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 void Coverage::getValues(FullMatrix* matrix, float d, vector< vector<float> >& data) {
  20         try {
  21                 vector<float> min;
  22                 vector<string> groups;
  23
  24                 //initialize data
  25                 data.resize(numUserGroups);
  26                 for (int l = 0; l < data.size(); l++) {
  27                         data[l].push_back(0.0);
  28                 }
  29
  30                 /**************************************/
  31                 //get the minimums for each comparision
  32                 /**************************************/
  33                 int count = 0;
  34                 int a = 0;
  35                 int b = 0;
  36                 for (int i = 0; i < numGroups; i++) {
  37                         for (int j = 0; j < numGroups; j++) {
  38
  39                                 //is this "box" one hte user wants analyzed?
  40                                 if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
  41
  42                                         min = matrix->getMins(count); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
  43
  44                                         //find the coverage at this distance
  45                                         sort(min.begin(), min.end());
  46 //cout << "minvector for : " << globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[j] << endl;
  47 //for(int h = 0; h<min.size(); h++) {
  48 // cout << min[h] << " ";
  49 //}
  50 //cout << endl;
  51                                         int index = -1;
  52                                         //find index in min where value is higher than d
  53                                         for (int m = 0; m < min.size(); m++) {
  54                                                 if (min[m] > d) { index = m; break;     }
  55                                         }
  56
  57                                         // if you don't find one than all the mins are less than d
  58                                         if (index == -1) { index = min.size();  }
  59
  60                                         //save value in data
  61                                         data[a][b] = 1.0 - ((min.size()-index)/(float)min.size());
  62 //cout << "D = " << d << "data " << a << b << " = " << data[a][b] << endl;
  63                                         if (b < numUserGroups-1) {  b++;  }
  64                                         else{ //you are moving to a new row of "boxes"
  65                                                 b = 0;
  66                                                 a++;
  67                                         }
  68                                 }
  69                                 count++;
  70                         }
  71                 }
  72         }
  73         catch(exception& e) {
  74                 cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  75                 exit(1);
  76         }
  77         catch(...) {
  78                 cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  79                 exit(1);
  80         }
  81 }
  82 //**********************************************************************************************************************
  83 //For the random matrices
  84 void Coverage::getValues(FullMatrix* matrix, float d, vector< vector<float> >& data, string r) {
  85         try {
  86                 vector<float> min;
  87                 vector<string> groups;
  88
  89                 //initialize data
  90                 data.resize(numUserGroups);
  91                 for (int l = 0; l < data.size(); l++) {
  92                         data[l].push_back(0.0);
  93                 }
  94
  95                 /**************************************/
  96                 //get the minimums for each comparision
  97                 /**************************************/
  98                 int count = 0;
  99                 int a = 0;
 100                 int b = 0;
 101                 for (int i = 0; i < numGroups; i++) {
 102                         for (int j = 0; j < numGroups; j++) {
 103
 104                                 //is this "box" one hte user wants analyzed?
 105                                 if ((inUsersGroups(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups) == true) && (inUsersGroups(globaldata->gGroupmap->namesOfGroups[j], globaldata->Groups) == true)) {
 106 cout << "combo " << a << b << endl;
 107 cout << "original matrix mins4rows " << endl;
 108 matrix->printMinsForRows(cout);
 109                                         //create random matrix for this comparison
 110                                         matrix->shuffle(count);
 111
 112                                         min = matrix->getMins(count);  //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
 113 cout << "shuffled matrix mins4rows " << endl;
 114 matrix->printMinsForRows(cout);
 115
 116                                         //find the coverage at this distance
 117                                         sort(min.begin(), min.end());
 118
 119                                         int index = -1;
 120                                         //find index in min where value is higher than d
 121                                         for (int m = 0; m < min.size(); m++) {
 122                                                 if (min[m] > d) { index = m; break;     }
 123                                         }
 124
 125                                         // if you don't find one than all the mins are less than d
 126                                         if (index == -1) { index = min.size();  }
 127
 128                                         //save value in data
 129                                         data[a][b] = 1.0 - ((min.size()-index)/(float)min.size());
 130 cout << "D = " << d << "data " << a << b << " = " << data[a][b] << endl;
 131                                         if (b < numUserGroups-1) {  b++;  }
 132                                         else{ //you are moving to a new row of "boxes"
 133                                                 b = 0;
 134                                                 a++;
 135                                         }
 136                                 }
 137                                 count++;
 138
 139                                 //restore matrix to original form for next shuffle
 140                                 matrix->restore();
 141 min = matrix->getMins(count-1);
 142 cout << "restored matrix mins4rows " << endl;
 143 matrix->printMinsForRows(cout);
 144                         }
 145                 }
 146         }
 147         catch(exception& e) {
 148                 cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 149                 exit(1);
 150         }
 151         catch(...) {
 152                 cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 153                 exit(1);
 154         }
 155 }
 156 //**********************************************************************************************************************
 157
 158