sharedchao1.cpp

   1 /*
   2  *  sharedchao1.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedchao1.h"
  11
  12 /***********************************************************************/
  13 EstOutput SharedChao1::getValues(vector<SharedRAbundVector*> shared){
  14         try {
  15                 data.resize(1,0);
  16                 vector<int> temp;
  17                 int numGroups = shared.size();
  18                 float Chao = 0.0; float leftvalue, rightvalue;
  19
  20                 // IntNode is defined in mothur.h
  21                 // The tree used here is a binary tree used to represent the f1+++, f+1++, f++1+, f+++1, f11++, f1+1+...
  22                 // combinations required to solve the chao estimator equation for any number of groups.  Conceptually, think
  23                 // of each node as having a 1 and a + value, or for f2 values a 2 and a + value, and 2 pointers to intnodes, and 2 coeffient values.
  24                 // The coeffient value is how many times you chose branch 1 to get to that fvalue.
  25                 // If you choose left you are selecting the 1 or 2 value and right means the + value.  For instance, to find
  26                 // the number of bins that have f1+1+ you would start at the root, go left, right, left, and select the rightvalue.
  27                 // the coeffient is 2.  Note: we only set the coeffient in f2 values.
  28
  29                 //create and initialize trees to 0.
  30                 initialTree(numGroups);
  31
  32                 //loop through vectors calculating the f11, f1A, f2A, f1B, f2B, S12 values
  33                 for (int i = 0; i < shared[0]->size(); i++) {
  34                         //get bin values and calc shared
  35                         bool sharedByAll = true;
  36                         temp.clear();
  37                         for (int j = 0; j < numGroups; j++) {
  38                                 temp.push_back(shared[j]->getAbundance(i));
  39                                 if (temp[j] == 0) { sharedByAll = false; }
  40                         }
  41
  42                         //they are shared
  43                         if (sharedByAll == true) {
  44                                 // cout << "temp = ";
  45                                 // for (int h = 0; h < temp.size(); h++) { cout << temp[h] << " "; } cout << endl;
  46                                 //find f1 and f2values
  47                                 updateTree(temp);
  48                         }
  49                 }
  50
  51
  52                 //cout << "Entering " << endl;
  53                 //calculate chao1, (numleaves-1) because numleaves contains the ++ values.
  54                 bool bias;
  55                 for(int i=0;i<numLeaves;i++){
  56                         if (f2leaves[i]->lvalue == 0) { bias = true;}// break;}
  57                 }
  58
  59                 if(bias){
  60                         for (int i = 0; i < numLeaves; i++) {
  61
  62                                 leftvalue = (float)(f1leaves[i]->lvalue * (f1leaves[i]->lvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * (f2leaves[i]->lvalue + 1));
  63                                 if (i != (numLeaves-1)) {
  64                                         rightvalue = (float)(f1leaves[i]->rvalue * (f1leaves[i]->rvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * (f2leaves[i]->rvalue + 1));
  65                                 }else{
  66                                         rightvalue = (float)(f1leaves[i]->rvalue);
  67                                 }
  68                                 Chao += leftvalue + rightvalue;
  69                         }
  70                 }
  71                 else{
  72
  73                         for (int i = 0; i < numLeaves; i++) {
  74
  75                                 leftvalue = (float)(f1leaves[i]->lvalue * f1leaves[i]->lvalue) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * f2leaves[i]->lvalue);
  76                                 if (i != (numLeaves-1)) {
  77                                         rightvalue = (float)(f1leaves[i]->rvalue * f1leaves[i]->rvalue) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * f2leaves[i]->rvalue);
  78                                 }else{
  79                                         rightvalue = (float)(f1leaves[i]->rvalue);
  80                                 }
  81                                 Chao += leftvalue + rightvalue;
  82                         }
  83                 }
  84
  85                 for (int i = 0; i < numNodes; i++) {
  86                         delete f1leaves[i];
  87                         delete f2leaves[i];
  88                 }
  89
  90         //      cout << "exiting " << endl;
  91                 data[0] = Chao;
  92                 return data;
  93         }
  94         catch(exception& e) {
  95                 cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98         catch(...) {
  99                 cout << "An unknown error has occurred in the SharedChao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 100                 exit(1);
 101         }
 102 }
 103
 104 /***********************************************************************/
 105 //builds trees structure with n leaf nodes initialized to 0.
 106 void SharedChao1::initialTree(int n) {
 107         try {
 108                 // (2^n) / 2. Divide by 2 because each leaf node contains 2 values. One for + and one for 1 or 2.
