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
  12 //**********************************************************************************************************************
  13 vector<string> DistanceCommand::setParameters(){
  14         try {
  15                 CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
  16                 CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
  19                 CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
  20                 CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
  21                 CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "DistanceCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string DistanceCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
  41                 helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors.  \n";
  42                 helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
  43                 helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
  44                 helpString += "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";
  45                 helpString += "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";
  46                 helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
  47                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
  48                 helpString += "The processors parameter allows you to specify number of processors to use.  The default is 1.\n";
  49                 helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n";
  50                 helpString += "The dist.seqs command should be in the following format: \n";
  51                 helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
  52                 helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "DistanceCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 DistanceCommand::DistanceCommand(){
  63         try {
  64                 abort = true; calledHelp = true;
  65                 setParameters();
  66                 vector<string> tempOutNames;
  67                 outputTypes["phylip"] = tempOutNames;
  68                 outputTypes["column"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 DistanceCommand::DistanceCommand(string option) {
  77         try {
  78                 abort = false; calledHelp = false;
  79                 Estimators.clear();
  80
  81                 //allow user to run help
  82                 if(option == "help") { help(); abort = true; calledHelp = true; }
  83                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  84
  85                 else {
  86                         vector<string> myArray = setParameters();
  87
  88                         OptionParser parser(option);
  89                         map<string, string> parameters = parser.getParameters();
  90
  91                         ValidParameters validParameter("dist.seqs");
  92                         map<string, string>::iterator it2;
  93
  94                         //check to make sure all parameters are valid for command
  95                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
  96                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
  97                         }
  98
  99                         //initialize outputTypes
 100                         vector<string> tempOutNames;
 101                         outputTypes["phylip"] = tempOutNames;
 102                         outputTypes["column"] = tempOutNames;
 103
 104                         //if the user changes the input directory command factory will send this info to us in the output parameter
 105                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 106                         if (inputDir == "not found"){   inputDir = "";          }
 107                         else {
 108                                 string path;
 109                                 it2 = parameters.find("fasta");
 110                                 //user has given a template file
 111                                 if(it2 != parameters.end()){
 112                                         path = m->hasPath(it2->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
 115                                 }
 116
 117                                 it2 = parameters.find("oldfasta");
 118                                 //user has given a template file
 119                                 if(it2 != parameters.end()){
 120                                         path = m->hasPath(it2->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["oldfasta"] = inputDir + it2->second;                }
 123                                 }
 124
 125                                 it2 = parameters.find("column");
 126                                 //user has given a template file
 127                                 if(it2 != parameters.end()){
 128                                         path = m->hasPath(it2->second);
 129                                         //if the user has not given a path then, add inputdir. else leave path alone.
 130                                         if (path == "") {       parameters["column"] = inputDir + it2->second;          }
 131                                 }
 132                         }
 133
 134                         //check for required parameters
 135                         fastafile = validParameter.validFile(parameters, "fasta", true);
 136                         if (fastafile == "not found") {
 137                                 fastafile = m->getFastaFile();
 138                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
 139                                         ifstream inFASTA;
 140                                         m->openInputFile(fastafile, inFASTA);
 141                                         alignDB = SequenceDB(inFASTA);
 142                                         inFASTA.close();
 143                                 }else {         m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 144                         }else if (fastafile == "not open") { abort = true; }
 145                         else{
 146                                 ifstream inFASTA;
 147                                 m->openInputFile(fastafile, inFASTA);
 148                                 alignDB = SequenceDB(inFASTA);
 149                                 inFASTA.close();
 150                                 m->setFastaFile(fastafile);
 151                         }
 152
 153                         oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
 154                         if (oldfastafile == "not found") { oldfastafile = ""; }
 155                         else if (oldfastafile == "not open") { abort = true; }
 156
 157                         column = validParameter.validFile(parameters, "column", true);
 158                         if (column == "not found") { column = ""; }
 159                         else if (column == "not open") { abort = true; }
 160                         else { m->setColumnFile(column); }
 161
 162                         //if the user changes the output directory command factory will send this info to us in the output parameter
 163                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 164                                 outputDir = "";
 165                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 166                         }
 167
 168                         //check for optional parameter and set defaults
 169                         // ...at some point should added some additional type checking...
