unweighted.cpp

   1 /*
   2  *  unweighted.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "unweighted.h"
  11
  12 /**************************************************************************************************/
  13
  14 EstOutput Unweighted::getValues(Tree* t, int p, string o) {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 processors = p;
  18                 outputDir = o;
  19
  20                 //if the users enters no groups then give them the score of all groups
  21                 int numGroups = globaldata->Groups.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 = r+1; l < numGroups; l++) {
  28                                 numComp++;
  29                                 vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
  30                                 namesOfGroupCombos.push_back(groups);
  31                         }
  32                 }
  33
  34                 if (numComp != 1) {
  35                         vector<string> groups;
  36                         if (numGroups == 0) {
  37                                 //get score for all users groups
  38                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
  39                                         if (tmap->namesOfGroups[i] != "xxx") {
  40                                                 groups.push_back(tmap->namesOfGroups[i]);
  41                                         }
  42                                 }
  43                                 namesOfGroupCombos.push_back(groups);
  44                         }else {
  45                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  46                                         groups.push_back(globaldata->Groups[i]);
  47                                 }
  48                                 namesOfGroupCombos.push_back(groups);
  49                         }
  50                 }
  51
  52                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  53                         if(processors == 1){
  54                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  55                         }else{
  56                                 int numPairs = namesOfGroupCombos.size();
  57
  58                                 int numPairsPerProcessor = numPairs / processors;
  59
  60                                 for (int i = 0; i < processors; i++) {
  61                                         int startPos = i * numPairsPerProcessor;
  62                                         if(i == processors - 1){
  63                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
  64                                         }
  65                                         lines.push_back(new linePair(startPos, numPairsPerProcessor));
  66                                 }
  67
  68                                 data = createProcesses(t, namesOfGroupCombos);
  69
  70                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
  71                         }
  72                 #else
  73                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  74                 #endif
  75
  76                 return data;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "Unweighted", "getValues");
  80                 exit(1);
  81         }
  82 }
  83 /**************************************************************************************************/
  84
  85 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
  86         try {
  87 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  88                 int process = 1;
  89                 int num = 0;
  90                 vector<int> processIDS;
  91
  92                 EstOutput results;
  93
  94                 //loop through and create all the processes you want
  95                 while (process != processors) {
  96                         int pid = fork();
  97
  98                         if (pid > 0) {
  99                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 100                                 process++;
 101                         }else if (pid == 0){
 102                                 EstOutput myresults;
 103                                 myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num);
 104
 105                                 if (m->control_pressed) { exit(0); }
 106
 107                                 m->mothurOut("Merging results."); m->mothurOutEndLine();
 108
 109                                 //pass numSeqs to parent
 110                                 ofstream out;
 111                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 112                                 m->openOutputFile(tempFile, out);
 113                                 out << myresults.size() << endl;
 114                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 115                                 out.close();
 116
 117                                 exit(0);
 118                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 119                 }
 120
 121                 results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num);
 122
 123                 //force parent to wait until all the processes are done
 124                 for (int i=0;i<(processors-1);i++) {
 125                         int temp = processIDS[i];
 126                         wait(&temp);
 127                 }
 128
 129                 if (m->control_pressed) { return results; }
 130
 131                 //get data created by processes
 132                 for (int i=0;i<(processors-1);i++) {
 133                         ifstream in;
 134                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 135                         m->openInputFile(s, in);
 136
 137                         //get quantiles
 138                         if (!in.eof()) {
 139                                 int num;
 140                                 in >> num; m->gobble(in);
 141
 142                                 if (m->control_pressed) { break; }
 143
 144                                 double w;
 145                                 for (int j = 0; j < num; j++) {
 146                                         in >> w;
 147                                         results.push_back(w);
 148                                 }
 149                                 m->gobble(in);
 150                         }
 151                         in.close();
 152                         remove(s.c_str());
 153                 }
 154
 155                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 156
 157                 return results;
 158 #endif
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "Unweighted", "createProcesses");
 162                 exit(1);
 163         }
 164 }
 165 /**************************************************************************************************/
 166 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
 167  try {
 168
 169                 EstOutput results; results.resize(num);
 170
 171                 int count = 0;
 172                 int total = num;
 173                 int twentyPercent = (total * 0.20);
 174
 175                 for (int h = start; h < (start+num); h++) {
 176
 177                         if (m->control_pressed) { return results; }
 178
 179                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 180                         double totalBL = 0.00;  //all branch lengths
 181                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 182
 183                         for(int i=0;i<t->getNumNodes();i++){
 184
 185                                 if (m->control_pressed) {  return data; }
 186
 187                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 188                                 //pcountSize = 2, not unique to one group
 189                                 //pcountSize = 1, unique to one group
 190
 191                                 int pcountSize = 0;
 192                                 for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 193                                         map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 194                                         if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 195                                 }
