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 = 0; l < r; 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
  63                                         if(i == processors - 1){
  64                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
  65                                         }
  66
  67                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
  68                                 }
  69
  70                                 data = createProcesses(t, namesOfGroupCombos);
  71                                 lines.clear();
  72                         }
  73                 #else
  74                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
  75                 #endif
  76
  77                 return data;
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "Unweighted", "getValues");
  81                 exit(1);
  82         }
  83 }
  84 /**************************************************************************************************/
  85
  86 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
  87         try {
  88 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  89                 int process = 1;
  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 {
 119                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 120                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 121                                 exit(0);
 122                         }
 123                 }
 124
 125                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
 126
 127                 //force parent to wait until all the processes are done
 128                 for (int i=0;i<(processors-1);i++) {
 129                         int temp = processIDS[i];
 130                         wait(&temp);
 131                 }
 132
 133                 if (m->control_pressed) { return results; }
 134
 135                 //get data created by processes
 136                 for (int i=0;i<(processors-1);i++) {
 137                         ifstream in;
 138                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 139                         m->openInputFile(s, in);
 140
 141                         //get quantiles
 142                         if (!in.eof()) {
 143                                 int num;
 144                                 in >> num; m->gobble(in);
 145
 146                                 if (m->control_pressed) { break; }
 147
 148                                 double w;
 149                                 for (int j = 0; j < num; j++) {
 150                                         in >> w;
 151                                         results.push_back(w);
 152                                 }
 153                                 m->gobble(in);
 154                         }
 155                         in.close();
 156                         remove(s.c_str());
 157                 }
 158
 159                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 160
 161                 return results;
 162 #endif
 163         }
 164         catch(exception& e) {
 165                 m->errorOut(e, "Unweighted", "createProcesses");
 166                 exit(1);
 167         }
 168 }
 169 /**************************************************************************************************/
 170 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
 171  try {
 172
 173                 EstOutput results; results.resize(num);
 174
 175                 int count = 0;
 176                 int numLeaves = t->getNumLeaves();
 177                 int total = num;
 178                 int twentyPercent = (total * 0.20);
 179                 if (twentyPercent == 0) { twentyPercent = 1; }
 180
 181
 182                 for (int h = start; h < (start+num); h++) {
 183         //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;
 184                         if (m->control_pressed) { return results; }
 185
 186                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 187                         double totalBL = 0.00;  //all branch lengths
 188                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 189                         map<int, double> tempTotals; //maps node to total Branch Length
 190                         map<int, int> nodePcountSize; //maps node to pcountSize
 191                         map<int, int>::iterator itCount;
 192
 193                         for(int i=0;i<t->getNumNodes();i++){
 194
 195                                 if (m->control_pressed) {  return data; }
 196
 197                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 198                                 //pcountSize = 2, not unique to one group
 199                                 //pcountSize = 1, unique to one group
 200
 201                                 int pcountSize = 0;
 202                                 for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 203                                         map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 204                                         if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 205                                 }
 206
 207                                 nodePcountSize[i] = pcountSize;
 208
 209                                 //cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t';
 210                                 if (pcountSize == 0) { }
 211                                 else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength()); }
 212
 213                                 //if you are a leaf from a users group add to total
 214                                 if (i < numLeaves) {
 215                                         if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {
 216                                         //cout << "added to total" << endl;
 217                                                 totalBL += abs(t->tree[i].getBranchLength());
 218                                         }
 219                                         tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
 220                                 }else{ //if you are not a leaf
 221                                         //do both your chidren have have descendants from the users groups?