 170                         calc = validParameter.validFile(parameters, "calc", false);
 171                         if (calc == "not found") { calc = "onegap";  }
 172                         else {
 173                                  if (calc == "default")  {  calc = "onegap";  }
 174                         }
 175                         m->splitAtDash(calc, Estimators);
 176
 177                         string temp;
 178                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 179                         convert(temp, countends);
 180
 181                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 182                         convert(temp, cutoff);
 183
 184                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 185                         m->setProcessors(temp);
 186                         convert(temp, processors);
 187
 188                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 189                         convert(temp, compress);
 190
 191                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 192
 193                         if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
 194
 195                         if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so."); m->mothurOutEndLine(); abort=true; }
 196
 197                         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"; }
 198
 199                 }
 200
 201         }
 202         catch(exception& e) {
 203                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 204                 exit(1);
 205         }
 206 }
 207 //**********************************************************************************************************************
 208
 209 int DistanceCommand::execute(){
 210         try {
 211
 212                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 213
 214                 int startTime = time(NULL);
 215
 216                 //save number of new sequence
 217                 numNewFasta = alignDB.getNumSeqs();
 218
 219                 //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
 220                 if ((oldfastafile != "") && (column != ""))  {  if (!(sanityCheck())) { return 0; }  }
 221
 222                 if (m->control_pressed) { return 0; }
 223
 224                 int numSeqs = alignDB.getNumSeqs();
 225                 cutoff += 0.005;
 226
 227                 if (!alignDB.sameLength()) {  m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
 228
 229                 string outputFile;
 230
 231                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 232                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
 233                         m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 234
 235                         //output numSeqs to phylip formatted dist file
 236                 }else if (output == "column") { //user wants column format
 237                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
 238                         outputTypes["column"].push_back(outputFile);
 239
 240                         //so we don't accidentally overwrite
 241                         if (outputFile == column) {
 242                                 string tempcolumn = column + ".old";
 243                                 rename(column.c_str(), tempcolumn.c_str());
 244                         }
 245
 246                         m->mothurRemove(outputFile);
 247                 }else { //assume square
 248                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
 249                         m->mothurRemove(outputFile);
 250                         outputTypes["phylip"].push_back(outputFile);
 251                 }
 252
 253
 254 #ifdef USE_MPI
 255
 256                 int pid, start, end;
 257                 int tag = 2001;
 258
 259                 MPI_Status status;
 260                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 261                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 262
 263                 //each process gets where it should start and stop in the file
 264                 if (output != "square") {
 265                         start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 266                         end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 267                 }else{
 268                         start = int ((float(pid)/float(processors)) * numSeqs);
 269                         end = int ((float(pid+1)/float(processors)) * numSeqs);
 270                 }
 271
 272                 if (output == "column") {
 273                         MPI_File outMPI;
 274                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 275
 276                         //char* filename = new char[outputFile.length()];
 277                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 278
 279                         char filename[1024];
 280                         strcpy(filename, outputFile.c_str());
 281
 282                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 283                         //delete filename;
 284
 285                         if (pid == 0) { //you are the root process
 286
 287                                 //do your part
 288                                 string outputMyPart;
 289
 290                                 driverMPI(start, end, outMPI, cutoff);
 291
 292                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);   return 0; }
 293
 294                                 //wait on chidren
 295                                 for(int i = 1; i < processors; i++) {
 296                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);    return 0; }
 297
 298                                         char buf[5];
 299                                         MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 300                                 }
 301                         }else { //you are a child process
 302                                 //do your part
 303                                 driverMPI(start, end, outMPI, cutoff);
 304
 305                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
 306
 307                                 char buf[5];
 308                                 strcpy(buf, "done");
 309                                 //tell parent you are done.
