                         }
 375                                 }
 376
 377                                 if(orderMap->count(seqName) == 0){
 378                                         cerr << seqName << " not found, check *.names file\n";
 379                                         exit(1);
 380                                 }
 381                                 ov.set((*orderMap)[seqName], i);
 382                         }
 383
 384                         ov.setLabel(label);
 385                         ov.getNumBins();
 386
 387                         return ov;
 388                 }
 389         }
 390         catch(exception& e) {
 391                 cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 392                 exit(1);
 393         }
 394         catch(...) {
 395                 cout << "An unknown error has occurred in the SharedListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 396                 exit(1);
 397         }
 398 }
 399
 400 /***********************************************************************/
 401