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()];\r
 204                         memcpy(filename, outputFile.c_str(), outputFile.length());
 205
 206                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 207                         delete filename;
 208
 209                         if (pid == 0) { //you are the root process
 210
 211                                 //do your part
 212                                 string outputMyPart;
 213                                 driverMPI(start, end, outMPI, cutoff);
 214
 215                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 216
 217                                 //wait on chidren
 218                                 for(int i = 1; i < processors; i++) {
 219                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 220
 221                                         char buf[4];
 222                                         MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 223                                 }
 224                         }else { //you are a child process
 225                                 //do your part
 226                                 driverMPI(start, end, outMPI, cutoff);
 227
 228                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 229
 230                                 char buf[4];
 231                                 strcpy(buf, "done");
 232                                 //tell parent you are done.
 233                                 MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 234                         }
 235
 236                         MPI_File_close(&outMPI);
 237
 238                 }else { //lower triangle format
 239                         if (pid == 0) { //you are the root process
 240
 241                                 //do your part
 242                                 string outputMyPart;
 243                                 long mySize;
 244                                 driverMPI(start, end, outputFile, mySize);
 245
 246                                 if (m->control_pressed) {  delete distCalculator;  return 0; }
 247
 248                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 249                                 MPI_File outMPI;
 250                                 MPI_File inMPI;
 251
 252                                 char* filename = new char[outputFile.length()];\r
 253                                 memcpy(filename, outputFile.c_str(), outputFile.length());
 254
 255                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 256                                 delete filename;
 257
 258                                 //wait on chidren
 259                                 for(int b = 1; b < processors; b++) {
 260                                         long fileSize;
 261
 262                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 263
 264                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 265
 266                                         string outTemp = outputFile + toString(b) + ".temp";
 267
 268                                         char* buf = new char[outTemp.length()];\r
 269                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 270
 271                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 272                                         delete buf;
 273
 274                                         int count = 0;
 275                                         while (count < fileSize) { //read 1000 characters at a time
 276                                                 //send freqs
 277                                                 char buf2[1];
 278                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 279                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 280                                                 count += 1;
 281                                         }
 282
 283                                         MPI_File_close(&inMPI); //deleted on close
 284                                 }
 285
 286                                 MPI_File_close(&outMPI);
 287                         }else { //you are a child process
 288                                 //do your part
 289                                 long size;
 290                                 driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
 291
 292                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 293
 294                                 //tell parent you are done.
 295                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 296                         }
 297                 }
 298 #else
 299
 300         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 301                 //if you don't need to fork anything
 302                 if(processors == 1){
 303                         driver(0, numSeqs, outputFile, cutoff);
 304                 }else{ //you have multiple processors
 305
 306                         for (int i = 0; i < processors; i++) {
 307                                 lines.push_back(new linePair());
 308                                 lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
 309                                 lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 310                         }
 311
 312                         createProcesses(outputFile);
 313
 314                         map<int, int>::iterator it = processIDS.begin();
 315                         rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
 316                         it++;
 317
 318                         //append and remove temp files
 319                         for (; it != processIDS.end(); it++) {
 320                                 appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
 321                                 remove((outputFile + toString(it->second) + ".temp").c_str());
 322                         }
 323                 }
 324         #else
 325                 ifstream inFASTA;
 326                 driver(0, numSeqs, outputFile, cutoff);
 327         #endif
 328
 329 #endif
 330                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 331
 332                 #ifdef USE_MPI
 333                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 334
