rarefact.cpp

   1 /*
   2  *  rarefact.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 11/18/08.
   6  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefact.h"
  11 //#include "ordervector.hpp"
  12
  13 /***********************************************************************/
  14
  15 void Rarefact::getCurve(int increment = 1, int nIters = 1000){
  16         try {
  17                 RarefactionCurveData* rcd = new RarefactionCurveData();
  18                 for(int i=0;i<displays.size();i++){
  19                         rcd->registerDisplay(displays[i]);
  20                 }
  21
  22                 for(int iter=0;iter<nIters;iter++){
  23
  24                         for(int i=0;i<displays.size();i++){
  25                                 displays[i]->init(label);
  26                         }
  27
  28                         RAbundVector* lookup    = new RAbundVector(order->getNumBins());
  29                         SAbundVector* rank      = new SAbundVector(order->getMaxRank()+1);
  30                         random_shuffle(order->begin(), order->end());
  31
  32                         for(int i=0;i<numSeqs;i++){
  33
  34                                 int binNumber = order->get(i);
  35                                 int abundance = lookup->get(binNumber);
  36
  37                                 rank->set(abundance, rank->get(abundance)-1);
  38                                 abundance++;
  39
  40                                 lookup->set(binNumber, abundance);
  41                                 rank->set(abundance, rank->get(abundance)+1);
  42
  43                                 if((i == 0) || (i+1) % increment == 0){
  44                                         rcd->updateRankData(rank);
  45                                 }
  46                         }
  47
  48                         if(numSeqs % increment != 0){
  49                                 rcd->updateRankData(rank);
  50                         }
  51
  52                         for(int i=0;i<displays.size();i++){
  53                                 displays[i]->reset();
  54                         }
  55
  56                         delete lookup;
  57                         delete rank;
  58                 }
  59
  60                 for(int i=0;i<displays.size();i++){
  61                         displays[i]->close();
  62                 }
  63                 delete rcd;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "Rarefact", "getCurve");
  67                 exit(1);
  68         }
  69 }
  70
  71 /***********************************************************************/
  72
  73 void Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
  74 try {
  75                 SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
  76
  77                 label = lookup[0]->getLabel();
  78
  79                 //register the displays
  80                 for(int i=0;i<displays.size();i++){
  81                         rcd->registerDisplay(displays[i]);
  82                 }
  83
  84                 //if jumble is false all iters will be the same
  85                 if (globaldata->jumble == false)  {  nIters = 1;  }
  86
  87                 for(int iter=0;iter<nIters;iter++){
  88
  89                         for(int i=0;i<displays.size();i++){
  90                                 displays[i]->init(label);
  91                         }
  92
  93                         if (globaldata->jumble == true)  {
  94                                 //randomize the groups
  95                                 random_shuffle(lookup.begin(), lookup.end());
  96                         }
  97
  98                         //make merge the size of lookup[0]
  99                         SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
 100
 101                         //make copy of lookup zero
 102                         for(int i = 0; i<lookup[0]->size(); i++) {
 103                                 merge->set(i, lookup[0]->getAbundance(i), "merge");
 104                         }
 105
 106                         vector<SharedRAbundVector*> subset;
 107                         //send each group one at a time
 108                         for (int k = 0; k < lookup.size(); k++) {
 109                                 subset.clear(); //clears out old pair of sharedrabunds
 110                                 //add in new pair of sharedrabunds
 111                                 subset.push_back(merge); subset.push_back(lookup[k]);
 112
 113                                 rcd->updateSharedData(subset, k+1, numGroupComb);
 114                                 mergeVectors(merge, lookup[k]);
 115                         }
 116
 117                         //resets output files
 118                         for(int i=0;i<displays.size();i++){
 119                                 displays[i]->reset();
 120                         }
 121
 122                         delete merge;
 123                 }
 124
 125                 for(int i=0;i<displays.size();i++){
 126                         displays[i]->close();
 127                 }
 128
 129                 delete rcd;
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "Rarefact", "getSharedCurve");
 133                 exit(1);
 134         }
 135 }
 136
 137 /**************************************************************************************/
 138 void Rarefact::mergeVectors(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
 139         try{
 140                 for (int k = 0; k < shared1->size(); k++) {
 141                         //merge new species into shared1
 142                         shared1->set(k, (shared1->getAbundance(k) + shared2->getAbundance(k)), "combo");  //set to 'combo' since this vector now contains multiple groups
 143                 }
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "Rarefact", "mergeVectors");
 147                 exit(1);
 148         }
 149 }
 150