distancecommand.cpp

   1 /*
   2  *  distancecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/7/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "distancecommand.h"
  11 #include "ignoregaps.h"
  12 #include "eachgapdist.h"
  13 #include "eachgapignore.h"
  14 #include "onegapdist.h"
  15 #include "onegapignore.h"
  16
  17 //**********************************************************************************************************************
  18
  19 DistanceCommand::DistanceCommand(string option) {
  20         try {
  21                 abort = false;
  22                 Estimators.clear();
  23
  24                 //allow user to run help
  25                 if(option == "help") { help(); abort = true; }
  26
  27                 else {
  28                         //valid paramters for this command
  29                         string Array[] =  {"fasta", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir"};
  30                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  31
  32                         OptionParser parser(option);
  33                         map<string, string> parameters = parser.getParameters();
  34
  35                         ValidParameters validParameter;
  36                         map<string, string>::iterator it2;
  37
  38                         //check to make sure all parameters are valid for command
  39                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
  40                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
  41                         }
  42
  43                         //if the user changes the input directory command factory will send this info to us in the output parameter
  44                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  45                         if (inputDir == "not found"){   inputDir = "";          }
  46                         else {
  47                                 string path;
  48                                 it2 = parameters.find("fasta");
  49                                 //user has given a template file
  50                                 if(it2 != parameters.end()){
  51                                         path = hasPath(it2->second);
  52                                         //if the user has not given a path then, add inputdir. else leave path alone.
  53                                         if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
  54                                 }
  55                         }
  56
  57                         //check for required parameters
  58                         fastafile = validParameter.validFile(parameters, "fasta", true);
  59                         if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the dist.seqs command."); m->mothurOutEndLine(); abort = true; }
  60                         else if (fastafile == "not open") { abort = true; }
  61                         else{
  62                                 ifstream inFASTA;
  63                                 openInputFile(fastafile, inFASTA);
  64                                 alignDB = SequenceDB(inFASTA);
  65                                 inFASTA.close();
  66                         }
  67
  68                         //if the user changes the output directory command factory will send this info to us in the output parameter
  69                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  70                                 outputDir = "";
  71                                 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
  72                         }
  73
  74                         //check for optional parameter and set defaults
  75                         // ...at some point should added some additional type checking...
  76                         calc = validParameter.validFile(parameters, "calc", false);
  77                         if (calc == "not found") { calc = "onegap";  }
  78                         else {
  79                                  if (calc == "default")  {  calc = "onegap";  }
  80                         }
  81                         splitAtDash(calc, Estimators);
  82
  83                         string temp;
  84                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
  85                         convert(temp, countends);
  86
  87                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
  88                         convert(temp, cutoff);
  89
  90                         temp = validParameter.validFile(parameters, "processors", false);       if(temp == "not found"){        temp = "1"; }
  91                         convert(temp, processors);
  92
  93                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
  94
  95                         if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
  96
  97                         ValidCalculators validCalculator;
  98
  99                         if (isTrue(countends) == true) {
 100                                 for (int i=0; i<Estimators.size(); i++) {
 101                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 102                                                 if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 103                                                 else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 104                                                 else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 105                                         }
 106                                 }
 107                         }else {
 108                                 for (int i=0; i<Estimators.size(); i++) {
 109                                         if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 110                                                 if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 111                                                 else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 112                                                 else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 113                                         }
 114                                 }
 115                         }
 116
 117                 }
 118
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 122                 exit(1);
 123         }
 124 }
 125
 126 //**********************************************************************************************************************
 127
 128 DistanceCommand::~DistanceCommand(){
 129
 130         for(int i=0;i<lines.size();i++){
 131                 delete lines[i];
 132         }
 133
 134 }
 135
 136 //**********************************************************************************************************************
 137
 138 void DistanceCommand::help(){
 139         try {
 140                 m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
 141                 m->mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors.  \n");
 142                 m->mothurOut("The fasta parameter is required.\n");
 143                 m->mothurOut("The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
 144                 m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n");