 196
 197                                 if (pcountSize == 0) { }
 198                                 else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());   }
 199
 200                                 if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
 201                                         totalBL += abs(t->tree[i].getBranchLength());
 202                                 }
 203                         }
 204
 205                         UW = (UniqueBL / totalBL);
 206
 207                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 208
 209                         results[count] = UW;
 210                         count++;
 211
 212                         //report progress
 213                         if((count) % twentyPercent == 0){       m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine();           }
 214                 }
 215
 216                 m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
 217
 218                 return results;
 219         }
 220         catch(exception& e) {
 221                 m->errorOut(e, "Unweighted", "driver");
 222                 exit(1);
 223         }
 224 }
 225 /**************************************************************************************************/
 226
 227 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 228  try {
 229         globaldata = GlobalData::getInstance();
 230
 231                 vector<string> groups;
 232                 double UniqueBL;  //a branch length is unique if it's chidren are from the same group
 233                 double totalBL; //all branch lengths
 234                 double UW;              //Unweighted Value = UniqueBL / totalBL;
 235                 copyTree = new Tree;
 236
 237                 //if the users enters no groups then give them the score of all groups
 238                 int numGroups = globaldata->Groups.size();
 239
 240                 //calculate number of comparsions
 241                 int numComp = 0;
 242                 for (int r=0; r<numGroups; r++) {
 243                         for (int l = r+1; l < numGroups; l++) {
 244                                 numComp++;
 245                         }
 246                 }
 247
 248                 //numComp+1 for AB, AC, BC, ABC
 249                 data.resize(numComp+1,0);
 250
 251                 int count = 0;
 252                 for (int a=0; a<numGroups; a++) {
 253                         for (int l = a+1; l < numGroups; l++) {
 254                                 UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 255                                 totalBL = 0.00; //all branch lengths
 256                                 UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 257
 258                                 //copy random tree passed in
 259                                 copyTree->getCopy(t);
 260
 261                                 //groups in this combo
 262                                 groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 263
 264                                 //swap labels in the groups you want to compare
 265                                 copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
 266
 267                                 if (m->control_pressed) { delete copyTree; return data; }
 268
 269                                 for(int i=0;i<copyTree->getNumNodes();i++){
 270
 271                                         if (m->control_pressed) {  return data; }
 272
 273                                         //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 274                                         //pcountSize = 2, not unique to one group
 275                                         //pcountSize = 1, unique to one group
 276
 277                                         int pcountSize = 0;
 278                                         for (int j = 0; j < groups.size(); j++) {
 279                                                 map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
 280                                                 if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; }
 281                                         }
 282
 283                                         if (pcountSize == 0) { }
 284                                         else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());     }
 285
 286                                         if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
 287                                                 totalBL += abs(copyTree->tree[i].getBranchLength());
 288                                         }
 289                                 }
 290
 291
 292                                 UW = (UniqueBL / totalBL);
 293
 294                                 if (isnan(UW) || isinf(UW)) { UW = 0; }
 295
 296                                 data[count] = UW;
 297                                 count++;
 298                                 groups.clear();
 299                         }
 300                 }
 301
 302
 303                 if (numComp != 1) {
 304                         if (numGroups == 0) {
 305                                 //get score for all users groups
 306                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 307                                         if (tmap->namesOfGroups[i] != "xxx") {
 308                                                 groups.push_back(tmap->namesOfGroups[i]);
 309                                         }
 310                                 }
 311                         }else {
 312                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 313                                         groups.push_back(globaldata->Groups[i]);
 314                                 }
 315                         }
 316
 317                         UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 318                         totalBL = 0.00; //all branch lengths
 319                         UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 320
 321                         //copy random tree passed in
 322                         copyTree->getCopy(t);
 323
 324                         //swap labels in all the groups you want to compare
 325                         copyTree->assembleRandomUnifracTree(groups);
 326
 327                         if (m->control_pressed) { delete copyTree; return data; }
 328
 329                         for(int i=0;i<copyTree->getNumNodes();i++){
 330
 331                                 if (m->control_pressed) {  return data; }
 332
 333                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 334                                 //pcountSize = 2, not unique to one group
 335                                 //pcountSize = 1, unique to one group
 336
 337                                 int pcountSize = 0;
 338                                 for (int j = 0; j < groups.size(); j++) {
 339                                         map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
 340                                         if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 341                                 }
 342
 343                                 if (pcountSize == 0) { }
 344                                 else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());     }
 345
 346                                 if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
 347                                         totalBL += abs(copyTree->tree[i].getBranchLength());
 348                                 }
 349                         }
 350
 351                         UW = (UniqueBL / totalBL);
 352
 353                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 354
 355                         data[count] = UW;
 356                 }
 357
 358                 delete copyTree;
 359
 360                 return data;
 361
 362         }
 363         catch(exception& e) {
 364                 m->errorOut(e, "Unweighted", "getValues");
 365                 exit(1);
 366         }
 367 }
 368
 369 /**************************************************************************************************/
 370
 371