 310                                 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 311                         }
 312
 313                         MPI_File_close(&outMPI);
 314
 315                 }else { //lower triangle format
 316                         if (pid == 0) { //you are the root process
 317
 318                                 //do your part
 319                                 string outputMyPart;
 320                                 unsigned long long mySize;
 321
 322                                 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 323                                 else { driverMPI(start, end, outputFile, mySize, output); }
 324
 325                                 if (m->control_pressed) {  outputTypes.clear();   return 0; }
 326
 327                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 328                                 MPI_File outMPI;
 329                                 MPI_File inMPI;
 330
 331                                 //char* filename = new char[outputFile.length()];
 332                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 333
 334                                 char filename[1024];
 335                                 strcpy(filename, outputFile.c_str());
 336
 337                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 338                                 //delete filename;
 339
 340                                 //wait on chidren
 341                                 for(int b = 1; b < processors; b++) {
 342                                         unsigned long long fileSize;
 343
 344                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
 345
 346                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 347
 348                                         string outTemp = outputFile + toString(b) + ".temp";
 349
 350                                         char* buf = new char[outTemp.length()];
 351                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 352
 353                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 354                                         delete buf;
 355
 356                                         int count = 0;
 357                                         while (count < fileSize) {
 358                                                 char buf2[1];
 359                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 360                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 361                                                 count += 1;
 362                                         }
 363
 364                                         MPI_File_close(&inMPI); //deleted on close
 365                                 }
 366
 367                                 MPI_File_close(&outMPI);
 368                         }else { //you are a child process
 369                                 //do your part
 370                                 unsigned long long size;
 371                                 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 372                                 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 373
 374                                 if (m->control_pressed) {  return 0; }
 375
 376                                 //tell parent you are done.
 377                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 378                         }
 379                 }
 380                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 381 #else
 382
 383         //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 384                 //if you don't need to fork anything
 385                 if(processors == 1){
 386                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 387                         else { driver(0, numSeqs, outputFile, "square");  }
 388                 }else{ //you have multiple processors
 389
 390                         unsigned long long numDists = 0;
 391
 392                         if (output == "square") {
 393                                  numDists = numSeqs * numSeqs;
 394                         }else {
 395                                 for(int i=0;i<numSeqs;i++){
 396                                         for(int j=0;j<i;j++){
 397                                                 numDists++;
 398                                                 if (numDists > processors) { break; }
 399                                         }
 400                                 }
 401                         }
 402
 403                         if (numDists < processors) { processors = numDists; }
 404
 405                         for (int i = 0; i < processors; i++) {
 406                                 distlinePair tempLine;
 407                                 lines.push_back(tempLine);
 408                                 if (output != "square") {
 409                                         lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 410                                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 411                                 }else{
 412                                         lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 413                                         lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 414                                 }
 415
 416                         }
 417
 418                         createProcesses(outputFile);
 419                 }
 420         //#else
 421                 //ifstream inFASTA;
 422                 //if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 423                 //else { driver(0, numSeqs, outputFile, "square");  }
 424         //#endif
 425
 426 #endif
 427                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 428
 429                 #ifdef USE_MPI
 430                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 431
 432                         if (pid == 0) { //only one process should output to screen
 433                 #endif
 434
 435                 //if (output == "square") {  convertMatrix(outputFile); }
 436
 437                 ifstream fileHandle;
 438                 fileHandle.open(outputFile.c_str());
 439                 if(fileHandle) {
 440                         m->gobble(fileHandle);
 441                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 442                 }
 443
 444                 //append the old column file to the new one
 445                 if ((oldfastafile != "") && (column != ""))  {
 446                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 447                         if (outputFile == column) {
 448                                 string tempcolumn = column + ".old";
 449                                 m->appendFiles(tempcolumn, outputFile);
 450                                 m->mothurRemove(tempcolumn);
 451                         }else{
 452                                 m->appendFiles(outputFile, column);
 453                                 m->mothurRemove(outputFile);
 454                                 outputFile = column;
 455                         }
 456
 457                         if (outputDir != "") {