 222                                         int lc = t->tree[i].getLChild();
 223                                         int rc = t->tree[i].getRChild();
 224
 225                                         //if yes, add your childrens tempTotals
 226                                         if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 227                                                 totalBL += tempTotals[lc] + tempTotals[rc];
 228                                                 //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
 229                                                 if (t->tree[i].getBranchLength() != -1) {
 230                                                         tempTotals[i] = abs(t->tree[i].getBranchLength());
 231                                                 }else {
 232                                                         tempTotals[i] = 0.0;
 233                                                 }
 234                                         }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
 235                                         }else { //if no, your tempTotal is your childrens temp totals + your branch length
 236                                                 tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength());
 237                                         }
 238                                         //cout << "temptotal = "<< tempTotals[i] << endl;
 239                                 }
 240
 241                         }
 242         //cout << UniqueBL << '\t' << totalBL << endl;
 243                         UW = (UniqueBL / totalBL);
 244
 245                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 246
 247                         results[count] = UW;
 248                         count++;
 249
 250                         //report progress
 251                         if((count % twentyPercent) == 0) {      float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
 252                 }
 253
 254                 //report progress
 255                 if((count % twentyPercent) != 0) {      float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine();       }
 256
 257                 return results;
 258         }
 259         catch(exception& e) {
 260                 m->errorOut(e, "Unweighted", "driver");
 261                 exit(1);
 262         }
 263 }
 264 /**************************************************************************************************/
 265
 266 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
 267  try {
 268                 globaldata = GlobalData::getInstance();
 269                 processors = p;
 270                 outputDir = o;
 271
 272
 273                 //if the users enters no groups then give them the score of all groups
 274                 int numGroups = globaldata->Groups.size();
 275
 276                 //calculate number of comparsions
 277                 int numComp = 0;
 278                 vector< vector<string> > namesOfGroupCombos;
 279                 for (int r=0; r<numGroups; r++) {
 280                         for (int l = 0; l < r; l++) {
 281                                 numComp++;
 282                                 vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
 283                                 namesOfGroupCombos.push_back(groups);
 284                         }
 285                 }
 286
 287                 if (numComp != 1) {
 288                         vector<string> groups;
 289                         if (numGroups == 0) {
 290                                 //get score for all users groups
 291                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 292                                         if (tmap->namesOfGroups[i] != "xxx") {
 293                                                 groups.push_back(tmap->namesOfGroups[i]);
 294                                         }
 295                                 }
 296                                 namesOfGroupCombos.push_back(groups);
 297                         }else {
 298                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 299                                         groups.push_back(globaldata->Groups[i]);
 300                                 }
 301                                 namesOfGroupCombos.push_back(groups);
 302                         }
 303                 }
 304
 305                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 306                         if(processors == 1){
 307                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 308                         }else{
 309                                 int numPairs = namesOfGroupCombos.size();
 310
 311                                 int numPairsPerProcessor = numPairs / processors;
 312
 313                                 for (int i = 0; i < processors; i++) {
 314                                         int startPos = i * numPairsPerProcessor;
 315                                         if(i == processors - 1){
 316                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
 317                                         }
 318                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
 319                                 }
 320
 321                                 data = createProcesses(t, namesOfGroupCombos, true);
 322
 323                                 lines.clear();
 324                         }
 325                 #else
 326                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 327                 #endif
 328
 329                 return data;
 330         }
 331         catch(exception& e) {
 332                 m->errorOut(e, "Unweighted", "getValues");
 333                 exit(1);
 334         }
 335 }
 336 /**************************************************************************************************/
 337
 338 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
 339         try {
 340 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 341                 int process = 1;
 342                 vector<int> processIDS;
 343
 344                 EstOutput results;
 345
 346                 //loop through and create all the processes you want
 347                 while (process != processors) {
 348                         int pid = fork();
 349
 350                         if (pid > 0) {
 351                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 352                                 process++;
 353                         }else if (pid == 0){
 354                                 EstOutput myresults;
 355                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
 356
 357                                 if (m->control_pressed) { exit(0); }
 358
 359                                 //pass numSeqs to parent
 360                                 ofstream out;
 361                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 362                                 m->openOutputFile(tempFile, out);
 363                                 out << myresults.size() << endl;
