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","column",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","phylip-column",false,true, true); parameters.push_back(pfasta);
  18                 CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false, true); 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, true); parameters.push_back(pprocessors);
  23                 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false, true); 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 string DistanceCommand::getOutputPattern(string type) {
  63     try {
  64         string pattern = "";
  65
  66         if (type == "phylip") {  pattern = "[filename],[outputtag],dist"; }
  67         else if (type == "column") { pattern = "[filename],dist"; }
  68         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  69
  70         return pattern;
  71     }
  72     catch(exception& e) {
  73         m->errorOut(e, "DistanceCommand", "getOutputPattern");
  74         exit(1);
  75     }
  76 }
  77 //**********************************************************************************************************************
  78 DistanceCommand::DistanceCommand(){
  79         try {
  80                 abort = true; calledHelp = true;
  81                 setParameters();
  82                 vector<string> tempOutNames;
  83                 outputTypes["phylip"] = tempOutNames;
  84                 outputTypes["column"] = tempOutNames;
  85         }
  86         catch(exception& e) {
  87                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
  88                 exit(1);
  89         }
  90 }
  91 //**********************************************************************************************************************
  92 DistanceCommand::DistanceCommand(string option) {
  93         try {
  94                 abort = false; calledHelp = false;
  95                 Estimators.clear();
  96
  97                 //allow user to run help
  98                 if(option == "help") { help(); abort = true; calledHelp = true; }
  99                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 100
 101                 else {
 102                         vector<string> myArray = setParameters();
 103
 104                         OptionParser parser(option);
 105                         map<string, string> parameters = parser.getParameters();
 106
 107                         ValidParameters validParameter("dist.seqs");
 108                         map<string, string>::iterator it2;
 109
 110                         //check to make sure all parameters are valid for command
 111                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 112                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 113                         }
 114
 115                         //initialize outputTypes
 116                         vector<string> tempOutNames;
 117                         outputTypes["phylip"] = tempOutNames;
 118                         outputTypes["column"] = tempOutNames;
 119
 120                         //if the user changes the input directory command factory will send this info to us in the output parameter
 121                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 122                         if (inputDir == "not found"){   inputDir = "";          }
 123                         else {
 124                                 string path;
 125                                 it2 = parameters.find("fasta");
 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["fasta"] = inputDir + it2->second;           }
 131                                 }
 132
 133                                 it2 = parameters.find("oldfasta");
 134                                 //user has given a template file
 135                                 if(it2 != parameters.end()){
 136                                         path = m->hasPath(it2->second);
 137                                         //if the user has not given a path then, add inputdir. else leave path alone.
 138                                         if (path == "") {       parameters["oldfasta"] = inputDir + it2->second;                }
 139                                 }
 140
 141                                 it2 = parameters.find("column");
 142                                 //user has given a template file
 143                                 if(it2 != parameters.end()){
 144                                         path = m->hasPath(it2->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["column"] = inputDir + it2->second;          }
 147                                 }
 148                         }
 149
 150                         //check for required parameters
 151                         fastafile = validParameter.validFile(parameters, "fasta", true);
 152                         if (fastafile == "not found") {
 153                                 fastafile = m->getFastaFile();
 154                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
 155                                         ifstream inFASTA;
 156                                         m->openInputFile(fastafile, inFASTA);
 157                                         alignDB = SequenceDB(inFASTA);
 158                                         inFASTA.close();
 159                                 }else {         m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 160                         }else if (fastafile == "not open") { abort = true; }
 161                         else{
 162                                 ifstream inFASTA;
 163                                 m->openInputFile(fastafile, inFASTA);
 164                                 alignDB = SequenceDB(inFASTA);
 165                                 inFASTA.close();
 166                                 m->setFastaFile(fastafile);
 167                         }
 168
 169                         oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
 170                         if (oldfastafile == "not found") { oldfastafile = ""; }
 171                         else if (oldfastafile == "not open") { abort = true; }
 172
 173                         column = validParameter.validFile(parameters, "column", true);
 174                         if (column == "not found") { column = ""; }
 175                         else if (column == "not open") { abort = true; }
 176                         else { m->setColumnFile(column); }
 177
 178                         //if the user changes the output directory command factory will send this info to us in the output parameter
 179                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 180                                 outputDir = "";
 181                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 182                         }
 183
 184                         //check for optional parameter and set defaults
 185                         // ...at some point should added some additional type checking...
