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, int p, string o) {
  15         try {
  16                 processors = p;
  17                 outputDir = o;
  18
  19                 //if the users enters no groups then give them the score of all groups
  20                 vector<string> mGroups = m->getGroups();
  21                 int numGroups = mGroups.size();
  22
  23                 //calculate number of comparsions
  24                 int numComp = 0;
  25                 vector< vector<string> > namesOfGroupCombos;
  26                 for (int r=0; r<numGroups; r++) {
  27                         for (int l = 0; l < r; l++) {
  28                                 numComp++;
  29                                 vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
  30                                 //cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
  31                                 namesOfGroupCombos.push_back(groups);
  32                         }
  33                 }
  34
  35                 //numComp+1 for AB, AC, BC, ABC
  36                 if (numComp != 1) {
  37                         vector<string> groups;
  38                         if (numGroups == 0) {
  39                                 //get score for all users groups
  40                                 vector<string> tGroups = tmap->getNamesOfGroups();
  41                                 for (int i = 0; i < tGroups.size(); i++) {
  42                                         if (tGroups[i] != "xxx") {
  43                                                 groups.push_back(tGroups[i]);
  44                                                 //cout << tmap->namesOfGroups[i] << endl;
  45                                         }
  46                                 }
  47                                 namesOfGroupCombos.push_back(groups);
  48                         }else {
  49                                 for (int i = 0; i < mGroups.size(); i++) {
  50                                         groups.push_back(mGroups[i]);
  51                                         //cout << globaldata->Groups[i] << endl;
  52                                 }
  53                                 namesOfGroupCombos.push_back(groups);
  54                         }
  55                 }
  56
  57         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  58                 if(processors == 1){
  59                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  60                 }else{
  61                         lines.clear();
  62                         int numPairs = namesOfGroupCombos.size();
  63
  64                         int numPairsPerProcessor = numPairs / processors;
  65
  66                         for (int i = 0; i < processors; i++) {
  67                                 int startPos = i * numPairsPerProcessor;
  68
  69                                 if(i == processors - 1){
  70                                         numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
  71                                 }
  72
  73                                 lines.push_back(linePair(startPos, numPairsPerProcessor));
  74                         }
  75
  76                         data = createProcesses(t, namesOfGroupCombos);
  77                 }
  78         #else
  79                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  80         #endif
  81
  82                 return data;
  83
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "Parsimony", "getValues");
  87                 exit(1);
  88         }
  89 }
  90 /**************************************************************************************************/
  91
  92 EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
  93         try {
  94 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  95                 int process = 1;
  96                 vector<int> processIDS;
  97
  98                 EstOutput results;
  99
 100                 //loop through and create all the processes you want
 101                 while (process != processors) {
 102                         int pid = fork();
 103
 104                         if (pid > 0) {
 105                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 106                                 process++;
 107                         }else if (pid == 0){
 108                                 EstOutput myresults;
 109                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
 110
 111                                 if (m->control_pressed) { exit(0); }
 112
 113                                 //pass numSeqs to parent
 114                                 ofstream out;
 115                                 string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
 116                                 m->openOutputFile(tempFile, out);
 117                                 out << myresults.size() << endl;
 118                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 119                                 out.close();
 120
 121                                 exit(0);
 122                         }else {
 123                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 124                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 125                                 exit(0);
 126                         }
 127                 }
 128
 129                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
 130
 131                 //force parent to wait until all the processes are done
 132                 for (int i=0;i<processIDS.size();i++) {
 133                         int temp = processIDS[i];
 134                         wait(&temp);
 135                 }
 136
 137                 if (m->control_pressed) { return results; }
 138
 139                 //get data created by processes
 140                 for (int i=0;i<processIDS.size();i++) {
 141                         ifstream in;
 142                         string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
 143                         m->openInputFile(s, in);
 144
 145                         //get scores
 146                         if (!in.eof()) {
 147                                 int num;
 148                                 in >> num; m->gobble(in);
 149
 150                                 if (m->control_pressed) { break; }
 151
 152                                 double w;
 153                                 for (int j = 0; j < num; j++) {
 154                                         in >> w;
 155                                         results.push_back(w);
 156                                 }
 157                                 m->gobble(in);
 158                         }
 159                         in.close();
 160                         m->mothurRemove(s);
 161                 }
 162
 163                 return results;
 164 #endif
 165         }
 166         catch(exception& e) {
 167                 m->errorOut(e, "Parsimony", "createProcesses");
 168                 exit(1);
 169         }
 170 }
 171 /**************************************************************************************************/
 172 EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
 173         try {
 174
 175                 EstOutput results; results.resize(num);
 176
 177                 Tree* copyTree = new Tree(tmap);
 178                 int count = 0;
 179
 180                 for (int h = start; h < (start+num); h++) {
 181
 182                         if (m->control_pressed) { delete copyTree; return results; }
 183
 184                         int score = 0;
 185
 186                         //groups in this combo
 187                         vector<string> groups = namesOfGroupCombos[h];
 188
 189                         //copy users tree so that you can redo pgroups
 190                         copyTree->getCopy(t);
 191
 192                         //create pgroups that reflect the groups the user want to use
 193                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 194                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 195                         }
 196
 197                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 198
 199                                 if (m->control_pressed) { return data; }
 200
 201                                 int lc = copyTree->tree[i].getLChild();
 202                                 int rc = copyTree->tree[i].getRChild();
 203
 204                                 int iSize = copyTree->tree[i].pGroups.size();
 205                                 int rcSize = copyTree->tree[rc].pGroups.size();
 206                                 int lcSize = copyTree->tree[lc].pGroups.size();
 207
 208                                 //if isize are 0 then that branch is to be ignored
 209                                 if (iSize == 0) { }
 210                                 else if ((rcSize == 0) || (lcSize == 0)) { }
 211                                 //if you have more groups than either of your kids then theres been a change.
 212                                 else if(iSize > rcSize || iSize > lcSize){
 213                                         score++;
 214                                 }
 215                         }
 216
 217                         results[count] = score;
 218                         count++;
 219                 }
 220
 221                 delete copyTree;
 222
 223                 return results;
 224         }
 225         catch(exception& e) {
 226                 m->errorOut(e, "Parsimony", "driver");
 227                 exit(1);
 228         }
 229 }
 230
 231 /**************************************************************************************************/
 232