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                 int num = 0;
  91                 vector<int> processIDS;
  92
  93                 EstOutput results;
  94
  95                 //loop through and create all the processes you want
  96                 while (process != processors) {
  97                         int pid = fork();
  98
  99                         if (pid > 0) {
 100                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 101                                 process++;
 102                         }else if (pid == 0){
 103                                 EstOutput myresults;
 104                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
 105
 106                                 if (m->control_pressed) { exit(0); }
 107
 108                                 m->mothurOut("Merging results."); m->mothurOutEndLine();
 109
 110                                 //pass numSeqs to parent
 111                                 ofstream out;
 112                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 113                                 m->openOutputFile(tempFile, out);
 114                                 out << myresults.size() << endl;
 115                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 116                                 out.close();
 117
 118                                 exit(0);
 119                         }else {
 120                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 121                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 122                                 exit(0);
 123                         }
 124                 }
 125
 126                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
 127
 128                 //force parent to wait until all the processes are done
 129                 for (int i=0;i<(processors-1);i++) {
 130                         int temp = processIDS[i];
 131                         wait(&temp);
 132                 }
 133
 134                 if (m->control_pressed) { return results; }
 135
 136                 //get data created by processes
 137                 for (int i=0;i<(processors-1);i++) {
 138                         ifstream in;
 139                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 140                         m->openInputFile(s, in);
 141
 142                         //get quantiles
 143                         if (!in.eof()) {
 144                                 int num;
 145                                 in >> num; m->gobble(in);
 146
 147                                 if (m->control_pressed) { break; }
 148
 149                                 double w;
 150                                 for (int j = 0; j < num; j++) {
 151                                         in >> w;
 152                                         results.push_back(w);
 153                                 }
 154                                 m->gobble(in);
 155                         }
 156                         in.close();
 157                         remove(s.c_str());
 158                 }
 159
 160                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 161
 162                 return results;
 163 #endif
 164         }
 165         catch(exception& e) {
 166                 m->errorOut(e, "Unweighted", "createProcesses");
 167                 exit(1);
 168         }
 169 }
 170 /**************************************************************************************************/
 171 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
 172  try {
 173
 174                 EstOutput results; results.resize(num);
 175
 176                 int count = 0;
 177                 int numLeaves = t->getNumLeaves();
 178                 int total = num;
 179                 int twentyPercent = (total * 0.20);
 180                 if (twentyPercent == 0) { twentyPercent = 1; }
 181
 182
 183                 for (int h = start; h < (start+num); h++) {
 184         //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;
 185                         if (m->control_pressed) { return results; }
 186
 187                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 188                         double totalBL = 0.00;  //all branch lengths
 189                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 190                         map<int, double> tempTotals; //maps node to total Branch Length
 191                         map<int, int> nodePcountSize; //maps node to pcountSize
 192                         map<int, int>::iterator itCount;
 193
 194                         for(int i=0;i<t->getNumNodes();i++){
 195
 196                                 if (m->control_pressed) {  return data; }
 197
 198                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 199                                 //pcountSize = 2, not unique to one group
 200                                 //pcountSize = 1, unique to one group
 201
 202                                 int pcountSize = 0;
 203                                 for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 204                                         map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 205                                         if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 206                                 }
 207
 208                                 nodePcountSize[i] = pcountSize;
 209
 210                                 //cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t';
 211                                 if (pcountSize == 0) { }
 212                                 else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength()); }
 213
 214                                 //if you are a leaf from a users group add to total
 215                                 if (i < numLeaves) {
 216                                         if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {
 217                                         //cout << "added to total" << endl;
 218                                                 totalBL += abs(t->tree[i].getBranchLength());
 219                                         }
 220                                         tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
 221                                 }else{ //if you are not a leaf
 222                                         //do both your chidren have have descendants from the users groups?
