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 #include "coverage.h"
  11
  12 //**********************************************************************************************************************
  13 Coverage::Coverage() {
  14                 globaldata = GlobalData::getInstance();
  15                 numUserGroups = globaldata->Groups.size();
  16                 numGroups = globaldata->gGroupmap->getNumGroups();
  17 }
  18
  19 //**********************************************************************************************************************
  20 void Coverage::getValues(FullMatrix* matrix, vector< vector< vector<float> > >& data, vector<float> dist, string mode) {
  21         try {
  22                 vector<float> min;
  23                 vector<string> groups;
  24
  25                 //initialize data
  26                 data.resize(dist.size());
  27                 for (int l = 0; l < data.size(); l++) {
  28                         data[l].resize(numGroups);
  29                         for (int k = 0; k < data[l].size(); k++) {
  30                                 data[l][k].push_back(0.0);
  31                         }
  32                 }
  33
  34                 /**************************************/
  35                 //get the minimums for each comparision
  36                 /**************************************/
  37                 int count = 0;
  38                 int a = 0;
  39                 int b = 0;
  40                 for (int i = 0; i < numGroups; i++) {
  41                         for (int j = 0; j < numGroups; j++) {
  42
  43                                 //is this "box" one hte user wants analyzed?
  44                                 if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
  45
  46                                         if (mode == "random") {
  47                                                 //create random matrix for this comparison
  48                                                 matrix->shuffle(globaldata->gGroupmap->namesOfGroups[i], globaldata->gGroupmap->namesOfGroups[j]);
  49                                         }
  50
  51                                         min = matrix->getMins(count);  //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
  52
  53                                         //find the coverage at this distance
  54                                         sort(min.begin(), min.end());
  55
  56                                         //loop through each distance and fill data
  57                                         for (int k = 0; k < data.size(); k++) {
  58
  59                                                 int index = -1;
  60                                                 //find index in min where value is higher than d
  61                                                 for (int m = 0; m < min.size(); m++) {
  62                                                         if (min[m] > dist[k])   { index = m; break;     }
  63                                                 }
  64
  65                                                 // if you don't find one than all the mins are less than d
  66                                                 if (index == -1) { index = min.size();  }
  67
  68                                                 //save value in data
  69                                                 data[k][a][b] = 1.0 - ((min.size()-index)/(float)min.size());
  70
  71                                         }
  72
  73                                         //move to next box
  74                                         if (b < numUserGroups-1) {  b++;  }
  75                                         else{ //you are moving to a new row of "boxes"
  76                                                 b = 0;
  77                                                 a++;
  78                                         }
  79
  80                                         count++;
  81
  82                                         if (mode == "random") {
  83                                                 //restore matrix to original form for next shuffle
  84                                                 matrix->restore();
  85                                         }
  86                                 }
  87                         }
  88                 }
  89
  90         }
  91         catch(exception& e) {
  92                 cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95         catch(...) {
  96                 cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99 }
 100 //**********************************************************************************************************************
 101
 102