 145                 m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
 146                 m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
 147                 m->mothurOut("The processors parameter allows you to specify number of processors to use.  The default is 1.\n");
 148                 m->mothurOut("The dist.seqs command should be in the following format: \n");
 149                 m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
 150                 m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
 151                 m->mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "DistanceCommand", "help");
 155                 exit(1);
 156         }
 157 }
 158 //**********************************************************************************************************************
 159
 160 int DistanceCommand::execute(){
 161         try {
 162
 163                 if (abort == true) { return 0; }
 164
 165                 int startTime = time(NULL);
 166
 167                 int numSeqs = alignDB.getNumSeqs();
 168                 cutoff += 0.005;
 169
 170                 string outputFile;
 171
 172                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 173                         outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
 174                         remove(outputFile.c_str());
 175
 176                         //output numSeqs to phylip formatted dist file
 177                 }else if (output == "column") { //user wants column format
 178                         outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
 179                         remove(outputFile.c_str());
 180                 }else { //assume square
 181                         outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "square.dist";
 182                         remove(outputFile.c_str());
 183                 }
 184
 185
 186 #ifdef USE_MPI
 187
 188                 int pid, start, end;
 189                 int tag = 2001;
 190
 191                 MPI_Status status;
 192                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 193                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 194
 195                 //each process gets where it should start and stop in the file
 196                 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 197                 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 198
 199                 if (output != "lt") {
 200                         MPI_File outMPI;
 201                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 202
 203                         //char* filename = new char[outputFile.length()];
 204                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 205
 206                         char filename[1024];
 207                         strcpy(filename, outputFile.c_str());
 208
 209                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 210                         //delete filename;
 211
 212                         if (pid == 0) { //you are the root process
 213
 214                                 //do your part
 215                                 string outputMyPart;
 216                                 driverMPI(start, end, outMPI, cutoff);
 217
 218                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 219
 220                                 //wait on chidren
 221                                 for(int i = 1; i < processors; i++) {
 222                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 223
 224                                         char buf[4];
 225                                         MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 226                                 }
 227                         }else { //you are a child process
 228                                 //do your part
 229                                 driverMPI(start, end, outMPI, cutoff);
 230
 231                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 232
 233                                 char buf[4];
 234                                 strcpy(buf, "done");
 235                                 //tell parent you are done.
 236                                 MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 237                         }
 238
 239                         MPI_File_close(&outMPI);
 240
 241                 }else { //lower triangle format
 242                         if (pid == 0) { //you are the root process
 243
 244                                 //do your part
 245                                 string outputMyPart;
 246                                 long mySize;
 247                                 driverMPI(start, end, outputFile, mySize);
 248
 249                                 if (m->control_pressed) {  delete distCalculator;  return 0; }
 250
 251                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 252                                 MPI_File outMPI;
 253                                 MPI_File inMPI;
 254
 255                                 //char* filename = new char[outputFile.length()];
 256                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 257
 258                                 char filename[1024];
 259                                 strcpy(filename, outputFile.c_str());
 260
 261                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 262                                 //delete filename;
 263
 264                                 //wait on chidren
 265                                 for(int b = 1; b < processors; b++) {
 266                                         long fileSize;
 267
 268                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 269
 270                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 271
 272                                         string outTemp = outputFile + toString(b) + ".temp";
 273
 274                                         char* buf = new char[outTemp.length()];
 275                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 276
 277                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 278                                         delete buf;
 279
 280                                         int count = 0;
 281                                         while (count < fileSize) {
 282                                                 char buf2[1];
 283                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 284                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 285                                                 count += 1;
 286                                         }
 287
 288                                         MPI_File_close(&inMPI); //deleted on close
 289                                 }
 290
 291                                 MPI_File_close(&outMPI);
 292                         }else { //you are a child process
 293                                 //do your part
 294                                 long size;
 295                                 driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
 296
 297                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 298
 299                                 //tell parent you are done.
