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                                 delete lookup;
  51                                 delete rank;
  52                                 delete ccd;
  53         }
  54         catch(exception& e) {
  55                 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58         catch(...) {
  59                 cout << "An unknown error has occurred in the Collect class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  60                 exit(1);
  61         }
  62
  63 }
  64
  65 /***********************************************************************/
  66 void Collect::getSharedCurve(int increment = 1){
  67 try {
  68                 globaldata = GlobalData::getInstance();
  69                 vector<SharedRAbundVector*> lookup;
  70                                 vector<SharedRAbundVector*> subset;
  71
  72                 //create and initialize vector of sharedvectors, one for each group
  73                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  74                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
  75                         temp->setLabel(sharedorder->getLabel());
  76                         temp->setGroup(globaldata->Groups[i]);
  77                         temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
  78                         lookup.push_back(temp);
  79                 }
  80
  81                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
  82
  83                 //initialize labels for output
  84                 //makes  'uniqueAB         uniqueAC  uniqueBC' if your groups are A, B, C
  85                 getGroupComb();
  86                 groupLabel = "";
  87                 for (int s = 0; s < groupComb.size(); s++) {
  88                         groupLabel = groupLabel + label + groupComb[s] + "\t";
  89                 }
  90
  91                                 //for multi displays
  92                                 string groupLabelAll = groupLabel + label + "all\t";
  93
  94                 for(int i=0;i<displays.size();i++){
  95                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  96                                                 if (displays[i]->isCalcMultiple() == true)  {   displays[i]->init(groupLabelAll); }
  97                                                 else {  displays[i]->init(groupLabel);  }
  98                 }
  99
 100                 //sample all the members
 101                 for(int i=0;i<numSeqs;i++){
 102                         //get first sample
 103                         individual chosen = sharedorder->get(i);
 104                         int abundance;
 105
 106                         //set info for sharedvector in chosens group
 107                         for (int j = 0; j < lookup.size(); j++) {
 108                                                         if (chosen.group == lookup[j]->getGroup()) {
 109                                                                 abundance = lookup[j]->getAbundance(chosen.bin);
 110                                                                 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 111                                                                 break;
 112                                                         }
 113                         }
 114
 115
 116                         //calculate at 0 and the given increment
 117                         if((i == 0) || (i+1) % increment == 0){
 118
 119                                                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 120
 121                                 int n = 1;
 122                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 123                                         for (int l = n; l < lookup.size(); l++) {
 124                                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 125                                                                                                 //add new pair of sharedrabund vectors
 126                                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 127                                                 ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
 128                                         }
 129                                         n++;
 130                                 }
 131                                                                 //if this is a calculator that can do multiples then do them
 132                                                                 ccd->updateSharedData(lookup, i+1, globaldata->Groups.size());
 133                         }
 134                         totalNumSeq = i+1;
 135                 }
 136
 137                 //calculate last line if you haven't already
 138                 if(numSeqs % increment != 0){
 139                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 140                         int n = 1;
 141                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 142                                 for (int l = n; l < lookup.size(); l++) {
 143                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 144                                                                                 //add new pair of sharedrabund vectors
 145                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 146                                                                                 ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
 147                                 }
 148                                 n++;
 149                         }
 150                                                 //if this is a calculator that can do multiples then do them
 151                                                 ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size());
 152                 }
 153
 154                 //resets output files
 155                 for(int i=0;i<displays.size();i++){
 156                         displays[i]->reset();
 157                 }
 158
 159                                 //memory cleanup
 160                                 delete ccd;
 161                                 for (int i = 0; i < lookup.size(); i++) {
 162                                         delete lookup[i];
 163                                 }
 164
 165         }
 166         catch(exception& e) {
 167                 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 168                 exit(1);
 169         }
 170         catch(...) {
 171                 cout << "An unknown error has occurred in the Collect class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 172                 exit(1);
 173         }
 174
 175 }
 176
 177 /**************************************************************************************/
 178
 179 void Collect::getGroupComb() {
 180         string group;
 181
 182         numGroupComb = 0;
 183
 184         int n = 1;
 185         for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
 186                 for (int l = n; l < globaldata->Groups.size(); l++) {
 187                         group = globaldata->Groups[i] + globaldata->Groups[l];
 188                         groupComb.push_back(group);
 189                         numGroupComb++;
 190                 }
 191                 n++;
 192         }
 193
 194 }
 195
 196 /**************************************************************************************/