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 = m->getNumNames(data[i]);
  32                                 numBins = i+1;
  33                                 if(binSize > maxRank)   {       maxRank = binSize;      }
  34                                 numSeqs += binSize;
  35                         }
  36                 }
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "ListVector", "ListVector");
  40                 exit(1);
  41         }
  42 }
  43
  44 /**********************************************************************/
  45
  46 ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
  47         try {
  48                 int hold;
  49                 f >> label >> hold;
  50
  51                 data.assign(hold, "");
  52                 string inputData = "";
  53
  54                 for(int i=0;i<hold;i++){
  55                         f >> inputData;
  56                         set(i, inputData);
  57                 }
  58                 m->gobble(f);
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "ListVector", "ListVector");
  62                 exit(1);
  63         }
  64 }
  65
  66 /***********************************************************************/
  67
  68 void ListVector::set(int binNumber, string seqNames){
  69         try {
  70                 int nNames_old = m->getNumNames(data[binNumber]);
  71                 data[binNumber] = seqNames;
  72                 int nNames_new = m->getNumNames(seqNames);
  73
  74                 if(nNames_old == 0)                     {       numBins++;                              }
  75                 if(nNames_new == 0)                     {       numBins--;                              }
  76                 if(nNames_new > maxRank)        {       maxRank = nNames_new;   }
  77
  78                 numSeqs += (nNames_new - nNames_old);
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "ListVector", "set");
  82                 exit(1);
  83         }
  84 }
  85
  86 /***********************************************************************/
  87
  88 string ListVector::get(int index){
  89         return data[index];
  90 }
  91
  92 /***********************************************************************/
  93
  94 void ListVector::push_back(string seqNames){
  95         try {
  96                 data.push_back(seqNames);
  97                 int nNames = m->getNumNames(seqNames);
  98
  99                 numBins++;
 100
 101                 if(nNames > maxRank)    {       maxRank = nNames;       }
 102
 103                 numSeqs += nNames;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "ListVector", "push_back");
 107                 exit(1);
 108         }
 109 }
 110
 111 /***********************************************************************/
 112
 113 void ListVector::resize(int size){
 114         data.resize(size);
 115 }
 116
 117 /***********************************************************************/
 118
 119 int ListVector::size(){
 120         return data.size();
 121 }
 122 /***********************************************************************/
 123
 124 void ListVector::clear(){
 125         numBins = 0;
 126         maxRank = 0;
 127         numSeqs = 0;
 128         return data.clear();
 129
 130 }
 131
 132 /***********************************************************************/
 133
 134 void ListVector::print(ostream& output){
 135         try {
 136                 output << label << '\t' << numBins << '\t';
 137
 138                 for(int i=0;i<data.size();i++){
 139                         if(data[i] != ""){
 140                                 output << data[i] << '\t';
 141                         }
 142                 }
 143                 output << endl;
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "ListVector", "print");
 147                 exit(1);
 148         }
 149 }
 150
 151
 152 /***********************************************************************/
 153
 154 RAbundVector ListVector::getRAbundVector(){
 155         try {
 156                 RAbundVector rav;
 157
 158                 for(int i=0;i<data.size();i++){
 159                         int binSize = m->getNumNames(data[i]);
 160                         rav.push_back(binSize);
 161                 }
 162
 163         //  This was here before to output data in a nice format, but it screws up the name mapping steps
 164         //      sort(rav.rbegin(), rav.rend());
 165         //
 166         //      for(int i=data.size()-1;i>=0;i--){
 167         //              if(rav.get(i) == 0){    rav.pop_back(); }
 168         //              else{
 169         //                      break;
 170         //              }
 171         //      }
 172                 rav.setLabel(label);
 173
 174                 return rav;
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "ListVector", "getRAbundVector");
 178                 exit(1);
 179         }
 180 }
 181
 182 /***********************************************************************/
 183
 184 SAbundVector ListVector::getSAbundVector(){
 185         try {
 186                 SAbundVector sav(maxRank+1);
 187
 188                 for(int i=0;i<data.size();i++){
 189                         int binSize = m->getNumNames(data[i]);
 190                         sav.set(binSize, sav.get(binSize) + 1);
 191                 }
 192                 sav.set(0, 0);
 193                 sav.setLabel(label);
 194
 195                 return sav;
 196         }
 197         catch(exception& e) {
 198                 m->errorOut(e, "ListVector", "getSAbundVector");
 199                 exit(1);
 200         }
 201 }
 202
 203 /***********************************************************************/
 204
 205 OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 206
 207         try {
 208                 if(orderMap == NULL){
 209                         OrderVector ov;
 210
 211                         for(int i=0;i<data.size();i++){
 212                                 int binSize = m->getNumNames(data[i]);
 213                                 for(int j=0;j<binSize;j++){
 214                                         ov.push_back(i);
 215                                 }
 216                         }
 217                         random_shuffle(ov.begin(), ov.end());
 218                         ov.setLabel(label);
 219                         ov.getNumBins();
 220
 221                         return ov;
 222
 223                 }
 224                 else{
 225                         OrderVector ov(numSeqs);
 226
 227                         for(int i=0;i<data.size();i++){
 228                                 string listOTU = data[i];
 229                                 int length = listOTU.size();
 230
 231                                 string seqName="";
 232
 233                                 for(int j=0;j<length;j++){
 234
 235                                         if(listOTU[j] != ','){
 236                                                 seqName += listOTU[j];
 237                                         }
 238                                         else{
 239                                                 if(orderMap->count(seqName) == 0){
 240                                                         m->mothurOut(seqName + " not found, check *.names file\n");
 241                                                         exit(1);
 242                                                 }
 243
 244                                                 ov.set((*orderMap)[seqName], i);
 245                                                 seqName = "";
 246                                         }
 247                                 }
 248
 249                                 if(orderMap->count(seqName) == 0){
 250                                         m->mothurOut(seqName + " not found, check *.names file\n");
 251                                         exit(1);
 252                                 }
 253                                 ov.set((*orderMap)[seqName], i);
 254                         }
 255
 256                         ov.setLabel(label);
 257                         ov.getNumBins();
 258
 259                         return ov;
 260                 }
 261         }
 262         catch(exception& e) {
 263                 m->errorOut(e, "ListVector", "getOrderVector");
 264                 exit(1);
 265         }
 266 }
 267
 268 /***********************************************************************/