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                 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
  59                 gobble(f);
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "ListVector", "ListVector");
  63                 exit(1);
  64         }
  65 }
  66
  67 /***********************************************************************/
  68
  69 void ListVector::set(int binNumber, string seqNames){
  70         try {
  71                 int nNames_old = getNumNames(data[binNumber]);
  72                 data[binNumber] = seqNames;
  73                 int nNames_new = getNumNames(seqNames);
  74
  75                 if(nNames_old == 0)                     {       numBins++;                              }
  76                 if(nNames_new == 0)                     {       numBins--;                              }
  77                 if(nNames_new > maxRank)        {       maxRank = nNames_new;   }
  78
  79                 numSeqs += (nNames_new - nNames_old);
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "ListVector", "set");
  83                 exit(1);
  84         }
  85 }
  86
  87 /***********************************************************************/
  88
  89 string ListVector::get(int index){
  90         return data[index];
  91 }
  92
  93 /***********************************************************************/
  94
  95 void ListVector::push_back(string seqNames){
  96         try {
  97                 data.push_back(seqNames);
  98                 int nNames = getNumNames(seqNames);
  99
 100                 numBins++;
 101
 102                 if(nNames > maxRank)    {       maxRank = nNames;       }
 103
 104                 numSeqs += nNames;
 105         }
 106         catch(exception& e) {
 107                 m->errorOut(e, "ListVector", "push_back");
 108                 exit(1);
 109         }
 110 }
 111
 112 /***********************************************************************/
 113
 114 void ListVector::resize(int size){
 115         data.resize(size);
 116 }
 117
 118 /***********************************************************************/
 119
 120 int ListVector::size(){
 121         return data.size();
 122 }
 123 /***********************************************************************/
 124
 125 void ListVector::clear(){
 126         numBins = 0;
 127         maxRank = 0;
 128         numSeqs = 0;
 129         return data.clear();
 130
 131 }
 132
 133 /***********************************************************************/
 134
 135 void ListVector::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                 m->errorOut(e, "ListVector", "print");
 148                 exit(1);
 149         }
 150 }
 151
 152
 153 /***********************************************************************/
 154
 155 RAbundVector ListVector::getRAbundVector(){
 156         try {
 157                 RAbundVector rav;
 158
 159                 for(int i=0;i<data.size();i++){
 160                         int binSize = getNumNames(data[i]);
 161                         rav.push_back(binSize);
 162                 }
 163
 164         //  This was here before to output data in a nice format, but it screws up the name mapping steps
 165         //      sort(rav.rbegin(), rav.rend());
 166         //
 167         //      for(int i=data.size()-1;i>=0;i--){
 168         //              if(rav.get(i) == 0){    rav.pop_back(); }
 169         //              else{
 170         //                      break;
 171         //              }
 172         //      }
 173                 rav.setLabel(label);
 174
 175                 return rav;
 176         }
 177         catch(exception& e) {
 178                 m->errorOut(e, "ListVector", "getRAbundVector");
 179                 exit(1);
 180         }
 181 }
 182
 183 /***********************************************************************/
 184
 185 SAbundVector ListVector::getSAbundVector(){
 186         try {
 187                 SAbundVector sav(maxRank+1);
 188
 189                 for(int i=0;i<data.size();i++){
 190                         int binSize = getNumNames(data[i]);
 191                         sav.set(binSize, sav.get(binSize) + 1);
 192                 }
 193                 sav.set(0, 0);
 194                 sav.setLabel(label);
 195
 196                 return sav;
 197         }
 198         catch(exception& e) {
 199                 m->errorOut(e, "ListVector", "getSAbundVector");
 200                 exit(1);
 201         }
 202 }
 203
 204 /***********************************************************************/
 205
 206 OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL){
 207
 208         try {
 209                 if(orderMap == NULL){
 210                         OrderVector ov;
 211
 212                         for(int i=0;i<data.size();i++){
 213                                 int binSize = getNumNames(data[i]);
 214                                 for(int j=0;j<binSize;j++){
 215                                         ov.push_back(i);
 216                                 }
 217                         }
 218                         random_shuffle(ov.begin(), ov.end());
 219                         ov.setLabel(label);
 220                         ov.getNumBins();
 221
 222                         return ov;
 223
 224                 }
 225                 else{
 226                         OrderVector ov(numSeqs);
 227
 228                         for(int i=0;i<data.size();i++){
 229                                 string listOTU = data[i];
 230                                 int length = listOTU.size();
 231
 232                                 string seqName="";
 233
 234                                 for(int j=0;j<length;j++){
 235
 236                                         if(listOTU[j] != ','){
 237                                                 seqName += listOTU[j];
 238                                         }
 239                                         else{
 240                                                 if(orderMap->count(seqName) == 0){
 241                                                         m->mothurOut(seqName + " not found, check *.names file\n");
 242                                                         exit(1);
 243                                                 }
 244
 245                                                 ov.set((*orderMap)[seqName], i);
 246                                                 seqName = "";
 247                                         }
 248                                 }
 249
 250                                 if(orderMap->count(seqName) == 0){
 251                                         m->mothurOut(seqName + " not found, check *.names file\n");
 252                                         exit(1);
 253                                 }
 254                                 ov.set((*orderMap)[seqName], i);
 255                         }
 256
 257                         ov.setLabel(label);
 258                         ov.getNumBins();
 259
 260                         return ov;
 261                 }
 262         }
 263         catch(exception& e) {
 264                 m->errorOut(e, "ListVector", "getOrderVector");
 265                 exit(1);
 266         }
 267 }
 268
 269 /***********************************************************************/