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                                 //find f1 and f2values
  45                                 updateTree(temp);
  46                         }
  47                 }
  48
  49
  50                 //calculate chao1, (numleaves-1) because numleaves contains the ++ values.
  51                 bool bias;
  52                 for(int i=0;i<numLeaves;i++){
  53                         if (f2leaves[i]->lvalue == 0) { bias = true;}// break;}
  54                 }
  55
  56                 if(bias){
  57                         for (int i = 0; i < numLeaves; i++) {
  58
  59                                 leftvalue = (float)(f1leaves[i]->lvalue * (f1leaves[i]->lvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * (f2leaves[i]->lvalue + 1));
  60                                 if (i != (numLeaves-1)) {
  61                                         rightvalue = (float)(f1leaves[i]->rvalue * (f1leaves[i]->rvalue - 1)) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * (f2leaves[i]->rvalue + 1));
  62                                 }else{
  63                                         rightvalue = (float)(f1leaves[i]->rvalue);
  64                                 }
  65                                 Chao += leftvalue + rightvalue;
  66                         }
  67                 }
  68                 else{
  69
  70                         for (int i = 0; i < numLeaves; i++) {
  71
  72                                 leftvalue = (float)(f1leaves[i]->lvalue * f1leaves[i]->lvalue) / (float)((pow(2, (float)f2leaves[i]->lcoef)) * f2leaves[i]->lvalue);
  73                                 if (i != (numLeaves-1)) {
  74                                         rightvalue = (float)(f1leaves[i]->rvalue * f1leaves[i]->rvalue) / (float)((pow(2, (float)f2leaves[i]->rcoef)) * f2leaves[i]->rvalue);
  75                                 }else{
  76                                         rightvalue = (float)(f1leaves[i]->rvalue);
  77                                 }
  78                                 Chao += leftvalue + rightvalue;
  79                         }
  80                 }
  81
  82                 for (int i = 0; i < numNodes; i++) {
  83                         delete f1leaves[i];
  84                         delete f2leaves[i];
  85                 }
  86
  87
  88                 data[0] = Chao;
  89                 return data;
  90         }
  91         catch(exception& e) {
  92                 errorOut(e, "SharedChao1", "getValues");
  93                 exit(1);
  94         }
  95 }
  96
  97 /***********************************************************************/
  98 //builds trees structure with n leaf nodes initialized to 0.
  99 void SharedChao1::initialTree(int n) {
 100         try {
 101                 // (2^n) / 2. Divide by 2 because each leaf node contains 2 values. One for + and one for 1 or 2.
 102                 numLeaves = pow(2, (float)n) / 2;
 103                 numNodes = 2*numLeaves - 1;
 104                 int countleft = 0;
 105                 int countright = 1;
 106
 107                 f1leaves.resize(numNodes);
 108                 f2leaves.resize(numNodes);
 109
 110                 //initialize leaf values
 111                 for (int i = 0; i < numLeaves; i++) {
 112                         f1leaves[i] = new IntNode;
 113                         f1leaves[i]->lvalue = 0;
 114                         f1leaves[i]->rvalue = 0;
 115                         f1leaves[i]->left = NULL;
 116                         f1leaves[i]->right = NULL;
 117
 118                         f2leaves[i] = new IntNode;
 119                         f2leaves[i]->lvalue = 0;
 120                         f2leaves[i]->rvalue = 0;
 121                         f2leaves[i]->left = NULL;
 122                         f2leaves[i]->right = NULL;
 123                 }
 124
 125                 //set pointers to children
 126                 for (int j = numLeaves; j < numNodes; j++) {
 127                         f1leaves[j] = new IntNode;
 128                         f1leaves[j]->left = f1leaves[countleft];
 129                         f1leaves[j]->right = f1leaves[countright];
 130
 131                         f2leaves[j] = new IntNode;
 132                         f2leaves[j]->left = f2leaves[countleft];
 133                         f2leaves[j]->right =f2leaves[countright];
 134
 135                         countleft = countleft + 2;
 136                         countright = countright + 2;
 137                 }
 138
 139                 //point to root
 140                 f1root = f1leaves[numNodes-1];
 141
 142                 //point to root
 143                 f2root = f2leaves[numNodes-1];
 144
 145                 //set coeffients
 146                 setCoef(f2root, 0);
 147         }
 148         catch(exception& e) {
 149                 errorOut(e, "SharedChao1", "initialTree");
 150                 exit(1);
 151         }
 152 }
 153
 154 /***********************************************************************/
 155 //take vector containing the abundance info. for a bin and updates trees.
