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