splitmatrix.cpp

   1 /*
   2  *  splitmatrix.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/19/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "splitmatrix.h"
  11 #include "phylotree.h"
  12 #include "distancecommand.h"
  13 #include "seqsummarycommand.h"
  14
  15 /***********************************************************************/
  16
  17 SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, string t, bool l){
  18         m = MothurOut::getInstance();
  19         distFile = distfile;
  20         cutoff = c;
  21         namefile = name;
  22         method = t;
  23         taxFile = tax;
  24         large = l;
  25 }
  26 /***********************************************************************/
  27
  28 SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, string output){
  29         m = MothurOut::getInstance();
  30         fastafile = ffile;
  31         namefile = name;
  32         taxFile = tax;
  33         cutoff = c;  //tax level cutoff
  34         distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
  35         method = t;
  36         processors = p;
  37         outputDir = output;
  38 }
  39
  40 /***********************************************************************/
  41
  42 int SplitMatrix::split(){
  43         try {
  44
  45                 if (method == "distance") {
  46                         splitDistance();
  47                 }else if ((method == "classify") || (method == "fasta")) {
  48                         splitClassify();
  49                 }else {
  50                         m->mothurOut("Unknown splitting method, aborting split."); m->mothurOutEndLine();
  51                         map<string, string> temp;
  52                         temp[distFile] = namefile;
  53                         dists.push_back(temp);
  54                 }
  55
  56                 return 0;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "SplitMatrix", "split");
  60                 exit(1);
  61         }
  62 }
  63 /***********************************************************************/
  64 int SplitMatrix::splitDistance(){
  65         try {
  66
  67                 if (large)      { splitDistanceLarge(); }
  68                 else            { splitDistanceRAM();   }
  69
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "SplitMatrix", "splitDistance");
  73                 exit(1);
  74         }
  75 }
  76
  77 /***********************************************************************/
  78 int SplitMatrix::splitClassify(){
  79         try {
  80                 cutoff = int(cutoff);
  81
  82                 map<string, int> seqGroup;
  83                 map<string, int>::iterator it;
  84                 map<string, int>::iterator it2;
  85
  86                 int numGroups = 0;
  87
  88                 //build tree from users taxonomy file
  89                 PhyloTree* phylo = new PhyloTree();
  90
  91                 ifstream in;
  92                 m->openInputFile(taxFile, in);
  93
  94                 //read in users taxonomy file and add sequences to tree
  95                 string seqname, tax;
  96                 while(!in.eof()){
  97                         in >> seqname >> tax; m->gobble(in);
  98                         phylo->addSeqToTree(seqname, tax);
  99                 }
 100                 in.close();
 101
 102                 phylo->assignHeirarchyIDs(0);
 103
 104                 //make sure the cutoff is not greater than maxlevel
 105                 if (cutoff > phylo->getMaxLevel()) { m->mothurOut("splitcutoff is greater than the longest taxonomy, using " + toString(phylo->getMaxLevel())); m->mothurOutEndLine(); cutoff = phylo->getMaxLevel(); }
 106
 107                 //for each node in tree
 108                 for (int i = 0; i < phylo->getNumNodes(); i++) {
 109
 110                         //is this node within the cutoff
 111                         TaxNode taxon = phylo->get(i);
 112
 113                         if (taxon.level == cutoff) {//if yes, then create group containing this nodes sequences
 114                                 if (taxon.accessions.size() > 1) { //if this taxon just has one seq its a singleton
 115                                         for (int j = 0; j < taxon.accessions.size(); j++) {
 116                                                 seqGroup[taxon.accessions[j]] = numGroups;
 117                                         }
 118                                         numGroups++;
 119                                 }
 120                         }
 121                 }
 122
 123                 delete phylo;
 124
 125                 if (method == "classify") {
 126                         splitDistanceFileByTax(seqGroup, numGroups);
 127                 }else {
 128                         createDistanceFilesFromTax(seqGroup, numGroups);
 129                 }
 130
 131                 return 0;
 132
 133         }
 134         catch(exception& e) {
 135                 m->errorOut(e, "SplitMatrix", "splitClassify");
 136                 exit(1);
 137         }
 138 }
 139 /***********************************************************************/
 140 int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numGroups){
 141         try {
 142                 map<string, int> copyGroups = seqGroup;
 143                 map<string, int>::iterator it;
 144                 set<string> names;
 145
 146                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 147                         remove((fastafile + "." + toString(i) + ".temp").c_str());
 148                 }
 149
 150                 ifstream in;
 151                 m->openInputFile(fastafile, in);