 458                                 string newOutputName = outputDir + m->getSimpleName(outputFile);
 459                                 rename(outputFile.c_str(), newOutputName.c_str());
 460                                 m->mothurRemove(outputFile);
 461                                 outputFile = newOutputName;
 462                         }
 463                 }
 464
 465
 466                 #ifdef USE_MPI
 467                         }
 468                 #endif
 469
 470                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 471
 472                 //set phylip file as new current phylipfile
 473                 string current = "";
 474                 itTypes = outputTypes.find("phylip");
 475                 if (itTypes != outputTypes.end()) {
 476                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 477                 }
 478
 479                 //set column file as new current columnfile
 480                 itTypes = outputTypes.find("column");
 481                 if (itTypes != outputTypes.end()) {
 482                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 483                 }
 484
 485                 m->mothurOutEndLine();
 486                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 487                 m->mothurOut(outputFile); m->mothurOutEndLine();
 488                 m->mothurOutEndLine();
 489                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 490
 491
 492                 if (m->isTrue(compress)) {
 493                         m->mothurOut("Compressing..."); m->mothurOutEndLine();
 494                         m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 495                         system(("gzip -v " + outputFile).c_str());
 496                         outputNames.push_back(outputFile + ".gz");
 497                 }else { outputNames.push_back(outputFile); }
 498
 499                 return 0;
 500
 501         }
 502         catch(exception& e) {
 503                 m->errorOut(e, "DistanceCommand", "execute");
 504                 exit(1);
 505         }
 506 }
 507 /**************************************************************************************************/
 508 void DistanceCommand::createProcesses(string filename) {
 509         try {
 510 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 511                 int process = 1;
 512                 processIDS.clear();
 513
 514                 //loop through and create all the processes you want
 515                 while (process != processors) {
 516                         int pid = fork();
 517
 518                         if (pid > 0) {
 519                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 520                                 process++;
 521                         }else if (pid == 0){
 522                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 523                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 524                                 exit(0);
 525                         }else {
 526                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
 527                                 perror(" : ");
 528                                 for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
 529                                 exit(0);
 530                         }
 531                 }
 532
 533                 //parent does its part
 534                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 535                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 536
 537
 538                 //force parent to wait until all the processes are done
 539                 for (int i=0;i<processIDS.size();i++) {
 540                         int temp = processIDS[i];
 541                         wait(&temp);
 542                 }
 543 #else
 544                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 545                 //Windows version shared memory, so be careful when passing variables through the distanceData struct.
 546                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 547                 //that's why the distance calculator was moved inside of the driver to make separate copies.
 548                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 549
 550                 vector<distanceData*> pDataArray; //[processors-1];
 551                 DWORD   dwThreadIdArray[processors-1];
 552                 HANDLE  hThreadArray[processors-1];
 553
 554                 //Create processor-1 worker threads.
 555                 for( int i=0; i<processors-1; i++ ){
 556
 557                         // Allocate memory for thread data.
 558                         distanceData* tempDist = new distanceData(lines[i+1].start, lines[i+1].end, (filename + toString(i) + ".temp"), cutoff, alignDB, Estimators, m, output, numNewFasta, countends);
 559                         pDataArray.push_back(tempDist);
 560                         processIDS.push_back(i);
 561
 562                         //MyDistThreadFunction is in header. It must be global or static to work with the threads.
 563                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 564                         hThreadArray[i] = CreateThread(NULL, 0, MyDistThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 565                 }
 566
 567                 //do your part
 568                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 569                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 570
 571                 //Wait until all threads have terminated.
 572                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 573
 574                 //Close all thread handles and free memory allocations.
 575                 for(int i=0; i < pDataArray.size(); i++){
 576                         CloseHandle(hThreadArray[i]);
 577                         delete pDataArray[i];
 578                 }
 579 #endif
 580
 581                 //append and remove temp files
 582                 for (int i=0;i<processIDS.size();i++) {
 583                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 584                         m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 585                 }
 586
 587         }
 588         catch(exception& e) {
 589                 m->errorOut(e, "DistanceCommand", "createProcesses");
 590                 exit(1);
 591         }
 592 }
 593 /**************************************************************************************************/
 594 /////// need to fix to work with calcs and sequencedb
 595 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 596         try {
 597                 ValidCalculators validCalculator;
 598                 Dist* distCalculator;
 599                 if (m->isTrue(countends) == true) {
 600                         for (int i=0; i<Estimators.size(); i++) {
 601                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 602                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 603                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 604                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 605                                 }
