parsimony.cpp

   1 /*
   2  *  parsimony.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/26/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "parsimony.h"
  11
  12 /**************************************************************************************************/
  13
  14 EstOutput Parsimony::getValues(Tree* t) {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 copyTree = new Tree();
  19
  20                 //if the users enters no groups then give them the score of all groups
  21                 int numGroups = globaldata->Groups.size();
  22                 if (numGroups == 0) {
  23                         numGroups++;
  24                         for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
  25                                 globaldata->Groups.push_back(tmap->namesOfGroups[i]);
  26                         }
  27                 }
  28
  29                 //calculate number of comparsions
  30                 int numComp = 0;
  31                 for (int r=0; r<numGroups; r++) {
  32                         for (int l = r+1; l < numGroups; l++) {
  33                                 numComp++;
  34                         }
  35                 }
  36
  37                 //numComp+1 for AB, AC, BC, ABC
  38                 data.resize(numComp+1,0);
  39                 vector<string> groups;
  40
  41                 int count = 0;
  42                 for (int a=0; a<numGroups; a++) {
  43                         for (int l = a+1; l < numGroups; l++) {
  44                                 int score = 0;
  45
  46                                 //groups in this combo
  47                                 groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
  48
  49                                 //copy users tree so that you can redo pgroups
  50                                 copyTree->getCopy(t);
  51
  52                                 //create pgroups that reflect the groups the user want to use
  53                                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  54                                         copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
  55                                 }
  56
  57                                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  58                                         int lc = copyTree->tree[i].getLChild();
  59                                         int rc = copyTree->tree[i].getRChild();
  60
  61                                         int iSize = copyTree->tree[i].pGroups.size();
  62                                         int rcSize = copyTree->tree[rc].pGroups.size();
  63                                         int lcSize = copyTree->tree[lc].pGroups.size();
  64
  65                                         //if isize are 0 then that branch is to be ignored
  66                                         if (iSize == 0) { }
  67                                         else if ((rcSize == 0) || (lcSize == 0)) { }
  68                                         //if you have more groups than either of your kids then theres been a change.
  69                                         else if(iSize > rcSize || iSize > lcSize){
  70                                                 score++;
  71                                         }
  72                                 }
  73
  74                                 data[count] = score;
  75                                 count++;
  76                                 groups.clear();
  77                         }
  78                 }
  79
  80                 //get score for all users groups
  81
  82                 //copy users tree so that you can redo pgroups
  83                 copyTree->getCopy(t);
  84                 int score = 0;
  85
  86                 //create pgroups that reflect the groups the user want to use
  87                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  88                         copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, globaldata->Groups));
  89                 }
  90
  91                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  92                         int lc = copyTree->tree[i].getLChild();
  93                         int rc = copyTree->tree[i].getRChild();
  94
  95                         int iSize = copyTree->tree[i].pGroups.size();
  96                         int rcSize = copyTree->tree[rc].pGroups.size();
  97                         int lcSize = copyTree->tree[lc].pGroups.size();
  98
  99                         //if isize are 0 then that branch is to be ignored
 100                         if (iSize == 0) { }
 101                         else if ((rcSize == 0) || (lcSize == 0)) { }
 102                         //if you have more groups than either of your kids then theres been a change.
 103                         else if(iSize > rcSize || iSize > lcSize){
 104                                 score++;
 105                         }
 106                 }
 107
 108                 data[count] = score;
 109
 110                 return data;
 111         }
 112         catch(exception& e) {
 113                 cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 114                 exit(1);
 115         }
 116         catch(...) {
 117                 cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 118                 exit(1);
 119         }
 120
 121 }
 122
 123 /**************************************************************************************************/
 124