 152
 153                 //parse fastafile
 154                 ofstream outFile;
 155                 while (!in.eof()) {
 156                         Sequence query(in); m->gobble(in);
 157                         if (query.getName() != "") {
 158
 159                                 it = seqGroup.find(query.getName());
 160
 161                                 //save names in case no namefile is given
 162                                 if (namefile == "") {  names.insert(query.getName()); }
 163
 164                                 if (it != seqGroup.end()) { //not singleton
 165                                         m->openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
 166                                         query.printSequence(outFile);
 167                                         outFile.close();
 168
 169                                         copyGroups.erase(query.getName());
 170                                 }
 171                         }
 172                 }
 173                 in.close();
 174
 175                 //warn about sequence in groups that are not in fasta file
 176                 for(it = copyGroups.begin(); it != copyGroups.end(); it++) {
 177                         m->mothurOut("ERROR: " + it->first + " is missing from your fastafile. This could happen if your taxonomy file is not unique and your fastafile is, or it could indicate and error."); m->mothurOutEndLine();
 178                         exit(1);
 179                 }
 180
 181                 copyGroups.clear();
 182
 183                 //process each distance file
 184                 for (int i = 0; i < numGroups; i++) {
 185
 186                         string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
 187
 188                         Command* command = new DistanceCommand(options);
 189
 190                         command->execute();
 191                         delete command;
 192
 193                         remove((fastafile + "." + toString(i) + ".temp").c_str());
 194
 195                         //remove old names files just in case
 196                         remove((namefile + "." + toString(i) + ".temp").c_str());
 197                 }
 198
 199                 singleton = namefile + ".extra.temp";
 200                 ofstream remainingNames;
 201                 m->openOutputFile(singleton, remainingNames);
 202
 203                 bool wroteExtra = false;
 204
 205                 ifstream bigNameFile;
 206                 m->openInputFile(namefile, bigNameFile);
 207
 208                 string name, nameList;
 209                 while(!bigNameFile.eof()){
 210                         bigNameFile >> name >> nameList;  m->gobble(bigNameFile);
 211
 212                         //did this sequence get assigned a group
 213                         it = seqGroup.find(name);
 214
 215                         if (it != seqGroup.end()) {
 216                                 m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
 217                                 outFile << name << '\t' << nameList << endl;
 218                                 outFile.close();
 219                         }else{
 220                                 wroteExtra = true;
 221                                 remainingNames << name << '\t' << nameList << endl;
 222                         }
 223                 }
 224                 bigNameFile.close();
 225
 226                 for(int i=0;i<numGroups;i++){
 227                         string tempNameFile = namefile + "." + toString(i) + ".temp";
 228                         if (outputDir == "") { outputDir = m->hasPath(fastafile); }
 229                         string tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
 230
 231                         //if there are valid distances
 232                         ifstream fileHandle;
 233                         fileHandle.open(tempDistFile.c_str());
 234                         if(fileHandle)  {
 235                                 m->gobble(fileHandle);
 236                                 if (!fileHandle.eof()) {  //check for blank file - this could occur if all dists in group are above cutoff
 237                                         map<string, string> temp;
 238                                         temp[tempDistFile] = tempNameFile;
 239                                         dists.push_back(temp);
 240                                 }else {
 241                                         ifstream in;
 242                                         m->openInputFile(tempNameFile, in);
 243
 244                                         while(!in.eof()) {
 245                                                 in >> name >> nameList;  m->gobble(in);
 246                                                 wroteExtra = true;
 247                                                 remainingNames << name << '\t' << nameList << endl;
 248                                         }
 249                                         in.close();
 250                                         remove(tempNameFile.c_str());
 251                                 }
 252                         }
 253                         fileHandle.close();
 254                 }
 255
 256                 remainingNames.close();
 257                 if (!wroteExtra) {
 258                         remove(singleton.c_str());
 259                         singleton = "none";
 260                 }
 261
 262                 if (m->control_pressed)  {  for (int i = 0; i < dists.size(); i++) { remove((dists[i].begin()->first).c_str()); remove((dists[i].begin()->second).c_str()); } dists.clear(); }
 263
