parsimony.h

   1 #ifndef PARSIMONY_H
   2 #define PARSIMONY_H
   3
   4
   5 /*
   6  *  parsimony.h
   7  *  Mothur
   8  *
   9  *  Created by Sarah Westcott on 1/26/09.
  10  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  11  *
  12  */
  13
  14 #include "treecalculator.h"
  15 #include "counttable.h"
  16
  17 /***********************************************************************/
  18
  19 class Parsimony : public TreeCalculator  {
  20
  21         public:
  22                 Parsimony() {};
  23                 ~Parsimony() {};
  24                 EstOutput getValues(Tree*, int, string);
  25
  26         private:
  27                 struct linePair {
  28                         int start;
  29                         int num;
  30                         linePair(int i, int j) : start(i), num(j) {}
  31                 };
  32                 vector<linePair> lines;
  33
  34                 EstOutput data;
  35                 int processors;
  36                 string outputDir;
  37
  38                 EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*);
  39                 EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
  40 };
  41 /***********************************************************************/
  42 struct parsData {
  43     int start;
  44         int num;
  45         MothurOut* m;
  46     EstOutput results;
  47     vector< vector<string> > namesOfGroupCombos;
  48     Tree* t;
  49     CountTable* ct;
  50
  51         parsData(){}
  52         parsData(MothurOut* mout, int st, int en, vector< vector<string> > ngc, Tree* tree, CountTable* count) {
  53         m = mout;
  54                 start = st;
  55                 num = en;
  56         namesOfGroupCombos = ngc;
  57         t = tree;
  58         ct = count;
  59         }
  60 };
  61
  62 /**************************************************************************************************/
  63 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  64 #else
  65 static DWORD WINAPI MyParsimonyThreadFunction(LPVOID lpParam){
  66         parsData* pDataArray;
  67         pDataArray = (parsData*)lpParam;
  68         try {
  69
  70         pDataArray->results.resize(pDataArray->num);
  71
  72                 Tree* copyTree = new Tree(pDataArray->ct);
  73                 int count = 0;
  74
  75                 for (int h = pDataArray->start; h < (pDataArray->start+pDataArray->num); h++) {
  76
  77                         if (pDataArray->m->control_pressed) { delete copyTree; return 0; }
  78
  79                         int score = 0;
  80
  81                         //groups in this combo
  82                         vector<string> groups = pDataArray->namesOfGroupCombos[h];
  83
  84                         //copy users tree so that you can redo pgroups
  85                         copyTree->getCopy(pDataArray->t);
  86
  87                         //create pgroups that reflect the groups the user want to use
  88                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  89                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
  90                         }
  91
  92                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
  93
  94                                 if (pDataArray->m->control_pressed) { return 0; }
  95
  96                                 int lc = copyTree->tree[i].getLChild();
  97                                 int rc = copyTree->tree[i].getRChild();
  98
  99                                 int iSize = copyTree->tree[i].pGroups.size();
 100                                 int rcSize = copyTree->tree[rc].pGroups.size();
 101                                 int lcSize = copyTree->tree[lc].pGroups.size();
 102
 103                                 //if isize are 0 then that branch is to be ignored
 104                                 if (iSize == 0) { }
 105                                 else if ((rcSize == 0) || (lcSize == 0)) { }
 106                                 //if you have more groups than either of your kids then theres been a change.
 107                                 else if(iSize > rcSize || iSize > lcSize){
 108                                         score++;
 109                                 }
 110                         }
 111
 112                         pDataArray->results[count] = score;
 113                         count++;
 114                 }
 115
 116                 delete copyTree;
 117
 118         return 0;
 119
 120     }
 121         catch(exception& e) {
 122                 pDataArray->m->errorOut(e, "Parsimony", "MyParsimonyThreadFunction");
 123                 exit(1);
 124         }
 125 }
 126 #endif
 127
 128 #endif