 335                         if (pid == 0) { //only one process should output to screen
 336                 #endif
 337
 338                 if (output == "square") {  convertMatrix(outputFile); }
 339
 340                 #ifdef USE_MPI
 341                         }
 342                 #endif
 343
 344                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 345
 346                 delete distCalculator;
 347
 348                 m->mothurOutEndLine();
 349                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 350                 m->mothurOut(outputFile); m->mothurOutEndLine();
 351                 m->mothurOutEndLine();
 352                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 353                 return 0;
 354
 355         }
 356         catch(exception& e) {
 357                 m->errorOut(e, "DistanceCommand", "execute");
 358                 exit(1);
 359         }
 360 }
 361 /**************************************************************************************************/
 362 void DistanceCommand::createProcesses(string filename) {
 363         try {
 364 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 365                 int process = 0;
 366                 processIDS.clear();
 367
 368                 //loop through and create all the processes you want
 369                 while (process != processors) {
 370                         int pid = fork();
 371
 372                         if (pid > 0) {
 373                                 processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
 374                                 process++;
 375                         }else if (pid == 0){
 376                                 driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
 377                                 exit(0);
 378                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 379                 }
 380
 381                 //force parent to wait until all the processes are done
 382                 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
 383                         int temp = it->second;
 384                         wait(&temp);
 385                 }
 386 #endif
 387         }
 388         catch(exception& e) {
 389                 m->errorOut(e, "DistanceCommand", "createProcesses");
 390                 exit(1);
 391         }
 392 }
 393
 394 /**************************************************************************************************/
 395 /////// need to fix to work with calcs and sequencedb
 396 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 397         try {
 398
 399                 int startTime = time(NULL);
 400
 401                 //column file
 402                 ofstream outFile(dFileName.c_str(), ios::trunc);
 403                 outFile.setf(ios::fixed, ios::showpoint);
 404                 outFile << setprecision(4);
 405
 406                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 407
 408                 for(int i=startLine;i<endLine;i++){
 409                         if(output == "lt")      {
 410                                 string name = alignDB.get(i).getName();
 411                                 if (name.length() < 10) { //pad with spaces to make compatible
 412                                         while (name.length() < 10) {  name += " ";  }
 413                                 }
 414                                 outFile << name << '\t';
 415                         }
 416                         for(int j=0;j<i;j++){
 417
 418                                 if (m->control_pressed) { outFile.close(); return 0;  }
 419
 420                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 421                                 double dist = distCalculator->getDist();
 422
 423                                 if(dist <= cutoff){
 424                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 425                                 }
 426                                 if (output == "lt") {  outFile << dist << '\t'; }
 427
 428                                 if (output == "square") { //make a square column you can convert to square phylip
 429                                         outFile << alignDB.get(i).getName() << '\t' << alignDB.get(j).getName() << '\t' << dist << endl;
 430                                         outFile << alignDB.get(j).getName() << '\t' << alignDB.get(i).getName() << '\t' << dist << endl;
 431                                 }
 432
 433                         }
 434
 435                         if (output == "lt") { outFile << endl; }
 436
 437                         if(i % 100 == 0){
 438                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 439                         }
 440
 441                 }
 442                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 443
 444                 outFile.close();
 445
 446                 return 1;
 447         }
 448         catch(exception& e) {
 449                 m->errorOut(e, "DistanceCommand", "driver");
 450                 exit(1);
 451         }
 452 }
 453 #ifdef USE_MPI
 454 /**************************************************************************************************/
 455 /////// need to fix to work with calcs and sequencedb
 456 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 457         try {
 458                 MPI_Status status;
 459                 int startTime = time(NULL);
 460
 461                 string outputString = "";
 462
 463                 for(int i=startLine;i<endLine;i++){
 464
 465                         for(int j=0;j<i;j++){
 466
 467                                 if (m->control_pressed) {  return 0;  }
 468
 469                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 470                                 double dist = distCalculator->getDist();
 471
 472                                 if(dist <= cutoff){
 473                                         if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
 474                                 }
 475
 476                                 if (output == "square") { //make a square column you can convert to square phylip
 477                                         outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 478                                         outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
