coverage.cpp

   1 /*
   2  *  coverage.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 /* This class library coverage at the given distances of the Cramer-von Mises statistic.
  11         you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
  12         paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
  13         DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
  14
  15
  16 #include "coverage.h"
  17
  18 //**********************************************************************************************************************
  19 Coverage::Coverage() {
  20                 globaldata = GlobalData::getInstance();
  21                 numUserGroups = globaldata->Groups.size();
  22                 numGroups = globaldata->gGroupmap->getNumGroups();
  23 }
  24
  25 //**********************************************************************************************************************
  26 void Coverage::getValues(FullMatrix* matrix, vector< vector< vector<float> > >& data, vector<float> dist, string mode) {
  27         try {
  28                 vector<float> min;
  29                 vector<string> groups;
  30
  31                 //initialize data
  32                 data.resize(dist.size());
  33                 for (int l = 0; l < data.size(); l++) {
  34                         data[l].resize(numGroups);
  35                         for (int k = 0; k < data[l].size(); k++) {
  36                                 data[l][k].push_back(0.0);
  37                         }
  38                 }
  39
  40                 /**************************************/
  41                 //get the minimums for each comparision
  42                 /**************************************/
  43                 int count = 0;
  44                 int a = 0;
  45                 int b = 0;
  46                 for (int i = 0; i < numGroups; i++) {
  47                         for (int j = 0; j < numGroups; j++) {
  48
  49                                 //is this "box" one hte user wants analyzed?
  50                                 if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
  51
  52                                         if (mode == "random") {
  53                                                 //create random matrix for this comparison
  54                                                 matrix->shuffle(globaldata->gGroupmap->namesOfGroups[i], globaldata->gGroupmap->namesOfGroups[j]);
  55                                         }
  56
  57                                         min = matrix->getMins(count);  //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
  58
  59                                         //find the coverage at this distance
  60                                         sort(min.begin(), min.end());
  61
  62                                         //loop through each distance and fill data
  63                                         for (int k = 0; k < data.size(); k++) {
  64
  65                                                 int index = -1;
  66                                                 //find index in min where value is higher than d
  67                                                 for (int m = 0; m < min.size(); m++) {
  68                                                         if (min[m] > dist[k])   { index = m; break;     }
  69                                                 }
  70
  71                                                 // if you don't find one than all the mins are less than d
  72                                                 if (index == -1) { index = min.size();  }
  73
  74                                                 //save value in data
  75                                                 data[k][a][b] = 1.0 - ((min.size()-index)/(float)min.size());
  76
  77                                         }
  78
  79                                         //move to next box
  80                                         if (b < numUserGroups-1) {  b++;  }
  81                                         else{ //you are moving to a new row of "boxes"
  82                                                 b = 0;
  83                                                 a++;
  84                                         }
  85
  86                                         count++;
  87
  88                                         if (mode == "random") {
  89                                                 //restore matrix to original form for next shuffle
  90                                                 matrix->restore();
  91                                         }
  92                                 }
  93                         }
  94                 }
  95
  96         }
  97         catch(exception& e) {
  98                 cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  99                 exit(1);
 100         }
 101         catch(...) {
 102                 cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107
 108