 264                 return 0;
 265         }
 266         catch(exception& e) {
 267                 m->errorOut(e, "SplitMatrix", "createDistanceFilesFromTax");
 268                 exit(1);
 269         }
 270 }
 271 /***********************************************************************/
 272 int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroups){
 273         try {
 274                 map<string, int>::iterator it;
 275                 map<string, int>::iterator it2;
 276
 277                 ifstream dFile;
 278                 m->openInputFile(distFile, dFile);
 279                 ofstream outFile;
 280
 281                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 282                         remove((distFile + "." + toString(i) + ".temp").c_str());
 283                 }
 284
 285                 //for buffering the io to improve speed
 286                  //allow for 10 dists to be stored, then output.
 287                 vector<string> outputs;  outputs.resize(numGroups, "");
 288                 vector<int> numOutputs;  numOutputs.resize(numGroups, 0);
 289
 290                 //you can have a group made, but their may be no distances in the file for this group if the taxonomy file and distance file don't match
 291                 //this can occur if we have converted the phylip to column, since we reduce the size at that step by using the cutoff value
 292                 vector<bool> validDistances;   validDistances.resize(numGroups, false);
 293
 294                 //for each distance
 295                 while(dFile){
 296                         string seqA, seqB;
 297                         float dist;
 298
 299                         if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { remove((distFile + "." + toString(i) + ".temp").c_str());        } }
 300
 301                         dFile >> seqA >> seqB >> dist;  m->gobble(dFile);
 302
 303                         //if both sequences are in the same group then they are within the cutoff
 304                         it = seqGroup.find(seqA);
 305                         it2 = seqGroup.find(seqB);
 306
 307                         if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons
 308                                 if (it->second == it2->second) { //they are from the same group so add the distance
 309                                         if (numOutputs[it->second] > 30) {
 310                                                 m->openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
 311                                                 outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl;
 312                                                 outFile.close();
 313                                                 outputs[it->second] = "";
 314                                                 numOutputs[it->second] = 0;
 315                                                 validDistances[it->second] = true;
 316                                         }else{
 317                                                 outputs[it->second] += seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 318                                                 numOutputs[it->second]++;
 319                                         }
 320                                 }
 321                         }
 322                 }
 323                 dFile.close();
 324
 325                 for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
 326                         remove((namefile + "." + toString(i) + ".temp").c_str());
 327
 328                         //write out any remaining buffers
 329                         if (numOutputs[i] > 0) {
 330                                 m->openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
 331                                 outFile << outputs[i];
 332                                 outFile.close();
 333                                 outputs[i] = "";
 334                                 numOutputs[i] = 0;
 335                                 validDistances[i] = true;
 336                         }
 337                 }
 338
 339                 ifstream bigNameFile;
 340                 m->openInputFile(namefile, bigNameFile);
 341
 342                 singleton = namefile + ".extra.temp";
 343                 ofstream remainingNames;
 344                 m->openOutputFile(singleton, remainingNames);
 345
 346                 bool wroteExtra = false;
 347
 348                 string name, nameList;
 349                 while(!bigNameFile.eof()){
 350                         bigNameFile >> name >> nameList;  m->gobble(bigNameFile);
 351
 352                         //did this sequence get assigned a group
 353                         it = seqGroup.find(name);
 354
 355                         if (it != seqGroup.end()) {
 356                                 m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
 357                                 outFile << name << '\t' << nameList << endl;
 358                                 outFile.close();
 359                         }else{
 360                                 wroteExtra = true;
 361                                 remainingNames << name << '\t' << nameList << endl;
 362                         }
 363                 }
 364                 bigNameFile.close();
 365
 366                 for(int i=0;i<numGroups;i++){
 367                         string tempNameFile = namefile + "." + toString(i) + ".temp";
 368                         string tempDistFile = distFile + "." + toString(i) + ".temp";
 369
 370                         //if there are valid distances
 371                         if (validDistances[i]) {