 156 void SharedChao1::updateTree(vector<int> bin) {
 157         try {
 158                 updateBranchf1(f1root, bin, 0);
 159                 updateBranchf2(f2root, bin, 0);
 160         }
 161         catch(exception& e) {
 162                 errorOut(e, "SharedChao1", "updateTree");
 163                 exit(1);
 164         }
 165 }
 166
 167 /***********************************************************************/
 168 void SharedChao1::updateBranchf1(IntNode* node, vector<int> bin, int index) {
 169         try {
 170                 //if you have more than one group
 171                 if (index == (bin.size()-1)) {
 172                         if (bin[index] == 1) { node->lvalue++; node->rvalue++; }
 173                         else { node->rvalue++;  }
 174                 }else {
 175                         if (bin[index] == 1) {
 176                                 //follow path as if you are 1
 177                                 updateBranchf1(node->left, bin, index+1);
 178                         }
 179                         //follow path as if you are +
 180                         updateBranchf1(node->right, bin, index+1);
 181                 }
 182         }
 183         catch(exception& e) {
 184                 errorOut(e, "SharedChao1", "updateBranchf1");
 185                 exit(1);
 186         }
 187 }
 188
 189 /***********************************************************************/
 190 void SharedChao1::updateBranchf2(IntNode* node, vector<int> bin, int index) {
 191         try {
 192                 //if you have more than one group
 193                 if (index == (bin.size()-1)) {
 194                         if (bin[index] == 2) { node->lvalue++; node->rvalue++; }
 195                         else { node->rvalue++;  }
 196                 }else {
 197                         if (bin[index] == 2) {
 198                                 //follow path as if you are 1
 199                                 updateBranchf2(node->left, bin, index+1);
 200                         }
 201                         //follow path as if you are +
 202                         updateBranchf2(node->right, bin, index+1);
 203                 }
 204         }
 205         catch(exception& e) {
 206                 errorOut(e, "SharedChao1", "updateBranchf2");
 207                 exit(1);
 208         }
 209 }
 210
 211 /***********************************************************************/
 212 void SharedChao1::setCoef(IntNode* node, int coef) {
 213         try {
 214                 if (node->left != NULL) {
 215                         setCoef(node->left, coef+1);
 216                         setCoef(node->right, coef);
 217                 }else {
 218                         node->lcoef = coef+1;
 219                         node->rcoef = coef;
 220                 }
 221         }
 222         catch(exception& e) {
 223                 errorOut(e, "SharedChao1", "setCoef");
 224                 exit(1);
 225         }
 226 }
 227
 228 /***********************************************************************/
 229 //for debugging purposes
 230 void SharedChao1::printTree() {
 231
 232         mothurOut("F1 leaves"); mothurOutEndLine();
 233         printBranch(f1root);
 234
 235         mothurOut("F2 leaves"); mothurOutEndLine();
 236         printBranch(f2root);
 237
 238
 239 }
 240 /*****************************************************************/
 241 void SharedChao1::printBranch(IntNode* node) {
 242         try {
 243
 244                 // you are not a leaf
 245                 if (node->left != NULL) {
 246                         printBranch(node->left);
 247                         printBranch(node->right);
 248                 }else { //you are a leaf
 249                         mothurOut(toString(node->lvalue)); mothurOutEndLine();
 250                         mothurOut(toString(node->rvalue)); mothurOutEndLine();
 251                 }
 252
 253         }
 254         catch(exception& e) {
 255                 errorOut(e, "SharedChao1", "printBranch");
 256                 exit(1);
 257         }
 258 }
 259
 260 /*****************************************************************/
 261
 262
 263
 264