 300                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 301                         }
 302                 }
 303 #else
 304
 305         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 306                 //if you don't need to fork anything
 307                 if(processors == 1){
 308                         driver(0, numSeqs, outputFile, cutoff);
 309                 }else{ //you have multiple processors
 310
 311                         for (int i = 0; i < processors; i++) {
 312                                 lines.push_back(new linePair());
 313                                 lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
 314                                 lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 315                         }
 316
 317                         createProcesses(outputFile);
 318
 319                         map<int, int>::iterator it = processIDS.begin();
 320                         rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
 321                         it++;
 322
 323                         //append and remove temp files
 324                         for (; it != processIDS.end(); it++) {
 325                                 appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
 326                                 remove((outputFile + toString(it->second) + ".temp").c_str());
 327                         }
 328                 }
 329         #else
 330                 ifstream inFASTA;
 331                 driver(0, numSeqs, outputFile, cutoff);
 332         #endif
 333
 334 #endif
 335                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 336
 337                 #ifdef USE_MPI
 338                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 339
 340                         if (pid == 0) { //only one process should output to screen
 341                 #endif
 342
 343                 if (output == "square") {  convertMatrix(outputFile); }
 344
 345                 ifstream fileHandle;
 346                 fileHandle.open(outputFile.c_str());
 347                 if(fileHandle) {
 348                         gobble(fileHandle);
 349                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 350                 }
 351
 352
 353                 #ifdef USE_MPI
 354                         }
 355                 #endif
 356
 357                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 358
 359                 delete distCalculator;
 360
 361                 m->mothurOutEndLine();
 362                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 363                 m->mothurOut(outputFile); m->mothurOutEndLine();
 364                 m->mothurOutEndLine();
 365                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 366                 return 0;
 367
 368         }
 369         catch(exception& e) {
 370                 m->errorOut(e, "DistanceCommand", "execute");
 371                 exit(1);
 372         }
 373 }
 374 /**************************************************************************************************/
 375 void DistanceCommand::createProcesses(string filename) {
 376         try {
 377 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 378                 int process = 0;
 379                 processIDS.clear();
 380
 381                 //loop through and create all the processes you want
 382                 while (process != processors) {
 383                         int pid = fork();
 384
 385                         if (pid > 0) {
 386                                 processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
 387                                 process++;
 388                         }else if (pid == 0){
 389                                 driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
 390                                 exit(0);
 391                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 392                 }
 393
 394                 //force parent to wait until all the processes are done
 395                 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
 396                         int temp = it->second;
 397                         wait(&temp);
 398                 }
 399 #endif
 400         }
 401         catch(exception& e) {
 402                 m->errorOut(e, "DistanceCommand", "createProcesses");
 403                 exit(1);
 404         }
 405 }
 406
 407 /**************************************************************************************************/
 408 /////// need to fix to work with calcs and sequencedb
 409 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 410         try {
 411
 412                 int startTime = time(NULL);
 413
 414                 //column file
 415                 ofstream outFile(dFileName.c_str(), ios::trunc);
 416                 outFile.setf(ios::fixed, ios::showpoint);
 417                 outFile << setprecision(4);
 418
 419                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 420
 421                 for(int i=startLine;i<endLine;i++){
 422                         if(output == "lt")      {
 423                                 string name = alignDB.get(i).getName();
 424                                 if (name.length() < 10) { //pad with spaces to make compatible
 425                                         while (name.length() < 10) {  name += " ";  }
 426                                 }
 427                                 outFile << name << '\t';
 428                         }
 429                         for(int j=0;j<i;j++){
 430
 431                                 if (m->control_pressed) { outFile.close(); return 0;  }
 432
 433                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 434                                 double dist = distCalculator->getDist();
 435
 436                                 if(dist <= cutoff){
 437                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 438                                 }
 439                                 if (output == "lt") {  outFile << dist << '\t'; }
 440
 441                                 if (output == "square") { //make a square column you can convert to square phylip
 442                                         outFile << alignDB.get(i).getName() << '\t' << alignDB.get(j).getName() << '\t' << dist << endl;
 443                                         outFile << alignDB.get(j).getName() << '\t' << alignDB.get(i).getName() << '\t' << dist << endl;
 444                                 }
 445
 446                         }
 447
 448                         if (output == "lt") { outFile << endl; }
 449
 450                         if(i % 100 == 0){
 451                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 452                         }
 453
 454                 }
 455                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 456
 457                 outFile.close();
 458
 459                 return 1;
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "DistanceCommand", "driver");
