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) { //read 1000 characters at a time
 282                                                 //send freqs
 283                                                 char buf2[1];
 284                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 285                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 286                                                 count += 1;
 287                                         }
 288
 289                                         MPI_File_close(&inMPI); //deleted on close
 290                                 }
 291
 292                                 MPI_File_close(&outMPI);
 293                         }else { //you are a child process
 294                                 //do your part
 295                                 long size;
 296                                 driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
 297
 298                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 299
 300                                 //tell parent you are done.
 301                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 302                         }
 303                 }
 304 #else
 305
 306         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 307                 //if you don't need to fork anything
 308                 if(processors == 1){
 309                         driver(0, numSeqs, outputFile, cutoff);
 310                 }else{ //you have multiple processors
 311
 312                         for (int i = 0; i < processors; i++) {
 313                                 lines.push_back(new linePair());
 314                                 lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
 315                                 lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 316                         }
 317
 318                         createProcesses(outputFile);
 319
 320                         map<int, int>::iterator it = processIDS.begin();
 321                         rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
 322                         it++;
 323
 324                         //append and remove temp files
 325                         for (; it != processIDS.end(); it++) {
 326                                 appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
 327                                 remove((outputFile + toString(it->second) + ".temp").c_str());
 328                         }
 329                 }
 330         #else
 331                 ifstream inFASTA;
 332                 driver(0, numSeqs, outputFile, cutoff);
 333         #endif
 334
 335 #endif
 336                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 337
 338                 #ifdef USE_MPI
 339                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 340
 341                         if (pid == 0) { //only one process should output to screen
 342                 #endif
 343
 344                 if (output == "square") {  convertMatrix(outputFile); }
 345
 346                 #ifdef USE_MPI
 347                         }
 348                 #endif
 349
 350                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 351
 352                 delete distCalculator;
 353
 354                 m->mothurOutEndLine();
 355                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 356                 m->mothurOut(outputFile); m->mothurOutEndLine();
 357                 m->mothurOutEndLine();
 358                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 359                 return 0;
 360
 361         }
 362         catch(exception& e) {
 363                 m->errorOut(e, "DistanceCommand", "execute");
 364                 exit(1);
 365         }
 366 }
 367 /**************************************************************************************************/
 368 void DistanceCommand::createProcesses(string filename) {
 369         try {
 370 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 371                 int process = 0;
 372                 processIDS.clear();
 373
 374                 //loop through and create all the processes you want
 375                 while (process != processors) {
 376                         int pid = fork();
 377
 378                         if (pid > 0) {
 379                                 processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
 380                                 process++;
 381                         }else if (pid == 0){
 382                                 driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
 383                                 exit(0);
 384                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 385                 }
 386
 387                 //force parent to wait until all the processes are done
 388                 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
 389                         int temp = it->second;
 390                         wait(&temp);
 391                 }
 392 #endif
 393         }
 394         catch(exception& e) {
 395                 m->errorOut(e, "DistanceCommand", "createProcesses");
 396                 exit(1);
 397         }
 398 }
 399
 400 /**************************************************************************************************/
 401 /////// need to fix to work with calcs and sequencedb
 402 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 403         try {
 404
 405                 int startTime = time(NULL);
 406
 407                 //column file
 408                 ofstream outFile(dFileName.c_str(), ios::trunc);
 409                 outFile.setf(ios::fixed, ios::showpoint);
 410                 outFile << setprecision(4);
 411
 412                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 413
 414                 for(int i=startLine;i<endLine;i++){
 415                         if(output == "lt")      {
 416                                 string name = alignDB.get(i).getName();
 417                                 if (name.length() < 10) { //pad with spaces to make compatible
 418                                         while (name.length() < 10) {  name += " ";  }
 419                                 }
 420                                 outFile << name << '\t';
 421                         }
 422                         for(int j=0;j<i;j++){
 423
 424                                 if (m->control_pressed) { outFile.close(); return 0;  }
 425
 426                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 427                                 double dist = distCalculator->getDist();
 428
 429                                 if(dist <= cutoff){
 430                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 431                                 }
 432                                 if (output == "lt") {  outFile << dist << '\t'; }
 433
 434                                 if (output == "square") { //make a square column you can convert to square phylip
 435                                         outFile << alignDB.get(i).getName() << '\t' << alignDB.get(j).getName() << '\t' << dist << endl;
 436                                         outFile << alignDB.get(j).getName() << '\t' << alignDB.get(i).getName() << '\t' << dist << endl;
