listvector.cpp

   1 /*
   2  *  list.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 8/8/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10
  11 #include "sabundvector.hpp"
  12 #include "rabundvector.hpp"
  13 #include "ordervector.hpp"
  14 #include "listvector.hpp"
  15
  16
  17 /***********************************************************************/
  18
  19 ListVector::ListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){}
  20
  21 /***********************************************************************/
  22
  23 ListVector::ListVector(int n):  DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){}
  24
  25 /***********************************************************************/
  26
  27 ListVector::ListVector(string id, vector<string> lv) : DataVector(id), data(lv){
  28         try {
  29                 for(int i=0;i<data.size();i++){
  30                         if(data[i] != ""){
  31                                 int binSize = getNumNames(data[i]);
  32                                 numBins = i+1;
  33                                 if(binSize > maxRank)   {       maxRank = binSize;      }
  34                                 numSeqs += binSize;
  35                         }
  36                 }
  37         }
  38         catch(exception& e) {
  39                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  40                 exit(1);
  41         }
  42         catch(...) {
  43                 cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  44                 exit(1);
  45         }
  46 }
  47
  48 /**********************************************************************/
  49
  50 ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
  51         try {
  52                 int hold;
  53                 f >> label >> hold;
  54
  55                 data.assign(hold, "");
  56                 string inputData = "";
  57
  58                 for(int i=0;i<hold;i++){
  59                         f >> inputData;
  60                         set(i, inputData);
  61                 }
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the ListVector class function ListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71 }
  72
  73 /***********************************************************************/
  74
  75 void ListVector::set(int binNumber, string seqNames){
  76         try {
  77                 int nNames_old = getNumNames(data[binNumber]);
  78                 data[binNumber] = seqNames;
  79                 int nNames_new = getNumNames(seqNames);
  80
  81                 if(nNames_old == 0)                     {       numBins++;                              }
  82                 if(nNames_new == 0)                     {       numBins--;                              }
  83                 if(nNames_new > maxRank)        {       maxRank = nNames_new;   }
  84
  85                 numSeqs += (nNames_new - nNames_old);
  86         }
  87         catch(exception& e) {
  88                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  89                 exit(1);
  90         }
  91         catch(...) {
  92                 cout << "An unknown error has occurred in the ListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95 }
  96
  97 /***********************************************************************/
  98
  99 string ListVector::get(int index){
 100         return data[index];
 101 }
 102
 103 /***********************************************************************/
 104
 105 void ListVector::push_back(string seqNames){
 106         try {
 107                 data.push_back(seqNames);
 108                 int nNames = getNumNames(seqNames);
 109
 110                 numBins++;
 111
 112                 if(nNames > maxRank)    {       maxRank = nNames;       }
 113
 114                 numSeqs += nNames;
 115         }
 116         catch(exception& e) {
 117                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 118                 exit(1);
 119         }
 120         catch(...) {
 121                 cout << "An unknown error has occurred in the ListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124 }
 125
 126 /***********************************************************************/
 127
 128 void ListVector::resize(int size){
 129         data.resize(size);
 130 }
 131
 132 /***********************************************************************/
 133
 134 int ListVector::size(){
 135         return data.size();
 136 }
 137 /***********************************************************************/
 138
 139 void ListVector::clear(){
 140         numBins = 0;
 141         maxRank = 0;
 142         numSeqs = 0;
 143         return data.clear();
 144
 145 }
 146
 147 /***********************************************************************/
 148
 149 void ListVector::print(ostream& output){
 150         try {
 151                 output << label << '\t' << numBins << '\t';
 152
 153                 for(int i=0;i<data.size();i++){
 154                         if(data[i] != ""){
 155                                 output << data[i] << '\t';
 156                         }
 157                 }
 158                 output << endl;
 159         }
 160         catch(exception& e) {
 161                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 162                 exit(1);
 163         }
 164         catch(...) {
