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
  53                                         if (m->control_pressed) { return data; }
  54
  55                                         int lc = copyTree->tree[i].getLChild();
  56                                         int rc = copyTree->tree[i].getRChild();
  57
  58                                         int iSize = copyTree->tree[i].pGroups.size();
  59                                         int rcSize = copyTree->tree[rc].pGroups.size();
  60                                         int lcSize = copyTree->tree[lc].pGroups.size();
  61
  62                                         //if isize are 0 then that branch is to be ignored
  63                                         if (iSize == 0) { }
  64                                         else if ((rcSize == 0) || (lcSize == 0)) { }
  65                                         //if you have more groups than either of your kids then theres been a change.
  66                                         else if(iSize > rcSize || iSize > lcSize){
  67                                                 score++;
  68                                         }
  69                                 }
  70
  71                                 data[count] = score;
  72                                 count++;
  73                                 groups.clear();
  74                         }
  75                 }
  76
  77                 if (numComp != 1) {
  78                         if (numGroups == 0) {
  79                                 //get score for all users groups
  80                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
  81                                         if (tmap->namesOfGroups[i] != "xxx") {
  82                                                 groups.push_back(tmap->namesOfGroups[i]);
  83                                         }
  84                                 }
  85                         }else {
  86                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  87                                         groups.push_back(globaldata->Groups[i]);
  88                                 }
  89                         }
  90
  91                         //copy users tree so that you can redo pgroups
  92                         copyTree->getCopy(t);
  93                         int score = 0;
  94
  95                         //create pgroups that reflect the groups the user want to use
  96                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  97                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
  98                         }
  99
 100 //                      map<string,int>::iterator it;
 101
 102                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 103
 104                                 if (m->control_pressed) { return data; }
 105
 106                                 int lc = copyTree->tree[i].getLChild();
 107                                 int rc = copyTree->tree[i].getRChild();
 108
 109                                 int iSize = copyTree->tree[i].pGroups.size();
 110                                 int rcSize = copyTree->tree[rc].pGroups.size();
 111                                 int lcSize = copyTree->tree[lc].pGroups.size();
 112
 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                         }
 122
 123                         data[count] = score;
 124
 125                 }
 126
 127                 delete copyTree;
 128
 129                 return data;
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "Parsimony", "getValues");
 133                 exit(1);
 134         }
 135 }
 136
 137 /**************************************************************************************************/
 138