 437                                 }
 438
 439                         }
 440
 441                         if (output == "lt") { outFile << endl; }
 442
 443                         if(i % 100 == 0){
 444                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 445                         }
 446
 447                 }
 448                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 449
 450                 outFile.close();
 451
 452                 return 1;
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "DistanceCommand", "driver");
 456                 exit(1);
 457         }
 458 }
 459 #ifdef USE_MPI
 460 /**************************************************************************************************/
 461 /////// need to fix to work with calcs and sequencedb
 462 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 463         try {
 464                 MPI_Status status;
 465                 int startTime = time(NULL);
 466
 467                 string outputString = "";
 468
 469                 for(int i=startLine;i<endLine;i++){
 470
 471                         for(int j=0;j<i;j++){
 472
 473                                 if (m->control_pressed) {  return 0;  }
 474
 475                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 476                                 double dist = distCalculator->getDist();
 477
 478                                 if(dist <= cutoff){
 479                                         if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
 480                                 }
 481
 482                                 if (output == "square") { //make a square column you can convert to square phylip
 483                                         outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 484                                         outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
 485                                 }
 486                         }
 487
 488                         if(i % 100 == 0){
 489                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 490                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 491                         }
 492
 493
 494                         //send results to parent
 495                         int length = outputString.length();
 496
 497                         char* buf = new char[length];
 498                         memcpy(buf, outputString.c_str(), length);
 499
 500                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 501                         outputString = "";
 502                         delete buf;
 503
 504                 }
 505
 506                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 507                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 508                 return 1;
 509         }
 510         catch(exception& e) {
 511                 m->errorOut(e, "DistanceCommand", "driverMPI");
 512                 exit(1);
 513         }
 514 }
 515 /**************************************************************************************************/
 516 /////// need to fix to work with calcs and sequencedb
 517 int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
 518         try {
 519                 MPI_Status status;
 520
 521                 MPI_File outMPI;
 522                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 523
 524                 //char* filename = new char[file.length()];
 525                 //memcpy(filename, file.c_str(), file.length());
 526
 527                 char filename[1024];
 528                 strcpy(filename, file.c_str());
 529
 530                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 531                 //delete filename;
 532
 533                 int startTime = time(NULL);
 534
 535                 string outputString = "";
 536                 size = 0;
 537
 538                 if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 539
 540                 for(int i=startLine;i<endLine;i++){
 541                         if(output == "lt")      {
 542                                 string name = alignDB.get(i).getName();
 543                                 if (name.length() < 10) { //pad with spaces to make compatible
 544                                         while (name.length() < 10) {  name += " ";  }
 545                                 }
 546                                 outputString += name + "\t";
 547                         }
 548                         for(int j=0;j<i;j++){
 549
 550                                 if (m->control_pressed) {  return 0;  }
 551
 552                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 553                                 double dist = distCalculator->getDist();
 554
 555                                 if (output == "lt") {  outputString += toString(dist) + "\t"; }
 556                         }
 557
 558                         if (output == "lt") { outputString += "\n"; }
 559
 560
 561                         if(i % 100 == 0){
 562                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 563                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 564                         }
 565
 566
 567                         //send results to parent
 568                         int length = outputString.length();
 569                         char* buf = new char[length];
 570                         memcpy(buf, outputString.c_str(), length);
 571
 572                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 573                         size += outputString.length();
 574                         outputString = "";
 575                         delete buf;
 576                 }
 577
 578                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 579                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 580                 MPI_File_close(&outMPI);
 581
 582                 return 1;
 583         }
 584         catch(exception& e) {
 585                 m->errorOut(e, "DistanceCommand", "driverMPI");
 586                 exit(1);
 587         }
 588 }
 589 #endif
 590 /**************************************************************************************************/
 591 int DistanceCommand::convertMatrix(string outputFile) {
 592         try{
 593
 594                 //sort file by first column so the distances for each row are together
 595                 string outfile = getRootName(outputFile) + "sorted.dist.temp";
 596
 597                 //use the unix sort
 598                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 599                         string command = "sort -n " + outputFile + " -o " + outfile;
 600                         system(command.c_str());
 601                 #else //sort using windows sort
 602                         string command = "sort " + outputFile + " /O " + outfile;
 603                         system(command.c_str());
 604                 #endif
 605
 606
 607                 //output to new file distance for each row and save positions in file where new row begins
 608                 ifstream in;
 609                 openInputFile(outfile, in);
 610
 611                 ofstream out;
 612                 openOutputFile(outputFile, out);
 613