 606                         }
 607                 }else {
 608                         for (int i=0; i<Estimators.size(); i++) {
 609                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 610                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 611                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 612                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 613                                 }
 614                         }
 615                 }
 616
 617                 int startTime = time(NULL);
 618
 619                 //column file
 620                 ofstream outFile(dFileName.c_str(), ios::trunc);
 621                 outFile.setf(ios::fixed, ios::showpoint);
 622                 outFile << setprecision(4);
 623
 624                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 625
 626                 for(int i=startLine;i<endLine;i++){
 627                         if(output == "lt")      {
 628                                 string name = alignDB.get(i).getName();
 629                                 if (name.length() < 10) { //pad with spaces to make compatible
 630                                         while (name.length() < 10) {  name += " ";  }
 631                                 }
 632                                 outFile << name << '\t';
 633                         }
 634                         for(int j=0;j<i;j++){
 635
 636                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 637
 638                                 //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
 639                                 //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
 640                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 641
 642                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 643                                 double dist = distCalculator->getDist();
 644
 645                                 if(dist <= cutoff){
 646                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 647                                 }
 648                                 if (output == "lt") {  outFile << dist << '\t'; }
 649                         }
 650
 651                         if (output == "lt") { outFile << endl; }
 652
 653                         if(i % 100 == 0){
 654                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 655                         }
 656
 657                 }
 658                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 659
 660                 outFile.close();
 661                 delete distCalculator;
 662
 663                 return 1;
 664         }
 665         catch(exception& e) {
 666                 m->errorOut(e, "DistanceCommand", "driver");
 667                 exit(1);
 668         }
 669 }
 670 /**************************************************************************************************/
 671 /////// need to fix to work with calcs and sequencedb
 672 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 673         try {
 674                 ValidCalculators validCalculator;
 675                 Dist* distCalculator;
 676                 if (m->isTrue(countends) == true) {
 677                         for (int i=0; i<Estimators.size(); i++) {
 678                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 679                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 680                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 681                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 682                                 }
 683                         }
 684                 }else {
 685                         for (int i=0; i<Estimators.size(); i++) {
 686                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 687                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 688                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 689                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 690                                 }
 691                         }
 692                 }
 693
 694                 int startTime = time(NULL);
 695
 696                 //column file
 697                 ofstream outFile(dFileName.c_str(), ios::trunc);
 698                 outFile.setf(ios::fixed, ios::showpoint);
 699                 outFile << setprecision(4);
 700
 701                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 702
 703                 for(int i=startLine;i<endLine;i++){
 704
 705                         string name = alignDB.get(i).getName();
 706                         //pad with spaces to make compatible
 707                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 708
 709                         outFile << name << '\t';
 710
 711                         for(int j=0;j<alignDB.getNumSeqs();j++){
 712
 713                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 714
 715                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 716                                 double dist = distCalculator->getDist();
 717
 718                                 outFile << dist << '\t';
 719                         }
 720
 721                         outFile << endl;
 722
 723                         if(i % 100 == 0){
 724                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 725                         }
 726
 727                 }
 728                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 729
 730                 outFile.close();
 731                 delete distCalculator;
 732
 733                 return 1;
 734         }
 735         catch(exception& e) {
 736                 m->errorOut(e, "DistanceCommand", "driver");
 737                 exit(1);
 738         }
 739 }
 740 #ifdef USE_MPI
 741 /**************************************************************************************************/
 742 /////// need to fix to work with calcs and sequencedb
 743 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 744         try {
 745
 746                 ValidCalculators validCalculator;
 747                 Dist* distCalculator;
 748                 if (m->isTrue(countends) == true) {
 749                         for (int i=0; i<Estimators.size(); i++) {
 750                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 751                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 752                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 753                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 754                                 }
 755                         }
 756                 }else {
 757                         for (int i=0; i<Estimators.size(); i++) {
 758                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 759                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 760                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 761                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 762                                 }
 763                         }
 764                 }
 765
