collect.cpp

   1 /*
   2  *  collect.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 "collect.h"
  11
  12 /***********************************************************************/
  13
  14 void Collect::getCurve(int increment = 1){
  15         try {
  16                 RAbundVector* lookup = new RAbundVector(order->getNumBins());
  17                 SAbundVector* rank        = new SAbundVector(order->getMaxRank()+1);
  18
  19                 CollectorsCurveData* ccd = new CollectorsCurveData();
  20
  21                 for(int i=0;i<displays.size();i++){
  22                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  23                         displays[i]->init(label);                   //sets displays label
  24                 }
  25                 for(int i=0;i<numSeqs;i++){
  26
  27                         int binNumber = order->get(i);
  28                         int abundance = lookup->get(binNumber);
  29
  30                         rank->set(abundance, rank->get(abundance)-1);
  31
  32                         abundance++;
  33
  34                         lookup->set(binNumber, abundance);
  35                         rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
  36
  37                         if((i == 0) || (i+1) % increment == 0){
  38                                 ccd->updateRankData(rank);
  39                         }
  40                 }
  41
  42                 if(numSeqs % increment != 0){
  43                         ccd->updateRankData(rank);
  44                 }
  45
  46                 for(int i=0;i<displays.size();i++){
  47                         displays[i]->reset();
  48                 }
  49         }
  50         catch(exception& e) {
  51                 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  52                 exit(1);
  53         }
  54         catch(...) {
  55                 cout << "An unknown error has occurred in the Collect class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58
  59 }
  60
  61 /***********************************************************************/
  62 void Collect::getSharedCurve(int increment = 1){
  63 try {
  64                 globaldata = GlobalData::getInstance();
  65                 vector<SharedRAbundVector*> lookup;
  66
  67                 //create and initialize vector of sharedvectors, one for each group
  68                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  69                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
  70                         temp->setLabel(sharedorder->getLabel());
  71                         temp->setGroup(globaldata->Groups[i]);
  72                         temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
  73                         lookup.push_back(temp);
  74                 }
  75
  76                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
  77
  78                 //initialize labels for output
  79                 //makes  'uniqueAB         uniqueAC  uniqueBC' if your groups are A, B, C
  80                 getGroupComb();
  81                 groupLabel = "";
  82                 for (int s = 0; s < groupComb.size(); s++) {
  83                         groupLabel = groupLabel + label + groupComb[s] + "\t";
  84                 }
  85
  86                 for(int i=0;i<displays.size();i++){
  87                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  88                         displays[i]->init(groupLabel);
  89                 }
  90
  91                 //sample all the members
  92                 for(int i=0;i<numSeqs;i++){
  93                         //get first sample
  94                         individual chosen = sharedorder->get(i);
  95                         int abundance;
  96
  97                         //set info for sharedvector in chosens group
  98                         for (int j = 0; j < lookup.size(); j++) {
  99                                                         if (chosen.group == lookup[j]->getGroup()) {
 100                                                                 abundance = lookup[j]->getAbundance(chosen.bin);
 101                                                                 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 102                                                                 break;
 103                                                         }
 104                         }
 105
 106
 107                         //calculate at 0 and the given increment
 108                         if((i == 0) || (i+1) % increment == 0){
 109                                 //randomize group order
 110                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 111                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 112                                 int n = 1;
 113                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 114                                         for (int l = n; l < lookup.size(); l++) {
 115                                                 ccd->updateSharedData(lookup[k], lookup[l], i+1, globaldata->Groups.size());
 116                                         }
 117                                         n++;
 118                                 }
 119                         }
 120                         totalNumSeq = i+1;
 121                 }
 122
 123                 //calculate last line if you haven't already
 124                 if(numSeqs % increment != 0){
 125                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 126                         int n = 1;
 127                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 128                                 for (int l = n; l < lookup.size(); l++) {
 129                                         ccd->updateSharedData(lookup[k], lookup[l], totalNumSeq, globaldata->Groups.size());
 130                                 }
 131                                 n++;
 132                         }
 133                 }
 134
 135                 //resets output files
 136                 for(int i=0;i<displays.size();i++){
 137                         displays[i]->reset();
 138                 }
 139         }
 140         catch(exception& e) {
 141                 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144         catch(...) {
 145                 cout << "An unknown error has occurred in the Collect class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148
 149 }
 150
 151 /**************************************************************************************/
 152
 153 void Collect::getGroupComb() {
 154         string group;
 155
 156         numGroupComb = 0;
 157
 158         int n = 1;
 159         for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
 160                 for (int l = n; l < globaldata->Groups.size(); l++) {
 161                         group = globaldata->Groups[i] + globaldata->Groups[l];
 162                         groupComb.push_back(group);
 163                         numGroupComb++;
 164                 }
 165                 n++;
 166         }
 167
 168 }
 169
 170 /**************************************************************************************/