 165                 cout << "An unknown error has occurred in the ListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 166                 exit(1);
 167         }
 168 }
 169
 170
 171 /***********************************************************************/
 172
 173 RAbundVector ListVector::getRAbundVector(){
 174         try {
 175                 RAbundVector rav;
 176
 177                 for(int i=0;i<data.size();i++){
 178                         int binSize = getNumNames(data[i]);
 179                         rav.push_back(binSize);
 180                 }
 181
 182         //  This was here before to output data in a nice format, but it screws up the name mapping steps
 183         //      sort(rav.rbegin(), rav.rend());
 184         //
 185         //      for(int i=data.size()-1;i>=0;i--){
 186         //              if(rav.get(i) == 0){    rav.pop_back(); }
 187         //              else{
 188         //                      break;
 189         //              }
 190         //      }
 191                 rav.setLabel(label);
 192
 193                 return rav;
 194         }
 195         catch(exception& e) {
 196                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 197                 exit(1);
 198         }
 199         catch(...) {
 200                 cout << "An unknown error has occurred in the ListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 201                 exit(1);
 202         }
 203 }
 204
 205 /***********************************************************************/
 206
 207 SAbundVector ListVector::getSAbundVector(){
 208         try {
 209                 SAbundVector sav(maxRank+1);
 210
 211                 for(int i=0;i<data.size();i++){
 212                         int binSize = getNumNames(data[i]);
 213                         sav.set(binSize, sav.get(binSize) + 1);
 214                 }
 215                 sav.set(0, 0);
 216                 sav.setLabel(label);
 217
 218                 return sav;
 219         }
 220         catch(exception& e) {
 221                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 222                 exit(1);
 223         }
 224         catch(...) {
 225                 cout << "An unknown error has occurred in the ListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 226                 exit(1);
 227         }
 228 }
 229
 230 /***********************************************************************/
 231
 232 OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 233
 234         try {
 235                 if(orderMap == NULL){
 236                         OrderVector ov;
 237
 238                         for(int i=0;i<data.size();i++){
 239                                 int binSize = getNumNames(data[i]);
 240                                 for(int j=0;j<binSize;j++){
 241                                         ov.push_back(i);
 242                                 }
 243                         }
 244                         random_shuffle(ov.begin(), ov.end());
 245                         ov.setLabel(label);
 246                         ov.getNumBins();
 247
 248                         return ov;
 249
 250                 }
 251                 else{
 252                         OrderVector ov(numSeqs);
 253
 254                         for(int i=0;i<data.size();i++){
 255                                 string listOTU = data[i];
 256                                 int length = listOTU.size();
 257
 258                                 string seqName="";
 259
 260                                 for(int j=0;j<length;j++){
 261
 262                                         if(listOTU[j] != ','){
 263                                                 seqName += listOTU[j];
 264                                         }
 265                                         else{
 266                                                 if(orderMap->count(seqName) == 0){
 267                                                         cerr << seqName << " not found, check *.names file\n";
 268                                                         exit(1);
 269                                                 }
 270
 271                                                 ov.set((*orderMap)[seqName], i);
 272                                                 seqName = "";
 273                                         }
 274                                 }
 275
 276                                 if(orderMap->count(seqName) == 0){
 277                                         cerr << seqName << " not found, check *.names file\n";
 278                                         exit(1);
 279                                 }
 280                                 ov.set((*orderMap)[seqName], i);
 281                         }
 282
 283                         ov.setLabel(label);
 284                         ov.getNumBins();
 285
 286                         return ov;
 287                 }
 288         }
 289         catch(exception& e) {
 290                 cout << "Standard Error: " << e.what() << " has occurred in the ListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 291                 exit(1);
 292         }
 293         catch(...) {
 294                 cout << "An unknown error has occurred in the ListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 295                 exit(1);
 296         }
 297 }
 298
 299 /***********************************************************************/