 186                         calc = validParameter.validFile(parameters, "calc", false);
 187                         if (calc == "not found") { calc = "onegap";  }
 188                         else {
 189                                  if (calc == "default")  {  calc = "onegap";  }
 190                         }
 191                         m->splitAtDash(calc, Estimators);
 192
 193                         string temp;
 194                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 195                         convert(temp, countends);
 196
 197                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 198                         m->mothurConvert(temp, cutoff);
 199
 200                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 201                         m->setProcessors(temp);
 202                         m->mothurConvert(temp, processors);
 203
 204                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 205                         convert(temp, compress);
 206
 207                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 208             if (output == "phylip") { output = "lt";  }
 209
 210                         if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
 211
 212                         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; }
 213
 214                         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"; }
 215
 216                 }
 217
 218         }
 219         catch(exception& e) {
 220                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 221                 exit(1);
 222         }
 223 }
 224 //**********************************************************************************************************************
 225
 226 int DistanceCommand::execute(){
 227         try {
 228
 229                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 230
 231                 int startTime = time(NULL);
 232
 233                 //save number of new sequence
 234                 numNewFasta = alignDB.getNumSeqs();
 235
 236                 //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
 237                 if ((oldfastafile != "") && (column != ""))  {  if (!(sanityCheck())) { return 0; }  }
 238
 239                 if (m->control_pressed) { return 0; }
 240
 241                 int numSeqs = alignDB.getNumSeqs();
 242                 cutoff += 0.005;
 243
 244                 if (!alignDB.sameLength()) {  m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
 245
 246                 string outputFile;
 247
 248         map<string, string> variables;
 249         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
 250                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 251             variables["[outputtag]"] = "phylip";
 252                         outputFile = getOutputFileName("phylip", variables);
 253                         m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 254
 255                         //output numSeqs to phylip formatted dist file
 256                 }else if (output == "column") { //user wants column format
 257                         outputFile = getOutputFileName("column", variables);
 258                         outputTypes["column"].push_back(outputFile);
 259
 260                         //so we don't accidentally overwrite
 261                         if (outputFile == column) {
 262                                 string tempcolumn = column + ".old";
 263                                 rename(column.c_str(), tempcolumn.c_str());
 264                         }
 265
 266                         m->mothurRemove(outputFile);
 267                 }else { //assume square
 268                         variables["[outputtag]"] = "square";
 269                         outputFile = getOutputFileName("phylip", variables);
 270                         m->mothurRemove(outputFile);
 271                         outputTypes["phylip"].push_back(outputFile);
 272                 }
 273
 274
 275 #ifdef USE_MPI
 276
 277                 int pid, start, end;
 278                 int tag = 2001;
 279
 280                 MPI_Status status;
 281                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 282                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 283
 284                 //each process gets where it should start and stop in the file
 285                 if (output != "square") {
 286                         start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 287                         end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 288                 }else{
 289                         start = int ((float(pid)/float(processors)) * numSeqs);
 290                         end = int ((float(pid+1)/float(processors)) * numSeqs);
 291                 }
 292
 293                 if (output == "column") {
 294                         MPI_File outMPI;
 295                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 296
 297                         //char* filename = new char[outputFile.length()];
 298                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 299
 300                         char filename[1024];
 301                         strcpy(filename, outputFile.c_str());
 302
 303                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 304                         //delete filename;
 305
 306                         if (pid == 0) { //you are the root process
 307
 308                                 //do your part
 309                                 string outputMyPart;
 310
 311                                 driverMPI(start, end, outMPI, cutoff);
 312
 313                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);   return 0; }
 314
 315                                 //wait on chidren
 316                                 for(int i = 1; i < processors; i++) {
 317                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);    return 0; }
 318
 319                                         char buf[5];
 320                                         MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 321                                 }
 322                         }else { //you are a child process
 323                                 //do your part
 324                                 driverMPI(start, end, outMPI, cutoff);
 325
 326                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
 327
 328                                 char buf[5];
 329                                 strcpy(buf, "done");
 330                                 //tell parent you are done.