 766
 767                 MPI_Status status;
 768                 int startTime = time(NULL);
 769
 770                 string outputString = "";
 771
 772                 for(int i=startLine;i<endLine;i++){
 773
 774                         for(int j=0;j<i;j++){
 775
 776                                 if (m->control_pressed) {  delete distCalculator; return 0;  }
 777
 778                                 //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
 779                                 //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
 780                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 781
 782                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 783                                 double dist = distCalculator->getDist();
 784
 785                                 if(dist <= cutoff){
 786                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 787                                 }
 788                         }
 789
 790                         if(i % 100 == 0){
 791                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 792                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 793                         }
 794
 795
 796                         //send results to parent
 797                         int length = outputString.length();
 798
 799                         char* buf = new char[length];
 800                         memcpy(buf, outputString.c_str(), length);
 801
 802                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 803                         outputString = "";
 804                         delete buf;
 805
 806                 }
 807
 808                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 809                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 810                 delete distCalculator;
 811                 return 1;
 812         }
 813         catch(exception& e) {
 814                 m->errorOut(e, "DistanceCommand", "driverMPI");
 815                 exit(1);
 816         }
 817 }
 818 /**************************************************************************************************/
 819 /////// need to fix to work with calcs and sequencedb
 820 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 821         try {
 822                 ValidCalculators validCalculator;
 823                 Dist* distCalculator;
 824                 if (m->isTrue(countends) == true) {
 825                         for (int i=0; i<Estimators.size(); i++) {
 826                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 827                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 828                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 829                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 830                                 }
 831                         }
 832                 }else {
 833                         for (int i=0; i<Estimators.size(); i++) {
 834                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 835                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 836                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 837                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 838                                 }
 839                         }
 840                 }
 841
 842
 843                 MPI_Status status;
 844
 845                 MPI_File outMPI;
 846                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 847
 848                 //char* filename = new char[file.length()];
 849                 //memcpy(filename, file.c_str(), file.length());
 850
 851                 char filename[1024];
 852                 strcpy(filename, file.c_str());
 853
 854                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 855                 //delete filename;
 856
 857                 int startTime = time(NULL);
 858
 859                 string outputString = "";
 860                 size = 0;
 861
 862                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 863
 864                 for(int i=startLine;i<endLine;i++){
 865
 866                         string name = alignDB.get(i).getName();
 867                         if (name.length() < 10) { //pad with spaces to make compatible
 868                                 while (name.length() < 10) {  name += " ";  }
 869                         }
 870                         outputString += name + "\t";
 871
 872                         for(int j=0;j<i;j++){
 873
 874                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 875
 876                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 877                                 double dist = distCalculator->getDist();
 878
 879                                 outputString += toString(dist) + "\t";
 880                         }
 881
 882                         outputString += "\n";
 883
 884
 885                         if(i % 100 == 0){
 886                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 887                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 888                         }
 889
 890
 891                         //send results to parent
 892                         int length = outputString.length();
 893                         char* buf = new char[length];
 894                         memcpy(buf, outputString.c_str(), length);
 895
 896                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 897                         size += outputString.length();
 898                         outputString = "";
 899                         delete buf;
 900                 }
 901
 902                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 903                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 904                 MPI_File_close(&outMPI);
 905                 delete distCalculator;
 906
 907                 return 1;
 908         }
 909         catch(exception& e) {
 910                 m->errorOut(e, "DistanceCommand", "driverMPI");
 911                 exit(1);
 912         }
 913 }
 914 /**************************************************************************************************/
 915 /////// need to fix to work with calcs and sequencedb
 916 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 917         try {
 918                 ValidCalculators validCalculator;
 919                 Dist* distCalculator;
 920                 if (m->isTrue(countends) == true) {
 921                         for (int i=0; i<Estimators.size(); i++) {
 922                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 923                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 924                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 925                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 926                                 }
 927                         }
 928                 }else {
 929                         for (int i=0; i<Estimators.size(); i++) {