 463                 exit(1);
 464         }
 465 }
 466 #ifdef USE_MPI
 467 /**************************************************************************************************/
 468 /////// need to fix to work with calcs and sequencedb
 469 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 470         try {
 471                 MPI_Status status;
 472                 int startTime = time(NULL);
 473
 474                 string outputString = "";
 475
 476                 for(int i=startLine;i<endLine;i++){
 477
 478                         for(int j=0;j<i;j++){
 479
 480                                 if (m->control_pressed) {  return 0;  }
 481
 482                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 483                                 double dist = distCalculator->getDist();
 484
 485                                 if(dist <= cutoff){
 486                                         if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
 487                                 }
 488
 489                                 if (output == "square") { //make a square column you can convert to square phylip
 490                                         outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 491                                         outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
 492                                 }
 493                         }
 494
 495                         if(i % 100 == 0){
 496                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 497                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 498                         }
 499
 500
 501                         //send results to parent
 502                         int length = outputString.length();
 503
 504                         char* buf = new char[length];
 505                         memcpy(buf, outputString.c_str(), length);
 506
 507                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 508                         outputString = "";
 509                         delete buf;
 510
 511                 }
 512
 513                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 514                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 515                 return 1;
 516         }
 517         catch(exception& e) {
 518                 m->errorOut(e, "DistanceCommand", "driverMPI");
 519                 exit(1);
 520         }
 521 }
 522 /**************************************************************************************************/
 523 /////// need to fix to work with calcs and sequencedb
 524 int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
 525         try {
 526                 MPI_Status status;
 527
 528                 MPI_File outMPI;
 529                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 530
 531                 //char* filename = new char[file.length()];
 532                 //memcpy(filename, file.c_str(), file.length());
 533
 534                 char filename[1024];
 535                 strcpy(filename, file.c_str());
 536
 537                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 538                 //delete filename;
 539
 540                 int startTime = time(NULL);
 541
 542                 string outputString = "";
 543                 size = 0;
 544
 545                 if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 546
 547                 for(int i=startLine;i<endLine;i++){
 548                         if(output == "lt")      {
 549                                 string name = alignDB.get(i).getName();
 550                                 if (name.length() < 10) { //pad with spaces to make compatible
 551                                         while (name.length() < 10) {  name += " ";  }
 552                                 }
 553                                 outputString += name + "\t";
 554                         }
 555                         for(int j=0;j<i;j++){
 556
 557                                 if (m->control_pressed) {  return 0;  }
 558
 559                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 560                                 double dist = distCalculator->getDist();
 561
 562                                 if (output == "lt") {  outputString += toString(dist) + "\t"; }
 563                         }
 564
 565                         if (output == "lt") { outputString += "\n"; }
 566
 567
 568                         if(i % 100 == 0){
 569                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 570                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 571                         }
 572
 573
 574                         //send results to parent
 575                         int length = outputString.length();
 576                         char* buf = new char[length];
 577                         memcpy(buf, outputString.c_str(), length);
 578
 579                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 580                         size += outputString.length();
 581                         outputString = "";
 582                         delete buf;
 583                 }
 584
 585                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 586                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 587                 MPI_File_close(&outMPI);
 588
 589                 return 1;
 590         }
 591         catch(exception& e) {
 592                 m->errorOut(e, "DistanceCommand", "driverMPI");
 593                 exit(1);
 594         }
 595 }
 596 #endif
 597 /**************************************************************************************************/
 598 int DistanceCommand::convertMatrix(string outputFile) {
 599         try{
 600
 601                 //sort file by first column so the distances for each row are together
 602                 string outfile = getRootName(outputFile) + "sorted.dist.temp";
 603
 604                 //use the unix sort
 605                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 606                         string command = "sort -n " + outputFile + " -o " + outfile;
 607                         system(command.c_str());
 608                 #else //sort using windows sort
 609                         string command = "sort " + outputFile + " /O " + outfile;
 610                         system(command.c_str());
 611                 #endif
 612
 613
 614                 //output to new file distance for each row and save positions in file where new row begins
 615                 ifstream in;
 616                 openInputFile(outfile, in);
 617
 618                 ofstream out;
 619                 openOutputFile(outputFile, out);
 620
 621                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 622
 623                 out << alignDB.getNumSeqs() << endl;
 624
 625                 //get first currentRow
 626                 string first, currentRow, second;
 627                 float dist;
