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 = 1;
  28                                 if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
  29                                 else { increment = percentFreq;  }
  30
  31                 for(int i=0;i<numSeqs;i++){
  32
  33                                                 if (m->control_pressed) { delete lookup; delete rank; delete ccd;  return 1;  }
  34
  35                         int binNumber = order->get(i);
  36                         int abundance = lookup->get(binNumber);
  37
  38                         rank->set(abundance, rank->get(abundance)-1);
  39
  40                         abundance++;
  41
  42                         lookup->set(binNumber, abundance);
  43                         rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
  44
  45                         if((i == 0) || (i+1) % increment == 0){
  46                                 ccd->updateRankData(rank);
  47                         }
  48                 }
  49
  50                 if(numSeqs % increment != 0){
  51                         ccd->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                                 delete ccd;
  61
  62                                 return 0;
  63         }
  64         catch(exception& e) {
  65                         m->errorOut(e, "Collect", "getCurve");
  66                         exit(1);
  67         }
  68 }
  69
  70 /***********************************************************************/
  71 int Collect::getSharedCurve(float percentFreq = 0.01){
  72 try {
  73                 vector<SharedRAbundVector*> lookup;
  74                                 vector<SharedRAbundVector*> subset;
  75
  76                 //create and initialize vector of sharedvectors, one for each group
  77                 for (int i = 0; i < m->Groups.size(); i++) {
  78                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
  79                         temp->setLabel(sharedorder->getLabel());
  80                         temp->setGroup(m->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
  90                 for(int i=0;i<displays.size();i++){
  91                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  92                                                 bool hasLciHci = displays[i]->hasLciHci();
  93                                                 groupLabel = "";
  94                                                 for (int s = 0; s < groupComb.size(); s++) {
  95                                                         if (hasLciHci) {  groupLabel = groupLabel + label + groupComb[s] + "\t" + label + groupComb[s] + "lci\t" + label + groupComb[s] + "hci\t"; }
  96                                                         else{  groupLabel = groupLabel + label + groupComb[s] + "\t";  }
  97                                                 }
  98
  99                                                 string groupLabelAll = groupLabel + label + "all\t";
 100                                                 if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) {   displays[i]->init(groupLabelAll); }
 101                                                 else {  displays[i]->init(groupLabel);  }
 102                 }
 103
 104                                 //convert freq percentage to number
 105                                 int increment = 1;
 106                                 if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
 107                                 else { increment = percentFreq;  }
 108
 109                 //sample all the members
 110                 for(int i=0;i<numSeqs;i++){
 111
 112                                                 if (m->control_pressed) { for (int j = 0; j < lookup.size(); j++) {  delete lookup[j]; } delete ccd;  return 1;  }
 113
 114                         //get first sample
 115                         individual chosen = sharedorder->get(i);
 116                         int abundance;
 117
 118                         //set info for sharedvector in chosens group
 119                         for (int j = 0; j < lookup.size(); j++) {
 120                                                         if (chosen.group == lookup[j]->getGroup()) {
 121                                                                 abundance = lookup[j]->getAbundance(chosen.bin);
 122                                                                 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 123                                                                 break;
 124                                                         }
 125                         }
 126
 127                         //calculate at 0 and the given increment
 128                         if((i == 0) || (i+1) % increment == 0){
 129
 130                                                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 131
 132                                 int n = 1;
 133                                                                 bool pair = true;
 134                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 135                                         for (int l = n; l < lookup.size(); l++) {
 136                                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 137                                                                                                 //add new pair of sharedrabund vectors
 138                                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 139
 140                                                                                                 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 141                                                                                                 for (int w = 0; w < lookup.size(); w++) {
 142                                                                                                         if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
 143                                                                                                 }
 144
 145                                                 ccd->updateSharedData(subset, i+1, m->Groups.size(), pair);
 146                                         }
 147                                         n++;
 148                                 }
 149
 150                                                                 //if this is a calculator that can do multiples then do them
 151                                                                 pair = false;
 152                                                                 ccd->updateSharedData(lookup, i+1, m->Groups.size(), pair);
 153
 154                         }
 155                         totalNumSeq = i+1;
 156                 }
 157
 158                 //calculate last label if you haven't already
 159                 if(numSeqs % increment != 0){
 160                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 161                         int n = 1;
 162                                                 bool pair = true;
 163                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 164                                 for (int l = n; l < lookup.size(); l++) {
 165                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 166                                                                                 //add new pair of sharedrabund vectors
 167                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 168
 169                                                                                 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 170                                                                                 for (int w = 0; w < lookup.size(); w++) {
 171                                                                                         if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
 172                                                                                 }
 173
 174                                                                                 ccd->updateSharedData(subset, totalNumSeq, m->Groups.size(), pair);
 175                                 }
 176                                 n++;
 177                         }
 178                                                 //if this is a calculator that can do multiples then do them
 179                                                 pair = false;
 180                                                 ccd->updateSharedData(lookup, totalNumSeq, m->Groups.size(), pair);
 181                 }
 182
 183                 //resets output files
 184                 for(int i=0;i<displays.size();i++){
 185                         displays[i]->reset();
 186                 }
 187
 188                                 //memory cleanup
 189                                 delete ccd;
 190                                 for (int i = 0; i < lookup.size(); i++) {
 191                                         delete lookup[i];
 192                                 }
 193
 194                                 return 0;
 195
 196         }
 197         catch(exception& e) {
 198                 m->errorOut(e, "Collect", "getSharedCurve");
 199                                 exit(1);
 200         }
 201 }
 202
 203 /**************************************************************************************/
 204
 205 void Collect::getGroupComb() {
 206         string group;
 207
 208         numGroupComb = 0;
 209
 210         int n = 1;
 211         for (int i = 0; i < (m->Groups.size() - 1); i++) {
 212                 for (int l = n; l < m->Groups.size(); l++) {
 213                         group = m->Groups[i] + m->Groups[l];
 214                         groupComb.push_back(group);
 215                         numGroupComb++;
 216                 }
 217                 n++;
 218         }
 219
 220 }
 221
 222 /**************************************************************************************/