 930                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 931                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 932                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 933                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 934                                 }
 935                         }
 936                 }
 937
 938                 MPI_Status status;
 939
 940                 MPI_File outMPI;
 941                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 942
 943                 //char* filename = new char[file.length()];
 944                 //memcpy(filename, file.c_str(), file.length());
 945
 946                 char filename[1024];
 947                 strcpy(filename, file.c_str());
 948
 949                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 950                 //delete filename;
 951
 952                 int startTime = time(NULL);
 953
 954                 string outputString = "";
 955                 size = 0;
 956
 957                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 958
 959                 for(int i=startLine;i<endLine;i++){
 960
 961                         string name = alignDB.get(i).getName();
 962                         if (name.length() < 10) { //pad with spaces to make compatible
 963                                 while (name.length() < 10) {  name += " ";  }
 964                         }
 965                         outputString += name + "\t";
 966
 967                         for(int j=0;j<alignDB.getNumSeqs();j++){
 968
 969                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 970
 971                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 972                                 double dist = distCalculator->getDist();
 973
 974                                 outputString += toString(dist) + "\t";
 975                         }
 976
 977                         outputString += "\n";
 978
 979
 980                         if(i % 100 == 0){
 981                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 982                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 983                         }
 984
 985
 986                         //send results to parent
 987                         int length = outputString.length();
 988                         char* buf = new char[length];
 989                         memcpy(buf, outputString.c_str(), length);
 990
 991                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 992                         size += outputString.length();
 993                         outputString = "";
 994                         delete buf;
 995                 }
 996
 997                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 998                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 999                 MPI_File_close(&outMPI);
1000                 delete distCalculator;
1001                 return 1;
1002         }
1003         catch(exception& e) {
1004                 m->errorOut(e, "DistanceCommand", "driverMPI");
1005                 exit(1);
1006         }
1007 }
1008 #endif
1009 /**************************************************************************************************
1010 int DistanceCommand::convertMatrix(string outputFile) {
1011         try{
1012
1013                 //sort file by first column so the distances for each row are together
1014                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1015
1016                 //use the unix sort
1017                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1018                         string command = "sort -n " + outputFile + " -o " + outfile;
1019                         system(command.c_str());
1020                 #else //sort using windows sort
1021                         string command = "sort " + outputFile + " /O " + outfile;
1022                         system(command.c_str());
1023                 #endif
1024
1025
1026                 //output to new file distance for each row and save positions in file where new row begins
1027                 ifstream in;
1028                 m->openInputFile(outfile, in);
1029
1030                 ofstream out;
1031                 m->openOutputFile(outputFile, out);
1032
1033                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1034
1035                 out << alignDB.getNumSeqs() << endl;
1036
1037                 //get first currentRow
1038                 string first, currentRow, second;
1039                 float dist;
1040                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1041                 map<string, float>::iterator it;
1042
1043                 in >> first;
1044                 currentRow = first;
1045
1046                 rowDists[first] = 0.00; //distance to yourself is 0.0
1047
1048                 in.seekg(0);
1049                 //m->openInputFile(outfile, in);
1050
1051                 while(!in.eof()) {
1052                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1053
1054                         in >> first >> second >> dist; m->gobble(in);
1055
1056                         if (first != currentRow) {
1057                                 //print out last row
1058                                 out << currentRow << '\t'; //print name
1059
1060                                 //print dists
1061                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1062                                         out << it->second << '\t';
1063                                 }
1064                                 out << endl;
1065
1066                                 //start new row
1067                                 currentRow = first;
1068                                 rowDists.clear();
1069                                 rowDists[first] = 0.00;
1070                                 rowDists[second] = dist;
1071                         }else{
1072                                 rowDists[second] = dist;
1073                         }
1074                 }
1075                 //print out last row
1076                 out << currentRow << '\t'; //print name
1077
1078                 //print dists
1079                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1080                         out << it->second << '\t';
1081                 }
1082                 out << endl;
1083
1084                 in.close();
1085                 out.close();
1086
1087                 m->mothurRemove(outfile);
1088
1089                 return 1;
1090
1091         }
1092         catch(exception& e) {
1093                 m->errorOut(e, "DistanceCommand", "convertMatrix");
1094                 exit(1);
1095         }
1096 }
1097 /**************************************************************************************************
1098 int DistanceCommand::convertToLowerTriangle(string outputFile) {
1099         try{
1100
1101                 //sort file by first column so the distances for each row are together
1102                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1103
1104                 //use the unix sort
1105                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1106                         string command = "sort -n " + outputFile + " -o " + outfile;