 628                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 629                 map<string, float>::iterator it;
 630
 631                 in >> first;
 632                 currentRow = first;
 633
 634                 rowDists[first] = 0.00; //distance to yourself is 0.0
 635
 636                 in.seekg(0);
 637                 //openInputFile(outfile, in);
 638
 639                 while(!in.eof()) {
 640                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 641
 642                         in >> first >> second >> dist; gobble(in);
 643
 644                         if (first != currentRow) {
 645                                 //print out last row
 646                                 out << currentRow << '\t'; //print name
 647
 648                                 //print dists
 649                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 650                                         out << it->second << '\t';
 651                                 }
 652                                 out << endl;
 653
 654                                 //start new row
 655                                 currentRow = first;
 656                                 rowDists.clear();
 657                                 rowDists[first] = 0.00;
 658                                 rowDists[second] = dist;
 659                         }else{
 660                                 rowDists[second] = dist;
 661                         }
 662                 }
 663                 //print out last row
 664                 out << currentRow << '\t'; //print name
 665
 666                 //print dists
 667                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 668                         out << it->second << '\t';
 669                 }
 670                 out << endl;
 671
 672                 in.close();
 673                 out.close();
 674
 675                 remove(outfile.c_str());
 676
 677                 return 1;
 678
 679         }
 680         catch(exception& e) {
 681                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 682                 exit(1);
 683         }
 684 }
 685 /**************************************************************************************************/
 686 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 687         try{
 688
 689                 //sort file by first column so the distances for each row are together
 690                 string outfile = getRootName(outputFile) + "sorted.dist.temp";
 691
 692                 //use the unix sort
 693                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 694                         string command = "sort -n " + outputFile + " -o " + outfile;
 695                         system(command.c_str());
 696                 #else //sort using windows sort
 697                         string command = "sort " + outputFile + " /O " + outfile;
 698                         system(command.c_str());
 699                 #endif
 700
 701
 702                 //output to new file distance for each row and save positions in file where new row begins
 703                 ifstream in;
 704                 openInputFile(outfile, in);
 705
 706                 ofstream out;
 707                 openOutputFile(outputFile, out);
 708
 709                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 710
 711                 out << alignDB.getNumSeqs() << endl;
 712
 713                 //get first currentRow
 714                 string first, currentRow, second;
 715                 float dist;
 716                 int i, j;
 717                 i = 0; j = 0;
 718                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 719                 map<string, float>::iterator it;
 720
 721                 in >> first;
 722                 currentRow = first;
 723
 724                 rowDists[first] = 0.00; //distance to yourself is 0.0
 725
 726                 in.seekg(0);
 727                 //openInputFile(outfile, in);
 728
 729                 while(!in.eof()) {
 730                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 731
 732                         in >> first >> second >> dist; gobble(in);
 733
 734                         if (first != currentRow) {
 735                                 //print out last row
 736                                 out << currentRow << '\t'; //print name
 737
 738                                 //print dists
 739                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 740                                         if (j >= i) { break; }
 741                                         out << it->second << '\t';
 742                                         j++;
 743                                 }
 744                                 out << endl;
 745
 746                                 //start new row
 747                                 currentRow = first;
 748                                 rowDists.clear();
 749                                 rowDists[first] = 0.00;
 750                                 rowDists[second] = dist;
 751                                 j = 0;
 752                                 i++;
 753                         }else{
 754                                 rowDists[second] = dist;
 755                         }
 756                 }
 757                 //print out last row
 758                 out << currentRow << '\t'; //print name
 759
 760                 //print dists
 761                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 762                         out << it->second << '\t';
 763                 }
 764                 out << endl;
 765
 766                 in.close();
 767                 out.close();
 768
 769                 remove(outfile.c_str());
 770
 771                 return 1;
 772
 773         }
 774         catch(exception& e) {
 775                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
 776                 exit(1);
 777         }
 778 }
 779 /**************************************************************************************************
 780 void DistanceCommand::appendFiles(string temp, string filename) {
 781         try{
 782                 ofstream output;
 783                 ifstream input;
 784
 785                 //open output file in append mode
 786                 openOutputFileAppend(filename, output);
 787                 openInputFile(temp, input);
 788
 789                 while(char c = input.get()){
 790                         if(input.eof())         {       break;                  }
 791                         else                            {       output << c;    }
 792                 }
 793
 794                 input.close();
 795                 output.close();
 796         }
 797         catch(exception& e) {
 798                 m->errorOut(e, "DistanceCommand", "appendFiles");
 799                 exit(1);
 800         }
 801 }
 802 /**************************************************************************************************/
 803
 804