 223                                         int lc = t->tree[i].getLChild();
 224                                         int rc = t->tree[i].getRChild();
 225
 226                                         //if yes, add your childrens tempTotals
 227                                         if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 228                                                 totalBL += tempTotals[lc] + tempTotals[rc];
 229                                                 //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
 230                                                 if (t->tree[i].getBranchLength() != -1) {
 231                                                         tempTotals[i] = abs(t->tree[i].getBranchLength());
 232                                                 }else {
 233                                                         tempTotals[i] = 0.0;
 234                                                 }
 235                                         }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
 236                                         }else { //if no, your tempTotal is your childrens temp totals + your branch length
 237                                                 tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength());
 238                                         }
 239                                         //cout << "temptotal = "<< tempTotals[i] << endl;
 240                                 }
 241
 242                         }
 243         //cout << UniqueBL << '\t' << totalBL << endl;
 244                         UW = (UniqueBL / totalBL);
 245
 246                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 247
 248                         results[count] = UW;
 249                         count++;
 250
 251                         //report progress
 252                         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();       }
 253                 }
 254
 255                 //report progress
 256                 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();       }
 257
 258                 return results;
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "Unweighted", "driver");
 262                 exit(1);
 263         }
 264 }
 265 /**************************************************************************************************/
 266
 267 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
 268  try {
 269                 globaldata = GlobalData::getInstance();
 270                 processors = p;
 271                 outputDir = o;
 272
 273
 274                 //if the users enters no groups then give them the score of all groups
 275                 int numGroups = globaldata->Groups.size();
 276
 277                 //calculate number of comparsions
 278                 int numComp = 0;
 279                 vector< vector<string> > namesOfGroupCombos;
 280                 for (int r=0; r<numGroups; r++) {
 281                         for (int l = 0; l < r; l++) {
 282                                 numComp++;
 283                                 vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
 284                                 namesOfGroupCombos.push_back(groups);
 285                         }
 286                 }
 287
 288                 if (numComp != 1) {
 289                         vector<string> groups;
 290                         if (numGroups == 0) {
 291                                 //get score for all users groups
 292                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 293                                         if (tmap->namesOfGroups[i] != "xxx") {
 294                                                 groups.push_back(tmap->namesOfGroups[i]);
 295                                         }
 296                                 }
 297                                 namesOfGroupCombos.push_back(groups);
 298                         }else {
 299                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 300                                         groups.push_back(globaldata->Groups[i]);
 301                                 }
 302                                 namesOfGroupCombos.push_back(groups);
 303                         }
 304                 }
 305
 306                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 307                         if(processors == 1){
 308                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 309                         }else{
 310                                 int numPairs = namesOfGroupCombos.size();
 311
 312                                 int numPairsPerProcessor = numPairs / processors;
 313
 314                                 for (int i = 0; i < processors; i++) {
 315                                         int startPos = i * numPairsPerProcessor;
 316                                         if(i == processors - 1){
 317                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
 318                                         }
 319                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
 320                                 }
 321
 322                                 data = createProcesses(t, namesOfGroupCombos, true);
 323
 324                                 lines.clear();
 325                         }
 326                 #else
 327                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 328                 #endif
 329
 330                 return data;
 331         }
 332         catch(exception& e) {
 333                 m->errorOut(e, "Unweighted", "getValues");
 334                 exit(1);
 335         }
 336 }
 337 /**************************************************************************************************/
 338
 339 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
 340         try {
 341 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 342                 int process = 1;
 343                 int num = 0;
 344                 vector<int> processIDS;
 345
 346                 EstOutput results;
 347
 348                 //loop through and create all the processes you want
 349                 while (process != processors) {
 350                         int pid = fork();
 351
 352                         if (pid > 0) {
 353                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 354                                 process++;
 355                         }else if (pid == 0){
 356                                 EstOutput myresults;
 357                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
 358
 359                                 if (m->control_pressed) { exit(0); }
 360
 361                                 //pass numSeqs to parent
 362                                 ofstream out;
 363                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 364                                 m->openOutputFile(tempFile, out);
 365                                 out << myresults.size() << endl;
