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                                 data = createProcesses(t, namesOfGroupCombos);
  70                                 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                 vector<int> processIDS;
  90
  91                 EstOutput results;
  92
  93                 //loop through and create all the processes you want
  94                 while (process != processors) {
  95                         int pid = fork();
  96
  97                         if (pid > 0) {
  98                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
  99                                 process++;
 100                         }else if (pid == 0){
 101                                 EstOutput myresults;
 102                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
 103
 104                                 if (m->control_pressed) { exit(0); }
 105
 106                                 m->mothurOut("Merging results."); m->mothurOutEndLine();
 107
 108                                 //pass numSeqs to parent
 109                                 ofstream out;
 110                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 111                                 m->openOutputFile(tempFile, out);
 112                                 out << myresults.size() << endl;
 113                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 114                                 out.close();
 115
 116                                 exit(0);
 117                         }else {
 118                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 119                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 120                                 exit(0);
 121                         }
 122                 }
 123
 124                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
 125
 126                 //force parent to wait until all the processes are done
 127                 for (int i=0;i<(processors-1);i++) {
 128                         int temp = processIDS[i];
 129                         wait(&temp);
 130                 }
 131
 132                 if (m->control_pressed) { return results; }
 133
 134                 //get data created by processes
 135                 for (int i=0;i<(processors-1);i++) {
 136                         ifstream in;
 137                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 138                         m->openInputFile(s, in);
 139
 140                         //get quantiles
 141                         if (!in.eof()) {
 142                                 int num;
 143                                 in >> num; m->gobble(in);
 144
 145                                 if (m->control_pressed) { break; }
 146
 147                                 double w;
 148                                 for (int j = 0; j < num; j++) {
 149                                         in >> w;
 150                                         results.push_back(w);
 151                                 }
 152                                 m->gobble(in);
 153                         }
 154                         in.close();
 155                         remove(s.c_str());
 156                 }
 157
 158                 m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
 159
 160                 return results;
 161 #endif
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "Unweighted", "createProcesses");
 165                 exit(1);
 166         }
 167 }
 168 /**************************************************************************************************/
 169 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
 170  try {
 171
 172                 EstOutput results; results.resize(num);
 173
 174                 int count = 0;
 175                 int numLeaves = t->getNumLeaves();
 176                 int total = num;
 177                 int twentyPercent = (total * 0.20);
 178                 if (twentyPercent == 0) { twentyPercent = 1; }
 179
 180
 181                 for (int h = start; h < (start+num); h++) {
 182         //cout << namesOfGroupCombos[h][0] << '\t' << namesOfGroupCombos[h][1] << endl;
 183                         if (m->control_pressed) { return results; }
 184
 185                         double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 186                         double totalBL = 0.00;  //all branch lengths
 187                         double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
 188                         map<int, double> tempTotals; //maps node to total Branch Length
 189                         map<int, int> nodePcountSize; //maps node to pcountSize
 190                         map<int, int>::iterator itCount;
 191
 192                         for(int i=0;i<t->getNumNodes();i++){
 193
 194                                 if (m->control_pressed) {  return data; }
 195
 196                                 //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
 197                                 //pcountSize = 2, not unique to one group
 198                                 //pcountSize = 1, unique to one group
 199
 200                                 int pcountSize = 0;
 201                                 for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
 202                                         map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
 203                                         if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
 204                                 }
 205
 206                                 nodePcountSize[i] = pcountSize;
 207
 208                                 //cout << i << '\t' << t->tree[i].getName() << " br = " << abs(t->tree[i].getBranchLength()) << '\t';
 209                                 if (pcountSize == 0) { }
 210                                 else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength()); }
 211
 212                                 //if you are a leaf from a users group add to total
 213                                 if (i < numLeaves) {
 214                                         if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {
 215                                         //cout << "added to total" << endl;
 216                                                 totalBL += abs(t->tree[i].getBranchLength());
 217                                         }
 218                                         tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
 219                                 }else{ //if you are not a leaf
 220                                         //do both your chidren have have descendants from the users groups?
