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
  15 void Collect::getCurve(int increment = 1){
  16         try {
  17                 RAbundVector* lookup = new RAbundVector(order->getNumBins());
  18                 SAbundVector* rank      = new SAbundVector(order->getMaxRank()+1);
  19
  20                 CollectorsCurveData* ccd = new CollectorsCurveData();
  21
  22                 for(int i=0;i<displays.size();i++){
  23                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  24                         displays[i]->init(label);                  //sets displays label
  25                 }
  26                 for(int i=0;i<numSeqs;i++){
  27
  28                         int binNumber = order->get(i);
  29                         int abundance = lookup->get(binNumber);
  30
  31                         rank->set(abundance, rank->get(abundance)-1);
  32
  33                         abundance++;
  34
  35                         lookup->set(binNumber, abundance);
  36                         rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
  37
  38                         if((i == 0) || (i+1) % increment == 0){
  39                                 ccd->updateRankData(rank);
  40                         }
  41                 }
  42
  43                 if(numSeqs % increment != 0){
  44                         ccd->updateRankData(rank);
  45                 }
  46
  47                 for(int i=0;i<displays.size();i++){
  48                         displays[i]->reset();
  49                 }
  50         }
  51         catch(exception& e) {
  52                 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55         catch(...) {
  56                 cout << "An unknown error has occurred in the Collect class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  57                 exit(1);
  58         }
  59
  60 }
  61
  62 /***********************************************************************/
  63 void Collect::getSharedCurve(int increment = 1){
  64 try {
  65                 globaldata = GlobalData::getInstance();
  66                 vector<SharedRAbundVector*> lookup;
  67                 vector<string> chosenGroups = globaldata->sharedGroups;
  68
  69                 //create and initialize vector of sharedvectors, one for each group
  70                 for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) {
  71                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
  72                         temp->setLabel(sharedorder->getLabel());
  73                         temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
  74                         temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]]);
  75                         lookup.push_back(temp);
  76                 }
  77
  78                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
  79
  80                 //initialize labels for output
  81                 //makes  'uniqueAB       uniqueAC  uniqueBC' if your groups are A, B, C
  82                 getGroupComb(chosenGroups);
  83                 groupLabel = "";
  84                 for (int s = 0; s < groupComb.size(); s++) {
  85                         groupLabel = groupLabel + label + groupComb[s] + "\t";
  86                 }
  87
  88                 for(int i=0;i<displays.size();i++){
  89                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
  90                         displays[i]->init(groupLabel);
  91                 }
  92
  93                 //sample all the members
  94                 for(int i=0;i<numSeqs;i++){
  95                         //get first sample
  96                         individual chosen = sharedorder->get(i);
  97                         int abundance;
  98                         //set info for sharedvector in chosens group
  99                         for (int j = 0; j < lookup.size(); j++) {
 100                                 if (chosen.group == lookup[j]->getGroup()) {
 101                                          abundance = lookup[j]->getAbundance(chosen.bin);
 102                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 103                                          break;
 104                                 }
 105                         }
 106
 107                         //calculate at 0 and the given increment
 108                         if((i == 0) || (i+1) % increment == 0){
 109                                 //randomize group order
 110                                 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
 111                                 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 112                                 int n = 1;
 113                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 114                                         for (int l = n; l < lookup.size(); l++) {
 115                                                 ccd->updateSharedData(lookup[k], lookup[l], i+1, globaldata->gGroupmap->namesOfGroups.size());
 116                                         }
 117                                         n++;
 118                                 }
 119                         totalNumSeq = i+1;
 120                         }
 121                 }
 122
 123                 //calculate last line if you haven't already
 124                 if(numSeqs % increment != 0){
 125                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 126                         int n = 1;
 127                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
 128                                 for (int l = n; l < lookup.size(); l++) {
 129                                         ccd->updateSharedData(lookup[k], lookup[l], totalNumSeq, globaldata->gGroupmap->namesOfGroups.size());
 130                                 }
 131                                 n++;
 132                         }
 133                 }
 134
 135                 //resets output files
 136                 for(int i=0;i<displays.size();i++){
 137                         displays[i]->reset();
 138                 }
 139         }
 140         catch(exception& e) {
 141                 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144         catch(...) {
 145                 cout << "An unknown error has occurred in the Collect class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148
 149 }
 150
 151 /**************************************************************************************/
 152
 153 void Collect::getGroupComb(vector<string> chosen) {
 154                 string group;
 155
 156                 numGroupComb = 0;
 157
 158                 int n = 1;
 159                 for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
 160                         for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
 161                                 string g1 = globaldata->gGroupmap->namesOfGroups[i];
 162                                 string g2 = globaldata->gGroupmap->namesOfGroups[l];
 163                                 if(validGroup(chosen, g1) && validGroup(chosen, g2)) {
 164                                         group = g1 + g2;
 165                                         groupComb.push_back(group);
 166                                         numGroupComb++;
 167                                 }
 168                         }
 169                         n++;
 170                 }
 171 }
 172
 173 /**************************************************************************************/
 174
 175 bool Collect::validGroup(vector<string> chosen, string group) {
 176         if(chosen.size() == 0)
 177                 return true;
 178         for(int i = 0; i < chosen.size(); i++)
 179                 if(chosen.at(i).compare(group) == 0)
 180                         return true;
 181         return false;
 182 }
 183
 184
 185