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