 372                                 map<string, string> temp;
 373                                 temp[tempDistFile] = tempNameFile;
 374                                 dists.push_back(temp);
 375                         }else{
 376                                 ifstream in;
 377                                 m->openInputFile(tempNameFile, in);
 378
 379                                 while(!in.eof()) {
 380                                         in >> name >> nameList;  m->gobble(in);
 381                                         wroteExtra = true;
 382                                         remainingNames << name << '\t' << nameList << endl;
 383                                 }
 384                                 in.close();
 385                                 remove(tempNameFile.c_str());
 386                         }
 387                 }
 388
 389                 remainingNames.close();
 390
 391                 if (!wroteExtra) {
 392                         remove(singleton.c_str());
 393                         singleton = "none";
 394                 }
 395
 396                 if (m->control_pressed)  {
 397                         for (int i = 0; i < dists.size(); i++) {
 398                                 remove((dists[i].begin()->first).c_str());
 399                                 remove((dists[i].begin()->second).c_str());
 400                         }
 401                         dists.clear();
 402                 }
 403
 404                 return 0;
 405         }
 406         catch(exception& e) {
 407                 m->errorOut(e, "SplitMatrix", "splitDistanceFileByTax");
 408                 exit(1);
 409         }
 410 }
 411 /***********************************************************************/
 412 int SplitMatrix::splitDistanceLarge(){
 413         try {
 414                 vector<set<string> > groups;
 415
 416                 //for buffering the io to improve speed
 417                  //allow for 30 dists to be stored, then output.
 418                 vector<string> outputs;
 419                 vector<int> numOutputs;
 420                 vector<bool> wroteOutPut;
 421
 422                 int numGroups = 0;
 423
 424                 ofstream outFile;
 425                 ifstream dFile;
 426                 m->openInputFile(distFile, dFile);
 427
 428                 while(dFile){
 429                         string seqA, seqB;
 430                         float dist;
 431
 432                         dFile >> seqA >> seqB >> dist;
 433
 434                         if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  remove((distFile + "." + toString(i) + ".temp").c_str()); }  } return 0; }
 435
 436                         if(dist < cutoff){
 437                                 //cout << "in cutoff: " << dist << endl;
 438                                 int groupIDA = -1;
 439                                 int groupIDB = -1;
 440                                 int groupID = -1;
 441
 442                                 for(int i=0;i<numGroups;i++){
 443                                         set<string>::iterator aIt = groups[i].find(seqA);
 444                                         set<string>::iterator bIt = groups[i].find(seqB);
 445
 446                                         if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
 447                                                 groups[i].insert(seqB);
 448                                                 groupIDA = i;
 449                                                 groupID = groupIDA;
 450
 451                                                 //cout << "in aIt: " << groupID << endl;
 452         //                                      break;
 453                                         }
 454                                         else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
 455                                                 groups[i].insert(seqA);
 456                                                 groupIDB = i;
 457                                                 groupID = groupIDB;
 458
 459                                         //      cout << "in bIt: " << groupID << endl;
 460         //                                      break;
 461                                         }
 462
 463                                         if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
 464                                                 if(groupIDA < groupIDB){
 465                                                 //      cout << "A: " << groupIDA << "\t" << groupIDB << endl;
 466                                                         groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
 467                                                         groups[groupIDB].clear();
 468                                                         groupID = groupIDA;
 469                                                 }
 470                                                 else{
 471                                                 //      cout << "B: " << groupIDA << "\t" << groupIDB << endl;
 472                                                         groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
 473                                                         groups[groupIDA].clear();
 474                                                         groupID = groupIDB;
 475                                                 }
 476                                                 break;
 477                                         }
 478                                 }
 479
 480         //windows is gonna gag on the reuse of outFile, will need to make it local...
