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