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