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                         errorOut(e, "Collect", "getCurve");
  56                         exit(1);
  57         }
  58 }
  59
  60 /***********************************************************************/
  61 void Collect::getSharedCurve(int increment = 1){
  62 try {
  63                 globaldata = GlobalData::getInstance();
  64                 vector<SharedRAbundVector*> lookup;
  65                                 vector<SharedRAbundVector*> subset;
  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 multi displays
  87                                 string groupLabelAll = groupLabel + label + "all\t";
  88
  89                 for(int i=0;i<displays.size();i++){
  90                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  91                                                 if (displays[i]->isCalcMultiple() == true)  {   displays[i]->init(groupLabelAll); }
  92                                                 else {  displays[i]->init(groupLabel);  }
  93                 }
  94
  95                 //sample all the members
  96                 for(int i=0;i<numSeqs;i++){
  97                         //get first sample
  98                         individual chosen = sharedorder->get(i);
  99                         int abundance;
 100
 101                         //set info for sharedvector in chosens group
 102                         for (int j = 0; j < lookup.size(); j++) {
 103                                                         if (chosen.group == lookup[j]->getGroup()) {
 104                                                                 abundance = lookup[j]->getAbundance(chosen.bin);
 105                                                                 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 106                                                                 break;
 107                                                         }
 108                         }
 109
 110
 111                         //calculate at 0 and the given increment
 112                         if((i == 0) || (i+1) % increment == 0){
 113
 114                                                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 115
 116                                 int n = 1;
 117                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 118                                         for (int l = n; l < lookup.size(); l++) {
 119                                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 120                                                                                                 //add new pair of sharedrabund vectors
 121                                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 122                                                 ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
 123                                         }
 124                                         n++;
 125                                 }
 126                                                                 //if this is a calculator that can do multiples then do them
 127                                                                 ccd->updateSharedData(lookup, i+1, globaldata->Groups.size());
 128                         }
 129                         totalNumSeq = i+1;
 130                 }
 131
 132                 //calculate last label if you haven't already
 133                 if(numSeqs % increment != 0){
 134                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 135                         int n = 1;
 136                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 137                                 for (int l = n; l < lookup.size(); l++) {
 138                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 139                                                                                 //add new pair of sharedrabund vectors
 140                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 141                                                                                 ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
 142                                 }
 143                                 n++;
 144                         }
 145                                                 //if this is a calculator that can do multiples then do them
 146                                                 ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size());
 147                 }
 148
 149                 //resets output files
 150                 for(int i=0;i<displays.size();i++){
 151                         displays[i]->reset();
 152                 }
 153
 154                                 //memory cleanup
 155                                 delete ccd;
 156                                 for (int i = 0; i < lookup.size(); i++) {
 157                                         delete lookup[i];
 158                                 }
 159
 160         }
 161         catch(exception& e) {
 162                 errorOut(e, "Collect", "getSharedCurve");
 163                                 exit(1);
 164         }
 165 }
 166
 167 /**************************************************************************************/
 168
 169 void Collect::getGroupComb() {
 170         string group;
 171
 172         numGroupComb = 0;
 173
 174         int n = 1;
 175         for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
 176                 for (int l = n; l < globaldata->Groups.size(); l++) {
 177                         group = globaldata->Groups[i] + globaldata->Groups[l];
 178                         groupComb.push_back(group);
 179                         numGroupComb++;
 180                 }
 181                 n++;
 182         }
 183
 184 }
 185
 186 /**************************************************************************************/