 364                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 365                                 out.close();
 366
 367                                 exit(0);
 368                         }else {
 369                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 370                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 371                                 exit(0);
 372                         }
 373                 }
 374
 375                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
 376
 377                 //force parent to wait until all the processes are done
 378                 for (int i=0;i<(processors-1);i++) {
 379                         int temp = processIDS[i];
 380                         wait(&temp);
 381                 }
 382
 383                 if (m->control_pressed) { return results; }
 384
 385                 //get data created by processes
 386                 for (int i=0;i<(processors-1);i++) {
 387                         ifstream in;
 388                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 389                         m->openInputFile(s, in);
 390
 391                         //get quantiles
 392                         if (!in.eof()) {
 393                                 int num;
 394                                 in >> num; m->gobble(in);
 395
 396                                 if (m->control_pressed) { break; }
 397
 398                                 double w;
 399                                 for (int j = 0; j < num; j++) {
 400                                         in >> w;
 401                                         results.push_back(w);
 402                                 }
 403                                 m->gobble(in);
 404                         }
 405                         in.close();
 406                         remove(s.c_str());
 407                 }
 408
 409                 return results;
 410 #endif
 411         }
 412         catch(exception& e) {
 413                 m->errorOut(e, "Unweighted", "createProcesses");
 414                 exit(1);
 415         }
 416 }
 417 /**************************************************************************************************/
 418 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
 419  try {
 420
 421                 EstOutput results; results.resize(num);
 422
 423                 int count = 0;
 424                 int numLeaves = t->getNumLeaves();
 425
 426                 Tree* copyTree = new Tree;
 427
 428                 for (int h = start; h < (start+num); h++) {
 429
 430                         if (m->control_pressed) { return results; }
 431
 432                         //copy random tree passed in
 433                         copyTree->getCopy(t);
 434
 435                         //swap labels in the groups you want to compare
 436                         copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
 437
 438                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 439                         double totalBL = 0.00;  //all branch lengths
 440                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 441                         map<int, double> tempTotals; //maps node to total Branch Length
 442                         map<int, int> nodePcountSize; //maps node to pcountSize
 443
 444                         for(int i=0;i<copyTree->getNumNodes();i++){
 445
 446                                 if (m->control_pressed) {  return data; }
 447
 448                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 449                                 //pcountSize = 2, not unique to one group
 450                                 //pcountSize = 1, unique to one group
 451
 452                                 int pcountSize = 0;
 453                                 for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 454                                         map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 455                                         if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 456                                 }
 457
 458                                 nodePcountSize[i] = pcountSize;
 459
 460                                 if (pcountSize == 0) { }
 461                                 else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());      }
 462
 463                                 //if you are a leaf from a users group add to total
 464                                 if (i < numLeaves) {
 465                                         if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) {
 466                                                 totalBL += abs(copyTree->tree[i].getBranchLength());
 467                                         }
 468                                         tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
 469                                 }else{ //if you are not a leaf
 470                                         //do both your chidren have have descendants from the users groups?
 471                                         int lc = copyTree->tree[i].getLChild();
 472                                         int rc = copyTree->tree[i].getRChild();
 473
 474                                         //if yes, add your childrens tempTotals
 475                                         if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 476                                                 totalBL += tempTotals[lc] + tempTotals[rc];
 477
 478                                                 if (copyTree->tree[i].getBranchLength() != -1) {
 479                                                         tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
 480                                                 }else {
 481                                                         tempTotals[i] = 0.0;
 482                                                 }
 483                                         }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
 484                                         }else { //if no, your tempTotal is your childrens temp totals + your branch length
 485                                                 tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength());
 486                                         }
 487
 488                                 }
 489
 490                         }
 491
 492                         UW = (UniqueBL / totalBL);
 493
 494                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 495
 496                         results[count] = UW;
 497                         count++;
 498
 499                 }
 500
 501                 delete copyTree;
 502
 503                 return results;
 504         }
 505         catch(exception& e) {
 506                 m->errorOut(e, "Unweighted", "driver");
 507                 exit(1);
 508         }
 509 }
 510 /**************************************************************************************************/
 511
 512