 479                                 }
 480                         }
 481
 482                         if(i % 100 == 0){
 483                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 484                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 485                         }
 486
 487
 488                         //send results to parent
 489                         int length = outputString.length();
 490
 491                         char* buf = new char[length];\r
 492                         memcpy(buf, outputString.c_str(), length);
 493
 494                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 495                         outputString = "";
 496                         delete buf;
 497
 498                 }
 499
 500                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 501                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 502                 return 1;
 503         }
 504         catch(exception& e) {
 505                 m->errorOut(e, "DistanceCommand", "driverMPI");
 506                 exit(1);
 507         }
 508 }
 509 /**************************************************************************************************/
 510 /////// need to fix to work with calcs and sequencedb
 511 int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
 512         try {
 513                 MPI_Status status;
 514
 515                 MPI_File outMPI;
 516                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 517
 518                 char* filename = new char[file.length()];\r
 519                 memcpy(filename, file.c_str(), file.length());
 520
 521                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 522                 delete filename;
 523
 524                 int startTime = time(NULL);
 525
 526                 string outputString = "";
 527                 size = 0;
 528
 529                 if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 530
 531                 for(int i=startLine;i<endLine;i++){
 532                         if(output == "lt")      {
 533                                 string name = alignDB.get(i).getName();
 534                                 if (name.length() < 10) { //pad with spaces to make compatible
 535                                         while (name.length() < 10) {  name += " ";  }
 536                                 }
 537                                 outputString += name + "\t";
 538                         }
 539                         for(int j=0;j<i;j++){
 540
 541                                 if (m->control_pressed) {  return 0;  }
 542
 543                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 544                                 double dist = distCalculator->getDist();
 545
 546                                 if (output == "lt") {  outputString += toString(dist) + "\t"; }
 547                         }
 548
 549                         if (output == "lt") { outputString += "\n"; }
 550
 551
 552                         if(i % 100 == 0){
 553                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 554                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 555                         }
 556
 557
 558                         //send results to parent
 559                         int length = outputString.length();
 560                         char* buf = new char[length];\r
 561                         memcpy(buf, outputString.c_str(), length);
 562
 563                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 564                         size += outputString.length();
 565                         outputString = "";
 566                         delete buf;
 567                 }
 568
 569                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 570                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 571                 MPI_File_close(&outMPI);
 572
 573                 return 1;
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "DistanceCommand", "driverMPI");
 577                 exit(1);
 578         }
 579 }
 580 #endif
 581 /**************************************************************************************************/
 582 int DistanceCommand::convertMatrix(string outputFile) {
 583         try{
 584
 585                 //sort file by first column so the distances for each row are together
 586                 string outfile = getRootName(outputFile) + "sorted.dist.temp";
 587
 588                 //use the unix sort
 589                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 590                         string command = "sort -n " + outputFile + " -o " + outfile;
 591                         system(command.c_str());
 592                 #else //sort using windows sort
 593                         string command = "sort " + outputFile + " /O " + outfile;
 594                         system(command.c_str());
 595                 #endif
 596
 597
 598                 //output to new file distance for each row and save positions in file where new row begins
 599                 ifstream in;
 600                 openInputFile(outfile, in);
 601
 602                 ofstream out;
 603                 openOutputFile(outputFile, out);
 604
 605                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 606
 607                 out << alignDB.getNumSeqs() << endl;
 608
 609                 //get first currentRow
 610                 string first, currentRow, second;
 611                 float dist;
 612                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 613                 map<string, float>::iterator it;
 614
 615                 in >> first;
 616                 currentRow = first;
 617
 618                 rowDists[first] = 0.00; //distance to yourself is 0.0
 619
 620                 in.seekg(0);
 621                 //openInputFile(outfile, in);
 622
 623                 while(!in.eof()) {
 624                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 625
 626                         in >> first >> second >> dist; gobble(in);
 627
 628                         if (first != currentRow) {
 629                                 //print out last row
 630                                 out << currentRow << '\t'; //print name
