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 int Collect::getCurve(float percentFreq = 0.01){
  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
  26                                 //convert freq percentage to number
  27                                 int increment = numSeqs * percentFreq;
  28
  29                 for(int i=0;i<numSeqs;i++){
  30
  31                                                 if (m->control_pressed) { delete lookup; delete rank; delete ccd;  return 1;  }
  32
  33                         int binNumber = order->get(i);
  34                         int abundance = lookup->get(binNumber);
  35
  36                         rank->set(abundance, rank->get(abundance)-1);
  37
  38                         abundance++;
  39
  40                         lookup->set(binNumber, abundance);
  41                         rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
  42
  43                         if((i == 0) || (i+1) % increment == 0){
  44                                 ccd->updateRankData(rank);
  45                         }
  46                 }
  47
  48                 if(numSeqs % increment != 0){
  49                         ccd->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                                 delete ccd;
  59
  60                                 return 0;
  61         }
  62         catch(exception& e) {
  63                         m->errorOut(e, "Collect", "getCurve");
  64                         exit(1);
  65         }
  66 }
  67
  68 /***********************************************************************/
  69 int Collect::getSharedCurve(float percentFreq = 0.01){
  70 try {
  71                                 globaldata = GlobalData::getInstance();
  72                 vector<SharedRAbundVector*> lookup;
  73                                 vector<SharedRAbundVector*> subset;
  74
  75                 //create and initialize vector of sharedvectors, one for each group
  76                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  77                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
  78                         temp->setLabel(sharedorder->getLabel());
  79                         temp->setGroup(globaldata->Groups[i]);
  80                         temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
  81                         lookup.push_back(temp);
  82                 }
  83
  84                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
  85
  86                 //initialize labels for output
  87                 //makes  'uniqueAB         uniqueAC  uniqueBC' if your groups are A, B, C
  88                 getGroupComb();
  89                 groupLabel = "";
  90                 for (int s = 0; s < groupComb.size(); s++) {
  91                         groupLabel = groupLabel + label + groupComb[s] + "\t";
  92                 }
  93
  94                                 //for multi displays
  95                                 string groupLabelAll = groupLabel + label + "all\t";
  96
  97                 for(int i=0;i<displays.size();i++){
  98                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  99                                                 if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) {   displays[i]->init(groupLabelAll); }
 100                                                 else {  displays[i]->init(groupLabel);  }
 101                 }
 102
 103                                 //convert freq percentage to number
 104                                 int increment = numSeqs * percentFreq;
 105
 106                 //sample all the members
 107                 for(int i=0;i<numSeqs;i++){
 108
 109                                                 if (m->control_pressed) { for (int j = 0; j < lookup.size(); j++) {  delete lookup[j]; } delete ccd;  return 1;  }
 110
 111                         //get first sample
 112                         individual chosen = sharedorder->get(i);
 113                         int abundance;
 114
 115                         //set info for sharedvector in chosens group
 116                         for (int j = 0; j < lookup.size(); j++) {
 117                                                         if (chosen.group == lookup[j]->getGroup()) {
 118                                                                 abundance = lookup[j]->getAbundance(chosen.bin);
 119                                                                 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 120                                                                 break;
 121                                                         }
 122                         }
 123
 124                         //calculate at 0 and the given increment
 125                         if((i == 0) || (i+1) % increment == 0){
 126
 127                                                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 128
 129                                 int n = 1;
 130                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 131                                         for (int l = n; l < lookup.size(); l++) {
 132                                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 133                                                                                                 //add new pair of sharedrabund vectors
 134                                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 135                                                 ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
 136                                         }
 137                                         n++;
 138                                 }
 139                                                                 //if this is a calculator that can do multiples then do them
 140                                                                 ccd->updateSharedData(lookup, i+1, globaldata->Groups.size());
 141                         }
 142                         totalNumSeq = i+1;
 143                 }
 144
 145                 //calculate last label if you haven't already
 146                 if(numSeqs % increment != 0){
 147                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 148                         int n = 1;
 149                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 150                                 for (int l = n; l < lookup.size(); l++) {
 151                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 152                                                                                 //add new pair of sharedrabund vectors
 153                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 154                                                                                 ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
 155                                 }
 156                                 n++;
 157                         }
 158                                                 //if this is a calculator that can do multiples then do them
 159                                                 ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size());
 160                 }
 161
 162                 //resets output files
 163                 for(int i=0;i<displays.size();i++){
 164                         displays[i]->reset();
 165                 }
 166
 167                                 //memory cleanup
 168                                 delete ccd;
 169                                 for (int i = 0; i < lookup.size(); i++) {
 170                                         delete lookup[i];
 171                                 }
 172
 173                                 return 0;
 174
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "Collect", "getSharedCurve");
 178                                 exit(1);
 179         }
 180 }
 181
 182 /**************************************************************************************/
 183
 184 void Collect::getGroupComb() {
 185         string group;
 186
 187         numGroupComb = 0;
 188
 189         int n = 1;
 190         for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
 191                 for (int l = n; l < globaldata->Groups.size(); l++) {
 192                         group = globaldata->Groups[i] + globaldata->Groups[l];
 193                         groupComb.push_back(group);
 194                         numGroupComb++;
 195                 }
 196                 n++;
 197         }
 198
 199 }
 200
 201 /**************************************************************************************/