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         CountTable* ct = t->getCountTable();
  19
  20                 //if the users enters no groups then give them the score of all groups
  21                 vector<string> mGroups = m->getGroups();
  22                 int numGroups = mGroups.size();
  23
  24                 //calculate number of comparsions
  25                 int numComp = 0;
  26                 vector< vector<string> > namesOfGroupCombos;
  27                 for (int r=0; r<numGroups; r++) {
  28                         for (int l = 0; l < r; l++) {
  29                                 numComp++;
  30                                 vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
  31                                 //cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
  32                                 namesOfGroupCombos.push_back(groups);
  33                         }
  34                 }
  35
  36                 //numComp+1 for AB, AC, BC, ABC
  37                 if (numComp != 1) {
  38                         vector<string> groups;
  39                         if (numGroups == 0) {
  40                                 //get score for all users groups
  41                                 vector<string> tGroups = ct->getNamesOfGroups();
  42                                 for (int i = 0; i < tGroups.size(); i++) {
  43                                         if (tGroups[i] != "xxx") {
  44                                                 groups.push_back(tGroups[i]);
  45                                                 //cout << tmap->namesOfGroups[i] << endl;
  46                                         }
  47                                 }
  48                                 namesOfGroupCombos.push_back(groups);
  49                         }else {
  50                                 for (int i = 0; i < mGroups.size(); i++) {
  51                                         groups.push_back(mGroups[i]);
  52                                         //cout << globaldata->Groups[i] << endl;
  53                                 }
  54                                 namesOfGroupCombos.push_back(groups);
  55                         }
  56                 }
  57
  58         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  59                 if(processors == 1){
  60                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
  61                 }else{
  62                         lines.clear();
  63                         int numPairs = namesOfGroupCombos.size();
  64
  65                         int numPairsPerProcessor = numPairs / processors;
  66
  67                         for (int i = 0; i < processors; i++) {
  68                                 int startPos = i * numPairsPerProcessor;
  69
  70                                 if(i == processors - 1){
  71                                         numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
  72                                 }
  73
  74                                 lines.push_back(linePair(startPos, numPairsPerProcessor));
  75                         }
  76
  77                         data = createProcesses(t, namesOfGroupCombos, ct);
  78                 }
  79         #else
  80                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
  81         #endif
  82
  83                 return data;
  84
  85         }
  86         catch(exception& e) {
  87                 m->errorOut(e, "Parsimony", "getValues");
  88                 exit(1);
  89         }
  90 }
  91 /**************************************************************************************************/
  92
  93 EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
  94         try {
  95 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  96                 int process = 1;
  97                 vector<int> processIDS;
  98
  99                 EstOutput results;
 100
 101                 //loop through and create all the processes you want
 102                 while (process != processors) {
 103                         int pid = fork();
 104
 105                         if (pid > 0) {
 106                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 107                                 process++;
 108                         }else if (pid == 0){
 109                                 EstOutput myresults;
 110                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
 111
 112                                 if (m->control_pressed) { exit(0); }
 113
 114                                 //pass numSeqs to parent
 115                                 ofstream out;
 116                                 string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
 117                                 m->openOutputFile(tempFile, out);
 118                                 out << myresults.size() << endl;
 119                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 120                                 out.close();
 121
 122                                 exit(0);
 123                         }else {
 124                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 125                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 126                                 exit(0);
 127                         }
 128                 }
 129
 130                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
 131
 132                 //force parent to wait until all the processes are done
 133                 for (int i=0;i<processIDS.size();i++) {
 134                         int temp = processIDS[i];
 135                         wait(&temp);
 136                 }
 137
 138                 if (m->control_pressed) { return results; }
 139
 140                 //get data created by processes
 141                 for (int i=0;i<processIDS.size();i++) {
 142                         ifstream in;
 143                         string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
 144                         m->openInputFile(s, in);
 145
 146                         //get scores
 147                         if (!in.eof()) {
 148                                 int num;
 149                                 in >> num; m->gobble(in);
 150
 151                                 if (m->control_pressed) { break; }
 152
 153                                 double w;
 154                                 for (int j = 0; j < num; j++) {
 155                                         in >> w;
 156                                         results.push_back(w);
 157                                 }
 158                                 m->gobble(in);
 159                         }
 160                         in.close();
 161                         m->mothurRemove(s);
 162                 }
 163
 164                 return results;
 165 #endif
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "Parsimony", "createProcesses");
 169                 exit(1);
 170         }
 171 }
 172 /**************************************************************************************************/
 173 EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
 174         try {
 175
 176                 EstOutput results; results.resize(num);
 177
 178                 Tree* copyTree = new Tree(ct);
 179                 int count = 0;
 180
 181                 for (int h = start; h < (start+num); h++) {
 182
 183                         if (m->control_pressed) { delete copyTree; return results; }
 184
 185                         int score = 0;
 186
 187                         //groups in this combo
 188                         vector<string> groups = namesOfGroupCombos[h];
 189
 190                         //copy users tree so that you can redo pgroups
 191                         copyTree->getCopy(t);
 192
 193                         //create pgroups that reflect the groups the user want to use
 194                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 195                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 196                         }
 197
 198                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 199
 200                                 if (m->control_pressed) { return data; }
 201
 202                                 int lc = copyTree->tree[i].getLChild();
 203                                 int rc = copyTree->tree[i].getRChild();
 204
 205                                 int iSize = copyTree->tree[i].pGroups.size();
 206                                 int rcSize = copyTree->tree[rc].pGroups.size();
 207                                 int lcSize = copyTree->tree[lc].pGroups.size();
 208
 209                                 //if isize are 0 then that branch is to be ignored
 210                                 if (iSize == 0) { }
 211                                 else if ((rcSize == 0) || (lcSize == 0)) { }
 212                                 //if you have more groups than either of your kids then theres been a change.
 213                                 else if(iSize > rcSize || iSize > lcSize){
 214                                         score++;
 215                                 }
 216                         }
 217
 218                         results[count] = score;
 219                         count++;
 220                 }
 221
 222                 delete copyTree;
 223
 224                 return results;
 225         }
 226         catch(exception& e) {
 227                 m->errorOut(e, "Parsimony", "driver");
 228                 exit(1);
 229         }
 230 }
 231
 232 /**************************************************************************************************/
 233