1107                         system(command.c_str());
1108                 #else //sort using windows sort
1109                         string command = "sort " + outputFile + " /O " + outfile;
1110                         system(command.c_str());
1111                 #endif
1112
1113
1114                 //output to new file distance for each row and save positions in file where new row begins
1115                 ifstream in;
1116                 m->openInputFile(outfile, in);
1117
1118                 ofstream out;
1119                 m->openOutputFile(outputFile, out);
1120
1121                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1122
1123                 out << alignDB.getNumSeqs() << endl;
1124
1125                 //get first currentRow
1126                 string first, currentRow, second;
1127                 float dist;
1128                 int i, j;
1129                 i = 0; j = 0;
1130                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1131                 map<string, float>::iterator it;
1132
1133                 in >> first;
1134                 currentRow = first;
1135
1136                 rowDists[first] = 0.00; //distance to yourself is 0.0
1137
1138                 in.seekg(0);
1139                 //m->openInputFile(outfile, in);
1140
1141                 while(!in.eof()) {
1142                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1143
1144                         in >> first >> second >> dist; m->gobble(in);
1145
1146                         if (first != currentRow) {
1147                                 //print out last row
1148                                 out << currentRow << '\t'; //print name
1149
1150                                 //print dists
1151                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1152                                         if (j >= i) { break; }
1153                                         out << it->second << '\t';
1154                                         j++;
1155                                 }
1156                                 out << endl;
1157
1158                                 //start new row
1159                                 currentRow = first;
1160                                 rowDists.clear();
1161                                 rowDists[first] = 0.00;
1162                                 rowDists[second] = dist;
1163                                 j = 0;
1164                                 i++;
1165                         }else{
1166                                 rowDists[second] = dist;
1167                         }
1168                 }
1169                 //print out last row
1170                 out << currentRow << '\t'; //print name
1171
1172                 //print dists
1173                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1174                         out << it->second << '\t';
1175                 }
1176                 out << endl;
1177
1178                 in.close();
1179                 out.close();
1180
1181                 m->mothurRemove(outfile);
1182
1183                 return 1;
1184
1185         }
1186         catch(exception& e) {
1187                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
1188                 exit(1);
1189         }
1190 }
1191 /**************************************************************************************************/
1192 //its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
1193 //but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
1194 //also check to make sure the 2 files have the same alignment length.
1195 bool DistanceCommand::sanityCheck() {
1196         try{
1197                 bool good = true;
1198
1199                 //make sure the 2 fasta files have the same alignment length
1200                 ifstream in;
1201                 m->openInputFile(fastafile, in);
1202                 int fastaAlignLength = 0;
1203                 if (in) {
1204                         Sequence tempIn(in);
1205                         fastaAlignLength = tempIn.getAligned().length();
1206                 }
1207                 in.close();
1208
1209                 ifstream in2;
1210                 m->openInputFile(oldfastafile, in2);
1211                 int oldfastaAlignLength = 0;
1212                 if (in2) {
1213                         Sequence tempIn2(in2);
1214                         oldfastaAlignLength = tempIn2.getAligned().length();
1215                 }
1216                 in2.close();
1217
1218                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1219
1220                 //read fasta file and save names as well as adding them to the alignDB
1221                 set<string> namesOldFasta;
1222
1223                 ifstream inFasta;
1224                 m->openInputFile(oldfastafile, inFasta);
1225
1226                 while (!inFasta.eof()) {
1227                         if (m->control_pressed) {  inFasta.close(); return good;  }
1228
1229                         Sequence temp(inFasta);
1230
1231                         if (temp.getName() != "") {
1232                                 namesOldFasta.insert(temp.getName());  //save name
1233                                 alignDB.push_back(temp);  //add to DB
1234                         }
1235
1236                         m->gobble(inFasta);
1237                 }
1238
1239                 inFasta.close();
1240
1241                 //read through the column file checking names and removing distances above the cutoff
1242                 ifstream inDist;
1243                 m->openInputFile(column, inDist);
1244
1245                 ofstream outDist;
1246                 string outputFile = column + ".temp";
1247                 m->openOutputFile(outputFile, outDist);
1248
1249                 string name1, name2;
1250                 float dist;
1251                 while (!inDist.eof()) {
1252                         if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
1253
1254                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1255
1256                         //both names are in fasta file and distance is below cutoff
1257                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1258                         else{
1259                                 if (dist <= cutoff) {
1260                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1261                                 }
1262                         }
1263                 }
1264
1265                 inDist.close();
1266                 outDist.close();
1267
1268                 if (good) {
1269                         m->mothurRemove(column);
1270                         rename(outputFile.c_str(), column.c_str());
1271                 }else{
1272                         m->mothurRemove(outputFile); //temp file is bad because file mismatch above
1273                 }
1274
1275                 return good;
1276
1277         }
1278         catch(exception& e) {
1279                 m->errorOut(e, "DistanceCommand", "sanityCheck");
1280                 exit(1);
1281         }
1282 }
1283 /**************************************************************************************************/
1284
1285
1286
1287