 481
 482                                 if(groupIDA == -1 && groupIDB == -1){ //we need a new group
 483                                         set<string> newGroup;
 484                                         newGroup.insert(seqA);
 485                                         newGroup.insert(seqB);
 486                                         groups.push_back(newGroup);
 487
 488                                         string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
 489                                         outputs.push_back(tempOut);
 490                                         numOutputs.push_back(1);
 491                                         wroteOutPut.push_back(false);
 492
 493                                         numGroups++;
 494                                 }
 495                                 else{
 496                                         string fileName = distFile + "." + toString(groupID) + ".temp";
 497
 498                                         //have we reached the max buffer size
 499                                         if (numOutputs[groupID] > 60) { //write out sequence
 500                                                 outFile.open(fileName.c_str(), ios::app);
 501                                                 outFile << outputs[groupID] << seqA << '\t' << seqB << '\t' << dist << endl;
 502                                                 outFile.close();
 503
 504                                                 outputs[groupID] = "";
 505                                                 numOutputs[groupID] = 0;
 506                                                 wroteOutPut[groupID] = true;
 507                                         }else {
 508                                                 outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 509                                                 numOutputs[groupID]++;
 510                                         }
 511
 512                                         if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
 513                                                 string row, column, distance;
 514                                                 if(groupIDA<groupIDB){
 515
 516                                                         //merge memory
 517                                                         numOutputs[groupID] += numOutputs[groupIDB];
 518                                                         outputs[groupID] += outputs[groupIDB];
 519
 520                                                         outputs[groupIDB] = "";
 521                                                         numOutputs[groupIDB] = 0;
 522
 523                                                         //if groupB is written to file it is above buffer size so read and write to new merged file
 524                                                         if (wroteOutPut[groupIDB]) {
 525                                                                 string fileName2 = distFile + "." + toString(groupIDB) + ".temp";
 526                                                                 ifstream fileB(fileName2.c_str(), ios::ate);
 527
 528                                                                 outFile.open(fileName.c_str(), ios::app);
 529
 530                                                                 long size;
 531                                                                 char* memblock;
 532
 533                                                                 size = fileB.tellg();
 534
 535                                                                 fileB.seekg (0, ios::beg);
 536
 537                                                                 int numRead = size / 1024;
 538                                                                 int lastRead = size % 1024;
 539
 540                                                                 for (int i = 0; i < numRead; i++) {
 541
 542                                                                         memblock = new char [1024];
 543
 544                                                                         fileB.read (memblock, 1024);
 545
 546                                                                         string temp = memblock;
 547                                                                         outFile << temp.substr(0, 1024);
 548
 549                                                                         delete memblock;
 550                                                                 }
 551
 552                                                                 memblock = new char [lastRead];
 553
 554                                                                 fileB.read (memblock, lastRead);
 555
 556                                                                 //not sure why but it will read more than lastRead char...??
