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 remainingPairs = namesOfGroupCombos.size();
  60         int startIndex = 0;
  61         for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
  62             int numPairs = remainingPairs; //case for last processor
  63             if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
  64             lines.push_back(linePair(startIndex, numPairs)); //startIndex, numPairs
  65             startIndex = startIndex + numPairs;
  66             remainingPairs = remainingPairs - numPairs;
  67         }
  68
  69         data = createProcesses(t, namesOfGroupCombos, ct);
  70
  71                 return data;
  72
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "Parsimony", "getValues");
  76                 exit(1);
  77         }
  78 }
  79 /**************************************************************************************************/
  80
  81 EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
  82         try {
  83         int process = 1;
  84                 vector<int> processIDS;
  85
  86                 EstOutput results;
  87
  88 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  89
  90                 //loop through and create all the processes you want
  91                 while (process != processors) {
  92                         int pid = fork();
  93
  94                         if (pid > 0) {
  95                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
  96                                 process++;
  97                         }else if (pid == 0){
  98                                 EstOutput myresults;
  99                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
 100
 101                                 if (m->control_pressed) { exit(0); }
 102
 103                                 //pass numSeqs to parent
 104                                 ofstream out;
 105                                 string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
 106                                 m->openOutputFile(tempFile, out);
 107                                 out << myresults.size() << endl;
 108                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 109                                 out.close();
 110
 111                                 exit(0);
 112                         }else {
 113                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 114                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 115                                 exit(0);
 116                         }
 117                 }
 118
 119                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
 120
 121                 //force parent to wait until all the processes are done
 122                 for (int i=0;i<processIDS.size();i++) {
 123                         int temp = processIDS[i];
 124                         wait(&temp);
 125                 }
 126
 127                 if (m->control_pressed) { return results; }
 128
 129                 //get data created by processes
 130                 for (int i=0;i<processIDS.size();i++) {
 131                         ifstream in;
 132                         string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
 133                         m->openInputFile(s, in);
 134
 135                         //get scores
 136                         if (!in.eof()) {
 137                                 int num;
 138                                 in >> num; m->gobble(in);
 139
 140                                 if (m->control_pressed) { break; }
 141
 142                                 double w;
 143                                 for (int j = 0; j < num; j++) {
 144                                         in >> w;
 145                                         results.push_back(w);
 146                                 }
 147                                 m->gobble(in);
 148                         }
 149                         in.close();
 150                         m->mothurRemove(s);
 151                 }
 152 #else
 153         //fill in functions
 154         vector<parsData*> pDataArray;
 155                 DWORD   dwThreadIdArray[processors-1];
 156                 HANDLE  hThreadArray[processors-1];
 157         vector<CountTable*> cts;
 158         vector<Tree*> trees;
 159
 160                 //Create processor worker threads.
 161                 for( int i=1; i<processors; i++ ){
 162             CountTable* copyCount = new CountTable();
 163             copyCount->copy(ct);
 164             Tree* copyTree = new Tree(copyCount);
 165             copyTree->getCopy(t);
 166
 167             cts.push_back(copyCount);
 168             trees.push_back(copyTree);
 169
 170             parsData* temppars = new parsData(m, lines[i].start, lines[i].num, namesOfGroupCombos, copyTree, copyCount);
 171                         pDataArray.push_back(temppars);
 172                         processIDS.push_back(i);
 173
 174                         hThreadArray[i-1] = CreateThread(NULL, 0, MyParsimonyThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 175                 }
 176
 177                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
 178
 179                 //Wait until all threads have terminated.
 180                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 181
 182                 //Close all thread handles and free memory allocations.
 183                 for(int i=0; i < pDataArray.size(); i++){
 184             for (int j = 0; j < pDataArray[i]->results.size(); j++) {  results.push_back(pDataArray[i]->results[j]);  }
 185                         delete cts[i];
 186             delete trees[i];
 187                         CloseHandle(hThreadArray[i]);
 188                         delete pDataArray[i];
 189                 }
 190
 191 #endif
 192         return results;
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "Parsimony", "createProcesses");
 196                 exit(1);
 197         }
 198 }
 199 /**************************************************************************************************/
 200 EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
 201         try {
 202
 203                 EstOutput results; results.resize(num);
 204
 205                 Tree* copyTree = new Tree(ct);
 206                 int count = 0;
 207
 208                 for (int h = start; h < (start+num); h++) {
 209
 210                         if (m->control_pressed) { delete copyTree; return results; }
 211
 212                         int score = 0;
 213
 214                         //groups in this combo
 215                         vector<string> groups = namesOfGroupCombos[h];
 216
 217                         //copy users tree so that you can redo pgroups
 218                         copyTree->getCopy(t);
 219
 220                         //create pgroups that reflect the groups the user want to use
 221                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 222                                 copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
 223                         }
 224
 225                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 226
 227                                 if (m->control_pressed) { return data; }
 228
 229                                 int lc = copyTree->tree[i].getLChild();
 230                                 int rc = copyTree->tree[i].getRChild();
 231
 232                                 int iSize = copyTree->tree[i].pGroups.size();
 233                                 int rcSize = copyTree->tree[rc].pGroups.size();
 234                                 int lcSize = copyTree->tree[lc].pGroups.size();
 235
 236                                 //if isize are 0 then that branch is to be ignored
 237                                 if (iSize == 0) { }
 238                                 else if ((rcSize == 0) || (lcSize == 0)) { }
 239                                 //if you have more groups than either of your kids then theres been a change.
 240                                 else if(iSize > rcSize || iSize > lcSize){
 241                                         score++;
 242                                 }
 243                         }
 244
 245                         results[count] = score;
 246                         count++;
 247                 }
 248
 249                 delete copyTree;
 250
 251                 return results;
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "Parsimony", "driver");
 255                 exit(1);
 256         }
 257 }
 258
 259 /**************************************************************************************************/
 260