 366                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 367                                 out.close();
 368
 369                                 exit(0);
 370                         }else {
 371                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 372                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 373                                 exit(0);
 374                         }
 375                 }
 376
 377                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
 378
 379                 //force parent to wait until all the processes are done
 380                 for (int i=0;i<(processors-1);i++) {
 381                         int temp = processIDS[i];
 382                         wait(&temp);
 383                 }
 384
 385                 if (m->control_pressed) { return results; }
 386
 387                 //get data created by processes
 388                 for (int i=0;i<(processors-1);i++) {
 389                         ifstream in;
 390                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 391                         m->openInputFile(s, in);
 392
 393                         //get quantiles
 394                         if (!in.eof()) {
 395                                 int num;
 396                                 in >> num; m->gobble(in);
 397
 398                                 if (m->control_pressed) { break; }
 399
 400                                 double w;
 401                                 for (int j = 0; j < num; j++) {
 402                                         in >> w;
 403                                         results.push_back(w);
 404                                 }
 405                                 m->gobble(in);
 406                         }
 407                         in.close();
 408                         remove(s.c_str());
 409                 }
 410
 411                 return results;
 412 #endif
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "Unweighted", "createProcesses");
 416                 exit(1);
 417         }
 418 }
 419 /**************************************************************************************************/
 420 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
 421  try {
 422
 423                 EstOutput results; results.resize(num);
 424
 425                 int count = 0;
 426                 int total = num;
 427                 int twentyPercent = (total * 0.20);
 428                 int numLeaves = t->getNumLeaves();
 429
 430                 Tree* copyTree = new Tree;
 431
 432                 for (int h = start; h < (start+num); h++) {
 433
 434                         if (m->control_pressed) { return results; }
 435
 436                         //copy random tree passed in
 437                         copyTree->getCopy(t);
 438
 439                         //swap labels in the groups you want to compare
 440                         copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
 441
 442                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 443                         double totalBL = 0.00;  //all branch lengths
 444                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 445                         map<int, double> tempTotals; //maps node to total Branch Length
 446                         map<int, int> nodePcountSize; //maps node to pcountSize
 447
 448                         for(int i=0;i<copyTree->getNumNodes();i++){
 449
 450                                 if (m->control_pressed) {  return data; }
 451
 452                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 453                                 //pcountSize = 2, not unique to one group
 454                                 //pcountSize = 1, unique to one group
 455
 456                                 int pcountSize = 0;
 457                                 for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 458                                         map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 459                                         if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 460                                 }
 461
 462                                 nodePcountSize[i] = pcountSize;
 463
 464                                 if (pcountSize == 0) { }
 465                                 else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());      }
 466
 467                                 //if you are a leaf from a users group add to total
 468                                 if (i < numLeaves) {
 469                                         if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) {
 470                                                 totalBL += abs(copyTree->tree[i].getBranchLength());
 471                                         }
 472                                         tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
 473                                 }else{ //if you are not a leaf
 474                                         //do both your chidren have have descendants from the users groups?
 475                                         int lc = copyTree->tree[i].getLChild();
 476                                         int rc = copyTree->tree[i].getRChild();
 477
 478                                         //if yes, add your childrens tempTotals
 479                                         if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 480                                                 totalBL += tempTotals[lc] + tempTotals[rc];
 481
 482                                                 if (copyTree->tree[i].getBranchLength() != -1) {
 483                                                         tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
 484                                                 }else {
 485                                                         tempTotals[i] = 0.0;
 486                                                 }
 487                                         }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
 488                                         }else { //if no, your tempTotal is your childrens temp totals + your branch length
 489                                                 tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength());
 490                                         }
 491
 492                                 }
 493
 494                         }
 495
 496                         UW = (UniqueBL / totalBL);
 497
 498                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 499
 500                         results[count] = UW;
 501                         count++;
 502
 503                 }
 504
 505                 delete copyTree;
 506
 507                 return results;
 508         }
 509         catch(exception& e) {
 510                 m->errorOut(e, "Unweighted", "driver");
 511                 exit(1);
 512         }
 513 }
 514 /**************************************************************************************************/
 515
 516