 557                                                                 string temp = memblock;
 558                                                                 outFile << temp.substr(0, lastRead);
 559                                                                 delete memblock;
 560
 561                                                                 fileB.close();
 562                                                                 remove(fileName2.c_str());
 563
 564                                                                 //write out the merged memory
 565                                                                 if (numOutputs[groupID] > 60) {
 566                                                                         outFile << outputs[groupID];
 567                                                                         outputs[groupID] = "";
 568                                                                         numOutputs[groupID] = 0;
 569                                                                 }
 570
 571                                                                 outFile.close();
 572
 573                                                                 wroteOutPut[groupID] = true;
 574                                                                 wroteOutPut[groupIDB] = false;
 575                                                         }else{ } //just merge b's memory with a's memory
 576                                                 }
 577                                                 else{
 578                                                         numOutputs[groupID] += numOutputs[groupIDA];
 579                                                         outputs[groupID] += outputs[groupIDA];
 580
 581                                                         outputs[groupIDA] = "";
 582                                                         numOutputs[groupIDA] = 0;
 583
 584                                                         if (wroteOutPut[groupIDA]) {
 585                                                                 string fileName2 = distFile + "." + toString(groupIDA) + ".temp";
 586                                                                 ifstream fileB(fileName2.c_str(), ios::ate);
 587
 588                                                                 outFile.open(fileName.c_str(), ios::app);
 589
 590                                                                 long size;
 591                                                                 char* memblock;
 592
 593                                                                 size = fileB.tellg();
 594
 595                                                                 fileB.seekg (0, ios::beg);
 596
 597                                                                 int numRead = size / 1024;
 598                                                                 int lastRead = size % 1024;
 599
 600                                                                 for (int i = 0; i < numRead; i++) {
 601
 602                                                                         memblock = new char [1024];
 603
 604                                                                         fileB.read (memblock, 1024);
 605                                                                         string temp = memblock;
 606                                                                         outFile << temp.substr(0, 1024);
 607
 608                                                                         delete memblock;
 609                                                                 }
 610
 611                                                                 memblock = new char [lastRead];
 612
 613                                                                 fileB.read (memblock, lastRead);
 614
 615                                                                 //not sure why but it will read more than lastRead char...??
 616                                                                 string temp = memblock;
 617                                                                 outFile << temp.substr(0, lastRead);
 618
 619                                                                 delete memblock;
 620
 621                                                                 fileB.close();
 622                                                                 remove(fileName2.c_str());
 623
 624                                                                 //write out the merged memory
 625                                                                 if (numOutputs[groupID] > 60) {
 626                                                                         outFile << outputs[groupID];
 627                                                                         outputs[groupID] = "";
 628                                                                         numOutputs[groupID] = 0;
 629                                                                 }
 630
 631                                                                 outFile.close();
 632
 633                                                                 wroteOutPut[groupID] = true;
 634                                                                 wroteOutPut[groupIDA] = false;
 635                                                         }else { } //just merge memory
 636                                                 }
 637                                         }
 638                                 }
 639                         }
 640                         m->gobble(dFile);
 641                 }
 642                 dFile.close();
 643
 644                 for (int i = 0; i < numGroups; i++) {
 645                         if (numOutputs[i] > 0) {
 646                                 string fileName = distFile + "." + toString(i) + ".temp";
 647                                 outFile.open(fileName.c_str(), ios::app);
 648                                 outFile << outputs[i];
 649                                 outFile.close();
 650                         }
 651                 }
 652
 653                 splitNames(groups);
 654
 655                 return 0;
 656         }
 657         catch(exception& e) {
 658                 m->errorOut(e, "SplitMatrix", "splitDistanceLarge");
 659                 exit(1);
 660         }
 661 }
 662 //********************************************************************************************************************
 663 int SplitMatrix::splitNames(vector<set<string> >& groups){
 664         try {
 665                 int numGroups = groups.size();
 666
 667                 ifstream bigNameFile(namefile.c_str());
 668                 if(!bigNameFile){
 669                         cerr << "Error: We can't open the name file\n";
 670                         exit(1);
 671                 }
 672
 673                 map<string, string> nameMap;
 674                 string name, nameList;
 675                 while(bigNameFile){
