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 int 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                                 if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0;  }
  35
  36                                 int binNumber = order->get(i);
  37                                 int abundance = lookup->get(binNumber);
  38
  39                                 rank->set(abundance, rank->get(abundance)-1);
  40                                 abundance++;
  41
  42                                 lookup->set(binNumber, abundance);
  43                                 rank->set(abundance, rank->get(abundance)+1);
  44
  45                                 if((i == 0) || (i+1) % increment == 0){
  46                                         rcd->updateRankData(rank);
  47                                 }
  48                         }
  49
  50                         if(numSeqs % increment != 0){
  51                                 rcd->updateRankData(rank);
  52                         }
  53
  54                         for(int i=0;i<displays.size();i++){
  55                                 displays[i]->reset();
  56                         }
  57
  58                         delete lookup;
  59                         delete rank;
  60                 }
  61
  62                 for(int i=0;i<displays.size();i++){
  63                         displays[i]->close();
  64                 }
  65                 delete rcd;
  66                 return 0;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "Rarefact", "getCurve");
  70                 exit(1);
  71         }
  72 }
  73
  74 /***********************************************************************/
  75
  76 int Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
  77 try {
  78                 SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
  79
  80                 label = lookup[0]->getLabel();
  81
  82                 //register the displays
  83                 for(int i=0;i<displays.size();i++){
  84                         rcd->registerDisplay(displays[i]);
  85                 }
  86
  87                 //if jumble is false all iters will be the same
  88                 if (globaldata->jumble == false)  {  nIters = 1;  }
  89
  90                 for(int iter=0;iter<nIters;iter++){
  91
  92                         for(int i=0;i<displays.size();i++){
  93                                 displays[i]->init(label);
  94                         }
  95
  96                         if (globaldata->jumble == true)  {
  97                                 //randomize the groups
  98                                 random_shuffle(lookup.begin(), lookup.end());
  99                         }
 100
 101                         //make merge the size of lookup[0]
 102                         SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
 103
 104                         //make copy of lookup zero
 105                         for(int i = 0; i<lookup[0]->size(); i++) {
 106                                 merge->set(i, lookup[0]->getAbundance(i), "merge");
 107                         }
 108
 109                         vector<SharedRAbundVector*> subset;
 110                         //send each group one at a time
 111                         for (int k = 0; k < lookup.size(); k++) {
 112                                 if (m->control_pressed) {  delete merge; delete rcd; return 0;  }
 113
 114                                 subset.clear(); //clears out old pair of sharedrabunds
 115                                 //add in new pair of sharedrabunds
 116                                 subset.push_back(merge); subset.push_back(lookup[k]);
 117
 118                                 rcd->updateSharedData(subset, k+1, numGroupComb);
 119                                 mergeVectors(merge, lookup[k]);
 120                         }
 121
 122                         //resets output files
 123                         for(int i=0;i<displays.size();i++){
 124                                 displays[i]->reset();
 125                         }
 126
 127                         delete merge;
 128                 }
 129
 130                 for(int i=0;i<displays.size();i++){
 131                         displays[i]->close();
 132                 }
 133
 134                 delete rcd;
 135                 return 0;
 136         }
 137         catch(exception& e) {
 138                 m->errorOut(e, "Rarefact", "getSharedCurve");
 139                 exit(1);
 140         }
 141 }
 142
 143 /**************************************************************************************/
 144 void Rarefact::mergeVectors(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
 145         try{
 146                 for (int k = 0; k < shared1->size(); k++) {
 147                         //merge new species into shared1
 148                         shared1->set(k, (shared1->getAbundance(k) + shared2->getAbundance(k)), "combo");  //set to 'combo' since this vector now contains multiple groups
 149                 }
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "Rarefact", "mergeVectors");
 153                 exit(1);
 154         }
 155 }
 156