 631
 632                                 //print dists
 633                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 634                                         out << it->second << '\t';
 635                                 }
 636                                 out << endl;
 637
 638                                 //start new row
 639                                 currentRow = first;
 640                                 rowDists.clear();
 641                                 rowDists[first] = 0.00;
 642                                 rowDists[second] = dist;
 643                         }else{
 644                                 rowDists[second] = dist;
 645                         }
 646                 }
 647                 //print out last row
 648                 out << currentRow << '\t'; //print name
 649
 650                 //print dists
 651                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 652                         out << it->second << '\t';
 653                 }
 654                 out << endl;
 655
 656                 in.close();
 657                 out.close();
 658
 659                 remove(outfile.c_str());
 660
 661                 return 1;
 662
 663         }
 664         catch(exception& e) {
 665                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 666                 exit(1);
 667         }
 668 }
 669 /**************************************************************************************************/
 670 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 671         try{
 672
 673                 //sort file by first column so the distances for each row are together
 674                 string outfile = getRootName(outputFile) + "sorted.dist.temp";
 675
 676                 //use the unix sort
 677                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 678                         string command = "sort -n " + outputFile + " -o " + outfile;
 679                         system(command.c_str());
 680                 #else //sort using windows sort
 681                         string command = "sort " + outputFile + " /O " + outfile;
 682                         system(command.c_str());
 683                 #endif
 684
 685
 686                 //output to new file distance for each row and save positions in file where new row begins
 687                 ifstream in;
 688                 openInputFile(outfile, in);
 689
 690                 ofstream out;
 691                 openOutputFile(outputFile, out);
 692
 693                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 694
 695                 out << alignDB.getNumSeqs() << endl;
 696
 697                 //get first currentRow
 698                 string first, currentRow, second;
 699                 float dist;
 700                 int i, j;
 701                 i = 0; j = 0;
 702                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 703                 map<string, float>::iterator it;
 704
 705                 in >> first;
 706                 currentRow = first;
 707
 708                 rowDists[first] = 0.00; //distance to yourself is 0.0
 709
 710                 in.seekg(0);
 711                 //openInputFile(outfile, in);
 712
 713                 while(!in.eof()) {
 714                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 715
 716                         in >> first >> second >> dist; gobble(in);
 717
 718                         if (first != currentRow) {
 719                                 //print out last row
 720                                 out << currentRow << '\t'; //print name
 721
 722                                 //print dists
 723                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 724                                         if (j >= i) { break; }
 725                                         out << it->second << '\t';
 726                                         j++;
 727                                 }
 728                                 out << endl;
 729
 730                                 //start new row
 731                                 currentRow = first;
 732                                 rowDists.clear();
 733                                 rowDists[first] = 0.00;
 734                                 rowDists[second] = dist;
 735                                 j = 0;
 736                                 i++;
 737                         }else{
 738                                 rowDists[second] = dist;
 739                         }
 740                 }
 741                 //print out last row
 742                 out << currentRow << '\t'; //print name
 743
 744                 //print dists
 745                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 746                         out << it->second << '\t';
 747                 }
 748                 out << endl;
 749
 750                 in.close();
 751                 out.close();
 752
 753                 remove(outfile.c_str());
 754
 755                 return 1;
 756
 757         }
 758         catch(exception& e) {
 759                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
 760                 exit(1);
 761         }
 762 }
 763 /**************************************************************************************************
 764 void DistanceCommand::appendFiles(string temp, string filename) {
 765         try{
 766                 ofstream output;
 767                 ifstream input;
 768
 769                 //open output file in append mode
 770                 openOutputFileAppend(filename, output);
 771                 openInputFile(temp, input);
 772
 773                 while(char c = input.get()){
 774                         if(input.eof())         {       break;                  }
 775                         else                            {       output << c;    }
 776                 }
 777
 778                 input.close();
 779                 output.close();
 780         }
 781         catch(exception& e) {
 782                 m->errorOut(e, "DistanceCommand", "appendFiles");
 783                 exit(1);
 784         }
 785 }
 786 /**************************************************************************************************/
 787
 788