 676                         bigNameFile >> name >> nameList;
 677                         nameMap[name] = nameList;
 678                         m->gobble(bigNameFile);
 679                 }
 680                 bigNameFile.close();
 681
 682                 for(int i=0;i<numGroups;i++){  //parse names file to match distance files
 683                         int numSeqsInGroup = groups[i].size();
 684
 685                         if(numSeqsInGroup > 0){
 686                                 string fileName = namefile + "." + toString(i) + ".temp";
 687                                 ofstream smallNameFile(fileName.c_str(), ios::ate);
 688
 689                                 for(set<string>::iterator gIt=groups[i].begin();gIt!=groups[i].end();gIt++){
 690                                         map<string,string>::iterator nIt = nameMap.find(*gIt);
 691                                         if (nIt != nameMap.end()) {
 692                                                 smallNameFile << nIt->first << '\t' << nIt->second << endl;
 693                                                 nameMap.erase(nIt);
 694                                         }else{
 695                                                 m->mothurOut((*gIt) + " is in your distance file and not in your namefile.  Please correct."); m->mothurOutEndLine(); exit(1);
 696                                         }
 697                                 }
 698                                 smallNameFile.close();
 699                         }
 700                 }
 701
 702                 //names of singletons
 703                 if (nameMap.size() != 0) {
 704                         singleton = namefile + ".extra.temp";
 705                         ofstream remainingNames(singleton.c_str(), ios::ate);
 706                         for(map<string,string>::iterator nIt=nameMap.begin();nIt!=nameMap.end();nIt++){
 707                                 remainingNames << nIt->first << '\t' << nIt->second << endl;
 708                         }
 709                         remainingNames.close();
 710                 }else { singleton = "none"; }
 711
 712                 for(int i=0;i<numGroups;i++){
 713                         if(groups[i].size() > 0){
 714                                 string tempNameFile = namefile + "." + toString(i) + ".temp";
 715                                 string tempDistFile = distFile + "." + toString(i) + ".temp";
 716
 717                                 map<string, string> temp;
 718                                 temp[tempDistFile] = tempNameFile;
 719                                 dists.push_back(temp);
 720                         }
 721                 }
 722
 723                 if (m->control_pressed)  {
 724                         for (int i = 0; i < dists.size(); i++) {
 725                                 remove((dists[i].begin()->first).c_str());
 726                                 remove((dists[i].begin()->second).c_str());
 727                         }
 728                         dists.clear();
 729                 }
 730
 731                 return 0;
 732         }
 733         catch(exception& e) {
 734                 m->errorOut(e, "SplitMatrix", "splitNames");
 735                 exit(1);
 736         }
 737 }
 738 //********************************************************************************************************************
 739 int SplitMatrix::splitDistanceRAM(){
 740         try {
 741                 vector<set<string> > groups;
 742                 vector<string> outputs;
 743
 744                 int numGroups = 0;
 745
 746                 ifstream dFile;
 747                 m->openInputFile(distFile, dFile);
 748
 749                 while(dFile){
 750                         string seqA, seqB;
 751                         float dist;
 752
 753                         dFile >> seqA >> seqB >> dist;
 754
 755                         if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){       if(groups[i].size() > 0){  remove((distFile + "." + toString(i) + ".temp").c_str()); }  } return 0; }
 756
 757                         if(dist < cutoff){
 758                                 //cout << "in cutoff: " << dist << endl;
 759                                 int groupIDA = -1;
 760                                 int groupIDB = -1;
 761                                 int groupID = -1;
 762
 763                                 for(int i=0;i<numGroups;i++){
 764                                         set<string>::iterator aIt = groups[i].find(seqA);
 765                                         set<string>::iterator bIt = groups[i].find(seqB);
 766
 767                                         if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
 768                                                 groups[i].insert(seqB);
 769                                                 groupIDA = i;
 770                                                 groupID = groupIDA;
 771
 772                                                 //cout << "in aIt: " << groupID << endl;
 773         //                                      break;
 774                                         }
 775                                         else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
 776                                                 groups[i].insert(seqA);
 777                                                 groupIDB = i;
 778                                                 groupID = groupIDB;
 779
 780                                         //      cout << "in bIt: " << groupID << endl;
 781         //                                      break;
 782                                         }
 783
 784                                         if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
 785                                                 if(groupIDA < groupIDB){
 786                                                 //      cout << "A: " << groupIDA << "\t" << groupIDB << endl;
 787                                                         groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
 788                                                         groups[groupIDB].clear();
 789                                                         groupID = groupIDA;
 790                                                 }
 791                                                 else{
 792                                                 //      cout << "B: " << groupIDA << "\t" << groupIDB << endl;
 793                                                         groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
 794                                                         groups[groupIDA].clear();
 795                                                         groupID = groupIDB;
 796                                                 }
 797                                                 break;
 798                                         }
 799                                 }
 800
 801         //windows is gonna gag on the reuse of outFile, will need to make it local...
