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(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                                                 if (m->control_pressed) { delete lookup; delete rank; delete ccd;  return 1;  }
  28
  29                         int binNumber = order->get(i);
  30                         int abundance = lookup->get(binNumber);
  31
  32                         rank->set(abundance, rank->get(abundance)-1);
  33
  34                         abundance++;
  35
  36                         lookup->set(binNumber, abundance);
  37                         rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
  38
  39                         if((i == 0) || (i+1) % increment == 0){
  40                                 ccd->updateRankData(rank);
  41                         }
  42                 }
  43
  44                 if(numSeqs % increment != 0){
  45                         ccd->updateRankData(rank);
  46                 }
  47
  48                 for(int i=0;i<displays.size();i++){
  49                         displays[i]->reset();
  50                 }
  51
  52                                 delete lookup;
  53                                 delete rank;
  54                                 delete ccd;
  55
  56                                 return 0;
  57         }
  58         catch(exception& e) {
  59                         m->errorOut(e, "Collect", "getCurve");
  60                         exit(1);
  61         }
  62 }
  63
  64 /***********************************************************************/
  65 int Collect::getSharedCurve(int increment = 1){
  66 try {
  67                 globaldata = GlobalData::getInstance();
  68                 vector<SharedRAbundVector*> lookup;
  69                                 vector<SharedRAbundVector*> subset;
  70
  71                 //create and initialize vector of sharedvectors, one for each group
  72                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  73                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
  74                         temp->setLabel(sharedorder->getLabel());
  75                         temp->setGroup(globaldata->Groups[i]);
  76                         temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
  77                         lookup.push_back(temp);
  78                 }
  79
  80                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
  81
  82                 //initialize labels for output
  83                 //makes  'uniqueAB         uniqueAC  uniqueBC' if your groups are A, B, C
  84                 getGroupComb();
  85                 groupLabel = "";
  86                 for (int s = 0; s < groupComb.size(); s++) {
  87                         groupLabel = groupLabel + label + groupComb[s] + "\t";
  88                 }
  89
  90                                 //for multi displays
  91                                 string groupLabelAll = groupLabel + label + "all\t";
  92
  93                 for(int i=0;i<displays.size();i++){
  94                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  95                                                 if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) {   displays[i]->init(groupLabelAll); }
  96                                                 else {  displays[i]->init(groupLabel);  }
  97                 }
  98
  99                 //sample all the members
 100                 for(int i=0;i<numSeqs;i++){
 101
 102                                                 if (m->control_pressed) { for (int j = 0; j < lookup.size(); j++) {  delete lookup[j]; } delete ccd;  return 1;  }
 103
 104                         //get first sample
 105                         individual chosen = sharedorder->get(i);
 106                         int abundance;
 107
 108                         //set info for sharedvector in chosens group
 109                         for (int j = 0; j < lookup.size(); j++) {
 110                                                         if (chosen.group == lookup[j]->getGroup()) {
 111                                                                 abundance = lookup[j]->getAbundance(chosen.bin);
 112                                                                 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 113                                                                 break;
 114                                                         }
 115                         }
 116
 117                         //calculate at 0 and the given increment
 118                         if((i == 0) || (i+1) % increment == 0){
 119
 120                                                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 121
 122                                 int n = 1;
 123                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 124                                         for (int l = n; l < lookup.size(); l++) {
 125                                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 126                                                                                                 //add new pair of sharedrabund vectors
 127                                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 128                                                 ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
 129                                         }
 130                                         n++;
 131                                 }
 132                                                                 //if this is a calculator that can do multiples then do them
 133                                                                 ccd->updateSharedData(lookup, i+1, globaldata->Groups.size());
 134                         }
 135                         totalNumSeq = i+1;
 136                 }
 137
 138                 //calculate last label if you haven't already
 139                 if(numSeqs % increment != 0){
 140                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 141                         int n = 1;
 142                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 143                                 for (int l = n; l < lookup.size(); l++) {
 144                                                                                 subset.clear(); //clear out old pair of sharedrabunds
 145                                                                                 //add new pair of sharedrabund vectors
 146                                                                                 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
 147                                                                                 ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
 148                                 }
 149                                 n++;
 150                         }
 151                                                 //if this is a calculator that can do multiples then do them
 152                                                 ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size());
 153                 }
 154
 155                 //resets output files
 156                 for(int i=0;i<displays.size();i++){
 157                         displays[i]->reset();
 158                 }
 159
 160                                 //memory cleanup
 161                                 delete ccd;
 162                                 for (int i = 0; i < lookup.size(); i++) {
 163                                         delete lookup[i];
 164                                 }
 165
 166                                 return 0;
 167
 168         }
 169         catch(exception& e) {
 170                 m->errorOut(e, "Collect", "getSharedCurve");
 171                                 exit(1);
 172         }
 173 }
 174
 175 /**************************************************************************************/
 176
 177 void Collect::getGroupComb() {
 178         string group;
 179
 180         numGroupComb = 0;
 181
 182         int n = 1;
 183         for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
 184                 for (int l = n; l < globaldata->Groups.size(); l++) {
 185                         group = globaldata->Groups[i] + globaldata->Groups[l];
 186                         groupComb.push_back(group);
 187                         numGroupComb++;
 188                 }
 189                 n++;
 190         }
 191
 192 }
 193
 194 /**************************************************************************************/