 221                                         int lc = t->tree[i].getLChild();
 222                                         int rc = t->tree[i].getRChild();
 223
 224                                         //if yes, add your childrens tempTotals
 225                                         if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 226                                                 totalBL += tempTotals[lc] + tempTotals[rc];
 227                                                 //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
 228                                                 if (t->tree[i].getBranchLength() != -1) {
 229                                                         tempTotals[i] = abs(t->tree[i].getBranchLength());
 230                                                 }else {
 231                                                         tempTotals[i] = 0.0;
 232                                                 }
 233                                         }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0;  //we don't care about you
 234                                         }else { //if no, your tempTotal is your childrens temp totals + your branch length
 235                                                 if (t->tree[i].getBranchLength() != -1) {
 236                                                         tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength());
 237                                                 }else {
 238                                                         tempTotals[i] = tempTotals[lc] + tempTotals[rc];
 239                                                 }
 240                                         }
 241                                         //cout << "temptotal = "<< tempTotals[i] << endl;
 242                                 }
 243
 244                         }
 245         //cout << UniqueBL << '\t' << totalBL << endl;
 246                         UW = (UniqueBL / totalBL);
 247
 248                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 249
 250                         results[count] = UW;
 251                         count++;
 252
 253                         //report progress
 254                         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();       }
 255                 }
 256
 257                 //report progress
 258                 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();       }
 259
 260                 return results;
 261         }
 262         catch(exception& e) {
 263                 m->errorOut(e, "Unweighted", "driver");
 264                 exit(1);
 265         }
 266 }
 267 /**************************************************************************************************/
 268
 269 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
 270  try {
 271                 globaldata = GlobalData::getInstance();
 272                 processors = p;
 273                 outputDir = o;
 274
 275
 276                 //if the users enters no groups then give them the score of all groups
 277                 int numGroups = globaldata->Groups.size();
 278
 279                 //calculate number of comparsions
 280                 int numComp = 0;
 281                 vector< vector<string> > namesOfGroupCombos;
 282                 for (int r=0; r<numGroups; r++) {
 283                         for (int l = 0; l < r; l++) {
 284                                 numComp++;
 285                                 vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
 286                                 namesOfGroupCombos.push_back(groups);
 287                         }
 288                 }
 289
 290                 if (numComp != 1) {
 291                         vector<string> groups;
 292                         if (numGroups == 0) {
 293                                 //get score for all users groups
 294                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 295                                         if (tmap->namesOfGroups[i] != "xxx") {
 296                                                 groups.push_back(tmap->namesOfGroups[i]);
 297                                         }
 298                                 }
 299                                 namesOfGroupCombos.push_back(groups);
 300                         }else {
 301                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 302                                         groups.push_back(globaldata->Groups[i]);
 303                                 }
 304                                 namesOfGroupCombos.push_back(groups);
 305                         }
 306                 }
 307
 308                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 309                         if(processors == 1){
 310                                 data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 311                         }else{
 312                                 int numPairs = namesOfGroupCombos.size();
 313
 314                                 int numPairsPerProcessor = numPairs / processors;
 315
 316                                 for (int i = 0; i < processors; i++) {
 317                                         int startPos = i * numPairsPerProcessor;
 318                                         if(i == processors - 1){
 319                                                 numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
 320                                         }
 321                                         lines.push_back(linePair(startPos, numPairsPerProcessor));
 322                                 }
 323
 324                                 data = createProcesses(t, namesOfGroupCombos, true);
 325
 326                                 lines.clear();
 327                         }
 328                 #else
 329                         data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
 330                 #endif
 331
 332                 return data;
 333         }
 334         catch(exception& e) {
 335                 m->errorOut(e, "Unweighted", "getValues");
 336                 exit(1);
 337         }
 338 }
 339 /**************************************************************************************************/
 340
 341 EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
 342         try {
 343 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 344                 int process = 1;
 345                 vector<int> processIDS;
 346
 347                 EstOutput results;
 348
 349                 //loop through and create all the processes you want
 350                 while (process != processors) {
 351                         int pid = fork();
 352
 353                         if (pid > 0) {
 354                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 355                                 process++;
 356                         }else if (pid == 0){
 357                                 EstOutput myresults;
 358                                 myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
 359
 360                                 if (m->control_pressed) { exit(0); }
 361
 362                                 //pass numSeqs to parent
 363                                 ofstream out;
 364                                 string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
 365                                 m->openOutputFile(tempFile, out);
 366                                 out << myresults.size() << endl;
 367                                 for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;
 368                                 out.close();
 369
 370                                 exit(0);
 371                         }else {
 372                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 373                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 374                                 exit(0);
 375                         }
 376                 }
 377
 378                 results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
 379
 380                 //force parent to wait until all the processes are done
 381                 for (int i=0;i<(processors-1);i++) {
 382                         int temp = processIDS[i];
 383                         wait(&temp);
 384                 }
 385
 386                 if (m->control_pressed) { return results; }
 387
 388                 //get data created by processes
 389                 for (int i=0;i<(processors-1);i++) {
 390                         ifstream in;
 391                         string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
 392                         m->openInputFile(s, in);
 393
 394                         //get quantiles
 395                         if (!in.eof()) {
 396                                 int num;
 397                                 in >> num; m->gobble(in);
 398
 399                                 if (m->control_pressed) { break; }
 400
 401                                 double w;
 402                                 for (int j = 0; j < num; j++) {
 403                                         in >> w;
 404
 405                                         results.push_back(w);
 406                                 }
 407                                 m->gobble(in);
 408                         }
 409                         in.close();
 410                         remove(s.c_str());
 411                 }
 412
 413                 return results;
 414 #endif
 415         }
 416         catch(exception& e) {
 417                 m->errorOut(e, "Unweighted", "createProcesses");
 418                 exit(1);
 419         }
 420 }
 421 /**************************************************************************************************/
 422 EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
 423  try {
 424
 425                 EstOutput results; results.resize(num);
 426
 427                 int count = 0;
 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                                                 if (t->tree[i].getBranchLength() != -1) {
 490                                                         tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength());
 491                                                 }else {
 492                                                         tempTotals[i] = tempTotals[lc] + tempTotals[rc];
 493                                                 }
 494                                         }
 495
 496                                 }
 497
 498                         }
 499
 500                         UW = (UniqueBL / totalBL);
 501
 502                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 503
 504                         results[count] = UW;
 505                         count++;
 506
 507                 }
 508
 509                 delete copyTree;
 510
 511                 return results;
 512         }
 513         catch(exception& e) {
 514                 m->errorOut(e, "Unweighted", "driver");
 515                 exit(1);
 516         }
 517 }
 518 /**************************************************************************************************/
 519
 520