 802
 803                                 if(groupIDA == -1 && groupIDB == -1){ //we need a new group
 804                                         set<string> newGroup;
 805                                         newGroup.insert(seqA);
 806                                         newGroup.insert(seqB);
 807                                         groups.push_back(newGroup);
 808
 809                                         string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
 810                                         outputs.push_back(tempOut);
 811                                         numGroups++;
 812                                 }
 813                                 else{
 814
 815                                         outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
 816
 817                                         if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
 818                                                 string row, column, distance;
 819                                                 if(groupIDA<groupIDB){
 820                                                         //merge memory
 821                                                         outputs[groupID] += outputs[groupIDB];
 822                                                         outputs[groupIDB] = "";
 823                                                 }else{
 824                                                         outputs[groupID] += outputs[groupIDA];
 825                                                         outputs[groupIDA] = "";
 826                                                 }
 827                                         }
 828                                 }
 829                         }
 830                         m->gobble(dFile);
 831                 }
 832                 dFile.close();
 833
 834                 for (int i = 0; i < numGroups; i++) {
 835                         if (outputs[i] != "") {
 836                                 ofstream outFile;
 837                                 string fileName = distFile + "." + toString(i) + ".temp";
 838                                 outFile.open(fileName.c_str(), ios::ate);
 839                                 outFile << outputs[i];
 840                                 outFile.close();
 841                         }
 842                 }
 843
 844                 splitNames(groups);
 845
 846                 return 0;
 847         }
 848         catch(exception& e) {
 849                 m->errorOut(e, "SplitMatrix", "splitDistanceRAM");
 850                 exit(1);
 851         }
 852 }
 853 //********************************************************************************************************************
 854 //sorts biggest to smallest
 855 inline bool compareFileSizes(map<string, string> left, map<string, string> right){
 856
 857         FILE * pFile;
 858         long leftsize = 0;
 859
 860         //get num bytes in file
 861         string filename = left.begin()->first;
 862         pFile = fopen (filename.c_str(),"rb");
 863         string error = "Error opening " + filename;
 864         if (pFile==NULL) perror (error.c_str());
 865         else{
 866                 fseek (pFile, 0, SEEK_END);
 867                 leftsize=ftell (pFile);
 868                 fclose (pFile);
 869         }
 870
 871         FILE * pFile2;
 872         long rightsize = 0;
 873
 874         //get num bytes in file
 875         filename = right.begin()->first;
 876         pFile2 = fopen (filename.c_str(),"rb");
 877         error = "Error opening " + filename;
 878         if (pFile2==NULL) perror (error.c_str());
 879         else{
 880                 fseek (pFile2, 0, SEEK_END);
 881                 rightsize=ftell (pFile2);
 882                 fclose (pFile2);
 883         }
 884
 885         return (leftsize > rightsize);
 886 }
 887 /***********************************************************************/
 888 //returns map of distance files -> namefile sorted by distance file size
 889 vector< map< string, string> > SplitMatrix::getDistanceFiles(){
 890         try {
 891
 892                 sort(dists.begin(), dists.end(), compareFileSizes);
 893
 894                 return dists;
 895         }
 896         catch(exception& e) {
 897                 m->errorOut(e, "SplitMatrix", "getDistanceFiles");
 898                 exit(1);
 899         }
 900 }
 901 /***********************************************************************/
 902 SplitMatrix::~SplitMatrix(){}
 903 /***********************************************************************/
 904