 109                 numLeaves = pow(2, (float)n) / 2;
 110                 numNodes = 2*numLeaves - 1;
 111                 int countleft = 0;
 112                 int countright = 1;
 113
 114                 f1leaves.resize(numNodes);
 115                 f2leaves.resize(numNodes);
 116
 117                 //initialize leaf values
 118                 for (int i = 0; i < numLeaves; i++) {
 119                         f1leaves[i] = new IntNode;
 120                         f1leaves[i]->lvalue = 0;
 121                         f1leaves[i]->rvalue = 0;
 122                         f1leaves[i]->left = NULL;
 123                         f1leaves[i]->right = NULL;
 124
 125                         f2leaves[i] = new IntNode;
 126                         f2leaves[i]->lvalue = 0;
 127                         f2leaves[i]->rvalue = 0;
 128                         f2leaves[i]->left = NULL;
 129                         f2leaves[i]->right = NULL;
 130                 }
 131
 132                 //set pointers to children
 133                 for (int j = numLeaves; j < numNodes; j++) {
 134                         f1leaves[j] = new IntNode;
 135                         f1leaves[j]->left = f1leaves[countleft];
 136                         f1leaves[j]->right = f1leaves[countright];
 137
 138                         f2leaves[j] = new IntNode;
 139                         f2leaves[j]->left = f2leaves[countleft];
 140                         f2leaves[j]->right =f2leaves[countright];
 141
 142                         countleft = countleft + 2;
 143                         countright = countright + 2;
 144                 }
 145
 146                 //point to root
 147                 f1root = f1leaves[numNodes-1];
 148
 149                 //point to root
 150                 f2root = f2leaves[numNodes-1];
 151
 152                 //set coeffients
 153                 setCoef(f2root, 0);
 154         }
 155         catch(exception& e) {
 156                 cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function initialTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159         catch(...) {
 160                 cout << "An unknown error has occurred in the SharedChao1 class function initialTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 161                 exit(1);
 162         }
 163 }
 164
 165 /***********************************************************************/
 166 //take vector containing the abundance info. for a bin and updates trees.
 167 void SharedChao1::updateTree(vector<int> bin) {
 168         try {
 169                 updateBranchf1(f1root, bin, 0);
 170                 updateBranchf2(f2root, bin, 0);
 171         }
 172         catch(exception& e) {
 173                 cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function updateTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176         catch(...) {
 177                 cout << "An unknown error has occurred in the SharedChao1 class function updateTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 178                 exit(1);
 179         }
 180 }
 181
 182 /***********************************************************************/
 183 void SharedChao1::updateBranchf1(IntNode* node, vector<int> bin, int index) {
 184         try {
 185                 //if you have more than one group
 186                 if (index == (bin.size()-1)) {
 187                         if (bin[index] == 1) { node->lvalue++; node->rvalue++; }
 188                         else { node->rvalue++;  }
 189                 }else {
 190                         if (bin[index] == 1) {
 191                                 //follow path as if you are 1
 192                                 updateBranchf1(node->left, bin, index+1);
 193                         }
 194                         //follow path as if you are +
 195                         updateBranchf1(node->right, bin, index+1);
 196                 }
 197         }
 198         catch(exception& e) {
 199                 cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function updateBranchf1. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 200                 exit(1);
 201         }
 202         catch(...) {
 203                 cout << "An unknown error has occurred in the SharedChao1 class function updateBranchf1. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 204                 exit(1);
 205         }
 206 }
 207
 208 /***********************************************************************/
 209 void SharedChao1::updateBranchf2(IntNode* node, vector<int> bin, int index) {
 210         try {
 211                 //if you have more than one group
 212                 if (index == (bin.size()-1)) {
 213                         if (bin[index] == 2) { node->lvalue++; node->rvalue++; }
 214                         else { node->rvalue++;  }
 215                 }else {
 216                         if (bin[index] == 2) {
 217                                 //follow path as if you are 1
 218                                 updateBranchf2(node->left, bin, index+1);
 219                         }
 220                         //follow path as if you are +
 221                         updateBranchf2(node->right, bin, index+1);
 222                 }
 223         }
 224         catch(exception& e) {
 225                 cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function updateBranchf2. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 226                 exit(1);
 227         }
 228         catch(...) {
 229                 cout << "An unknown error has occurred in the SharedChao1 class function updateBranchf2. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 230                 exit(1);
 231         }
 232 }
 233
 234 /***********************************************************************/
 235 void SharedChao1::setCoef(IntNode* node, int coef) {
 236         try {
 237                 if (node->left != NULL) {
 238                         setCoef(node->left, coef+1);
 239                         setCoef(node->right, coef);
 240                 }else {
 241                         node->lcoef = coef+1;
 242                         node->rcoef = coef;
 243                 }
 244         }
 245         catch(exception& e) {
 246                 cout << "Standard Error: " << e.what() << " has occurred in the SharedChao1 class Function getCoef. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 247                 exit(1);
 248         }
 249         catch(...) {
 250                 cout << "An unknown error has occurred in the SharedChao1 class function getCoef. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 251                 exit(1);
 252         }
 253 }
 254
 255 /***********************************************************************/
 256 //for debugging purposes
 257 void SharedChao1::printTree() {
 258
 259         cout << "F1 leaves" << endl;
 260         printBranch(f1root);
 261
 262         cout << "F2 leaves" << endl;
 263         printBranch(f2root);
 264
 265
 266 }
 267 /*****************************************************************/
 268 void SharedChao1::printBranch(IntNode* node) {
 269         try {
 270
 271                 // you are not a leaf
 272                 if (node->left != NULL) {
 273                         printBranch(node->left);
 274                         printBranch(node->right);
 275                 }else { //you are a leaf
 276                         cout << node->lvalue << endl;
 277                         cout << node->rvalue << endl;
 278                 }
 279
 280         }
 281         catch(exception& e) {
 282                 cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 283                 exit(1);
 284         }
 285         catch(...) {
 286                 cout << "An unknown error has occurred in the Tree class function printBranch. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 287                 exit(1);
 288         }
 289 }
 290
 291 /*****************************************************************/
 292
 293
 294
 295