 614                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 615
 616                 out << alignDB.getNumSeqs() << endl;
 617
 618                 //get first currentRow
 619                 string first, currentRow, second;
 620                 float dist;
 621                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 622                 map<string, float>::iterator it;
 623
 624                 in >> first;
 625                 currentRow = first;
 626
 627                 rowDists[first] = 0.00; //distance to yourself is 0.0
 628
 629                 in.seekg(0);
 630                 //openInputFile(outfile, in);
 631
 632                 while(!in.eof()) {
 633                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 634
 635                         in >> first >> second >> dist; gobble(in);
 636
 637                         if (first != currentRow) {
 638                                 //print out last row
 639                                 out << currentRow << '\t'; //print name
 640
 641                                 //print dists
 642                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 643                                         out << it->second << '\t';
 644                                 }
 645                                 out << endl;
 646
 647                                 //start new row
 648                                 currentRow = first;
 649                                 rowDists.clear();
 650                                 rowDists[first] = 0.00;
 651                                 rowDists[second] = dist;
 652                         }else{
 653                                 rowDists[second] = dist;
 654                         }
 655                 }
 656                 //print out last row
 657                 out << currentRow << '\t'; //print name
 658
 659                 //print dists
 660                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 661                         out << it->second << '\t';
 662                 }
 663                 out << endl;
 664
 665                 in.close();
 666                 out.close();
 667
 668                 remove(outfile.c_str());
 669
 670                 return 1;
 671
 672         }
 673         catch(exception& e) {
 674                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 675                 exit(1);
 676         }
 677 }
 678 /**************************************************************************************************/
 679 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 680         try{
 681
 682                 //sort file by first column so the distances for each row are together
 683                 string outfile = getRootName(outputFile) + "sorted.dist.temp";
 684
 685                 //use the unix sort
 686                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 687                         string command = "sort -n " + outputFile + " -o " + outfile;
 688                         system(command.c_str());
 689                 #else //sort using windows sort
 690                         string command = "sort " + outputFile + " /O " + outfile;
 691                         system(command.c_str());
 692                 #endif
 693
 694
 695                 //output to new file distance for each row and save positions in file where new row begins
 696                 ifstream in;
 697                 openInputFile(outfile, in);
 698
 699                 ofstream out;
 700                 openOutputFile(outputFile, out);
 701
 702                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 703
 704                 out << alignDB.getNumSeqs() << endl;
 705
 706                 //get first currentRow
 707                 string first, currentRow, second;
 708                 float dist;
 709                 int i, j;
 710                 i = 0; j = 0;
 711                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 712                 map<string, float>::iterator it;
 713
 714                 in >> first;
 715                 currentRow = first;
 716
 717                 rowDists[first] = 0.00; //distance to yourself is 0.0
 718
 719                 in.seekg(0);
 720                 //openInputFile(outfile, in);
 721
 722                 while(!in.eof()) {
 723                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 724
 725                         in >> first >> second >> dist; gobble(in);
 726
 727                         if (first != currentRow) {
 728                                 //print out last row
 729                                 out << currentRow << '\t'; //print name
 730
 731                                 //print dists
 732                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 733                                         if (j >= i) { break; }
 734                                         out << it->second << '\t';
 735                                         j++;
 736                                 }
 737                                 out << endl;
 738
 739                                 //start new row
 740                                 currentRow = first;
 741                                 rowDists.clear();
 742                                 rowDists[first] = 0.00;
 743                                 rowDists[second] = dist;
 744                                 j = 0;
 745                                 i++;
 746                         }else{
 747                                 rowDists[second] = dist;
 748                         }
 749                 }
 750                 //print out last row
 751                 out << currentRow << '\t'; //print name
 752
 753                 //print dists
 754                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 755                         out << it->second << '\t';
 756                 }
 757                 out << endl;
 758
 759                 in.close();
 760                 out.close();
 761
 762                 remove(outfile.c_str());
 763
 764                 return 1;
 765
 766         }
 767         catch(exception& e) {
 768                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
 769                 exit(1);
 770         }
 771 }
 772 /**************************************************************************************************
 773 void DistanceCommand::appendFiles(string temp, string filename) {
 774         try{
 775                 ofstream output;
 776                 ifstream input;
 777
 778                 //open output file in append mode
 779                 openOutputFileAppend(filename, output);
 780                 openInputFile(temp, input);
 781
 782                 while(char c = input.get()){
 783                         if(input.eof())         {       break;                  }
 784                         else                            {       output << c;    }
 785                 }
 786
 787                 input.close();
 788                 output.close();
 789         }
 790         catch(exception& e) {
 791                 m->errorOut(e, "DistanceCommand", "appendFiles");
 792                 exit(1);
 793         }
 794 }
 795 /**************************************************************************************************/
 796
 797