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                 vector<string> groups;
  18
  19                 copyTree = new Tree();
  20
  21                 //if the users enters no groups then give them the score of all groups
  22                 int numGroups = globaldata->Groups.size();
  23
  24                 //calculate number of comparsions
  25                 int numComp = 0;
  26                 for (int r=0; r<numGroups; r++) {
  27                         for (int l = r+1; l < numGroups; l++) {
  28                                 numComp++;
  29                         }
  30                 }
  31
  32                 //numComp+1 for AB, AC, BC, ABC
  33                 data.resize(numComp+1,0);
  34
  35                 int count = 0;
  36                 for (int a=0; a<numGroups; a++) {
  37                         for (int l = a+1; l < numGroups; l++) {
  38                                 int score = 0;
  39
  40                                 //groups in this combo
  41                                 groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
  42
  43                                 //copy users tree so that you can redo pgroups
  44                                 copyTree->getCopy(t);
  45
  46                                 //create pgroups that reflect the groups the user want to use
  47                                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  48                                         copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
  49                                 }
  50
  51                                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  52                                         int lc = copyTree->tree[i].getLChild();
  53                                         int rc = copyTree->tree[i].getRChild();
  54
  55                                         int iSize = copyTree->tree[i].pGroups.size();
  56                                         int rcSize = copyTree->tree[rc].pGroups.size();
  57                                         int lcSize = copyTree->tree[lc].pGroups.size();
  58
  59                                         //if isize are 0 then that branch is to be ignored
  60                                         if (iSize == 0) { }
  61                                         else if ((rcSize == 0) || (lcSize == 0)) { }
  62                                         //if you have more groups than either of your kids then theres been a change.
  63                                         else if(iSize > rcSize || iSize > lcSize){
  64                                                 score++;
  65                                         }
  66                                 }
  67
  68                                 data[count] = score;
  69                                 count++;
  70                                 groups.clear();
  71                         }
  72                 }
  73
  74                 if (numComp != 1) {
  75                         if (numGroups == 0) {
  76                                 //get score for all users groups
  77                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
  78                                         groups.push_back(tmap->namesOfGroups[i]);
  79                                 }
  80                         }else {
  81                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  82                                         groups.push_back(globaldata->Groups[i]);
  83                                 }
  84                         }
  85
  86                         //copy users tree so that you can redo pgroups
  87                         copyTree->getCopy(t);
  88                         int score = 0;
  89
  90                         //create pgroups that reflect the groups the user want to use
  91                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  92 //                              cout << i << "..." << endl;
  93                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
  94                         }
  95
  96 //                      map<string,int>::iterator it;
  97
  98                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  99                                 int lc = copyTree->tree[i].getLChild();
 100                                 int rc = copyTree->tree[i].getRChild();
 101
 102                                 int iSize = copyTree->tree[i].pGroups.size();
 103                                 int rcSize = copyTree->tree[rc].pGroups.size();
 104                                 int lcSize = copyTree->tree[lc].pGroups.size();
 105
 106 //                              cout << i+1 << '\t' << lc+1 << '\t' << rc+1 << ":\t";
 107
 108 //                              for(it=copyTree->tree[i].pGroups.begin();it!=copyTree->tree[i].pGroups.end();it++){
 109 //                                      cout << it->first << '\t';
 110 //                              }
 111
 112 //                              cout << " : " << iSize << '\t' << rcSize << '\t' << lcSize << '\t';
 113
 114                                 //if isize are 0 then that branch is to be ignored
 115                                 if (iSize == 0) { }
 116                                 else if ((rcSize == 0) || (lcSize == 0)) { }
 117                                 //if you have more groups than either of your kids then theres been a change.
 118                                 else if(iSize > rcSize || iSize > lcSize){
 119                                         score++;
 120                                 }
 121 //                              cout << score << endl;
 122                         }
 123
 124                         data[count] = score;
 125                         string hold;
 126 //                      cin >> hold;
 127                 }
 128
 129                 delete copyTree;
 130
 131                 return data;
 132         }
 133         catch(exception& e) {
 134                 cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 135                 exit(1);
 136         }
 137         catch(...) {
 138                 cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 139                 exit(1);
 140         }
 141
 142 }
 143
 144 /**************************************************************************************************/
 145