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         lines.clear();
  59         int numPairs = namesOfGroupCombos.size();
  60         int numPairsPerProcessor = numPairs / processors;
  61
  62         for (int i = 0; i < processors; i++) {
  63             int startPos = i * numPairsPerProcessor;
  64             if(i == processors - 1){ numPairsPerProcessor = numPairs - i * numPairsPerProcessor; }
  65             lines.push_back(linePair(startPos, numPairsPerProcessor));
  66         }
  67
  68         data = createProcesses(t, namesOfGroupCombos, ct);
  69
  70                 return data;
  71
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "Parsimony", "getValues");
  75                 exit(1);
  76         }
  77 }
  78 /**************************************************************************************************/
  79
  80 EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
  81         try {
  82         int process = 1;
  83                 vector<int> processIDS;
  84
  85                 EstOutput results;
  86
  87 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  88
  89                 //loop through and create all the processes you want
  90                 while (process != processors) {
  91                         int pid = fork();
  92
  93                         if (pid > 0) {
  94                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
  95                                 process++;
  96                         }else if (pid == 0){
  97                                 EstOutput myresults;
  98                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
  99
 100                                 if (m->control_pressed) { exit(0); }
 101
 102                                 //pass numSeqs to parent
 103                                 ofstream out;
 104                                 string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
 105                                 m->openOutputFile(tempFile, out);
 106                                 out << myresults.size() << endl;
 107                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 108                                 out.close();
 109
 110                                 exit(0);
 111                         }else {
 112                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 113                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 114                                 exit(0);
 115                         }
 116                 }
 117
 118                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
 119
 120                 //force parent to wait until all the processes are done
 121                 for (int i=0;i<processIDS.size();i++) {
 122                         int temp = processIDS[i];
 123                         wait(&temp);
 124                 }
 125
 126                 if (m->control_pressed) { return results; }
 127
 128                 //get data created by processes
 129                 for (int i=0;i<processIDS.size();i++) {
 130                         ifstream in;
 131                         string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
 132                         m->openInputFile(s, in);
 133
 134                         //get scores
 135                         if (!in.eof()) {
 136                                 int num;
 137                                 in >> num; m->gobble(in);
 138
 139                                 if (m->control_pressed) { break; }
 140
 141                                 double w;
 142                                 for (int j = 0; j < num; j++) {
 143                                         in >> w;
 144                                         results.push_back(w);
 145                                 }
 146                                 m->gobble(in);
 147                         }
 148                         in.close();
 149                         m->mothurRemove(s);
 150                 }
 151 #else
 152         //fill in functions
 153         vector<parsData*> pDataArray;
 154                 DWORD   dwThreadIdArray[processors-1];
 155                 HANDLE  hThreadArray[processors-1];
 156         vector<CountTable*> cts;
 157         vector<Tree*> trees;
 158
 159                 //Create processor worker threads.
 160                 for( int i=1; i<processors; i++ ){
 161             CountTable* copyCount = new CountTable();
 162             copyCount->copy(ct);
 163             Tree* copyTree = new Tree(copyCount);
 164             copyTree->getCopy(t);
 165
 166             cts.push_back(copyCount);
 167             trees.push_back(copyTree);
 168
 169             parsData* temppars = new parsData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount);
 170                         pDataArray.push_back(temppars);
 171                         processIDS.push_back(i);
 172
 173                         hThreadArray[i-1] = CreateThread(NULL, 0, MyParsimonyThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 174                 }
 175
 176                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
 177
 178                 //Wait until all threads have terminated.
 179                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 180
 181                 //Close all thread handles and free memory allocations.
 182                 for(int i=0; i < pDataArray.size(); i++){
 183             for (int j = 0; j < pDataArray[i]->results.size(); j++) {  results.push_back(pDataArray[i]->results[j]);  }
 184                         delete cts[i];
 185             delete trees[i];
 186                         CloseHandle(hThreadArray[i]);
 187                         delete pDataArray[i];
 188                 }
 189
 190 #endif
 191         return results;
 192         }
 193         catch(exception& e) {
 194                 m->errorOut(e, "Parsimony", "createProcesses");
 195                 exit(1);
 196         }
 197 }
 198 /**************************************************************************************************/
 199 EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
 200         try {
 201
 202                 EstOutput results; results.resize(num);
 203
 204                 Tree* copyTree = new Tree(ct);
 205                 int count = 0;
 206
 207                 for (int h = start; h < (start+num); h++) {
 208
 209                         if (m->control_pressed) { delete copyTree; return results; }
 210
 211                         int score = 0;
 212
 213                         //groups in this combo
 214                         vector<string> groups = namesOfGroupCombos[h];
 215
 216                         //copy users tree so that you can redo pgroups
 217                         copyTree->getCopy(t);
 218
 219                         //create pgroups that reflect the groups the user want to use
 220                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 221                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 222                         }
 223
 224                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 225
 226                                 if (m->control_pressed) { return data; }
 227
 228                                 int lc = copyTree->tree[i].getLChild();
 229                                 int rc = copyTree->tree[i].getRChild();
 230
 231                                 int iSize = copyTree->tree[i].pGroups.size();
 232                                 int rcSize = copyTree->tree[rc].pGroups.size();
 233                                 int lcSize = copyTree->tree[lc].pGroups.size();
 234
 235                                 //if isize are 0 then that branch is to be ignored
 236                                 if (iSize == 0) { }
 237                                 else if ((rcSize == 0) || (lcSize == 0)) { }
 238                                 //if you have more groups than either of your kids then theres been a change.
 239                                 else if(iSize > rcSize || iSize > lcSize){
 240                                         score++;
 241                                 }
 242                         }
 243
 244                         results[count] = score;
 245                         count++;
 246                 }
 247
 248                 delete copyTree;
 249
 250                 return results;
 251         }
 252         catch(exception& e) {
 253                 m->errorOut(e, "Parsimony", "driver");
 254                 exit(1);
 255         }
 256 }
 257
 258 /**************************************************************************************************/
 259