 331                                 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 332                         }
 333
 334                         MPI_File_close(&outMPI);
 335
 336                 }else { //lower triangle format
 337                         if (pid == 0) { //you are the root process
 338
 339                                 //do your part
 340                                 string outputMyPart;
 341                                 unsigned long long mySize;
 342
 343                                 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 344                                 else { driverMPI(start, end, outputFile, mySize, output); }
 345
 346                                 if (m->control_pressed) {  outputTypes.clear();   return 0; }
 347
 348                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 349                                 MPI_File outMPI;
 350                                 MPI_File inMPI;
 351
 352                                 //char* filename = new char[outputFile.length()];
 353                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 354
 355                                 char filename[1024];
 356                                 strcpy(filename, outputFile.c_str());
 357
 358                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 359                                 //delete filename;
 360
 361                                 //wait on chidren
 362                                 for(int b = 1; b < processors; b++) {
 363                                         unsigned long long fileSize;
 364
 365                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
 366
 367                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 368
 369                                         string outTemp = outputFile + toString(b) + ".temp";
 370
 371                                         char* buf = new char[outTemp.length()];
 372                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 373
 374                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 375                                         delete buf;
 376
 377                                         int count = 0;
 378                                         while (count < fileSize) {
 379                                                 char buf2[1];
 380                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 381                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 382                                                 count += 1;
 383                                         }
 384
 385                                         MPI_File_close(&inMPI); //deleted on close
 386                                 }
 387
 388                                 MPI_File_close(&outMPI);
 389                         }else { //you are a child process
 390                                 //do your part
 391                                 unsigned long long size;
 392                                 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 393                                 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 394
 395                                 if (m->control_pressed) {  return 0; }
 396
 397                                 //tell parent you are done.
 398                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 399                         }
 400                 }
 401                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 402 #else
 403
 404         //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 405                 //if you don't need to fork anything
 406                 if(processors == 1){
 407                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 408                         else { driver(0, numSeqs, outputFile, "square");  }
 409                 }else{ //you have multiple processors
 410
 411                         unsigned long long numDists = 0;
 412
 413                         if (output == "square") {
 414                                  numDists = numSeqs * numSeqs;
 415                         }else {
 416                                 for(int i=0;i<numSeqs;i++){
 417                                         for(int j=0;j<i;j++){
 418                                                 numDists++;
 419                                                 if (numDists > processors) { break; }
 420                                         }
 421                                 }
 422                         }
 423
 424                         if (numDists < processors) { processors = numDists; }
 425
 426                         for (int i = 0; i < processors; i++) {
 427                                 distlinePair tempLine;
 428                                 lines.push_back(tempLine);
 429                                 if (output != "square") {
 430                                         lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 431                                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 432                                 }else{
 433                                         lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 434                                         lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 435                                 }
 436
 437                         }
 438
 439                         createProcesses(outputFile);
 440                 }
 441         //#else
 442                 //ifstream inFASTA;
 443                 //if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 444                 //else { driver(0, numSeqs, outputFile, "square");  }
 445         //#endif
 446
 447 #endif
 448                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 449
 450                 #ifdef USE_MPI
 451                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 452
 453                         if (pid == 0) { //only one process should output to screen
 454                 #endif
 455
 456                 //if (output == "square") {  convertMatrix(outputFile); }
 457
 458                 ifstream fileHandle;
 459                 fileHandle.open(outputFile.c_str());
 460                 if(fileHandle) {
 461                         m->gobble(fileHandle);
 462                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 463                 }
 464
 465                 //append the old column file to the new one
 466                 if ((oldfastafile != "") && (column != ""))  {
 467                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 468                         if (outputFile == column) {
 469                                 string tempcolumn = column + ".old";
 470                                 m->appendFiles(tempcolumn, outputFile);
 471                                 m->mothurRemove(tempcolumn);
 472                         }else{
 473                                 m->appendFiles(outputFile, column);
 474                                 m->mothurRemove(outputFile);
 475                                 outputFile = column;
 476                         }
 477
 478                         if (outputDir != "") {
 479                                 string newOutputName = outputDir + m->getSimpleName(outputFile);
 480                                 rename(outputFile.c_str(), newOutputName.c_str());
 481                                 m->mothurRemove(outputFile);
 482                                 outputFile = newOutputName;
 483                         }
 484                 }
 485
 486
 487                 #ifdef USE_MPI
 488                         }
 489                 #endif
 490
 491                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 492
 493                 //set phylip file as new current phylipfile
 494                 string current = "";
 495                 itTypes = outputTypes.find("phylip");
 496                 if (itTypes != outputTypes.end()) {
 497                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 498                 }
 499
 500                 //set column file as new current columnfile
 501                 itTypes = outputTypes.find("column");
 502                 if (itTypes != outputTypes.end()) {
 503                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 504                 }
 505
 506                 m->mothurOutEndLine();
 507                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 508                 m->mothurOut(outputFile); m->mothurOutEndLine();
 509                 m->mothurOutEndLine();
 510                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 511
 512
 513                 if (m->isTrue(compress)) {
 514                         m->mothurOut("Compressing..."); m->mothurOutEndLine();
 515                         m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 516                         system(("gzip -v " + outputFile).c_str());
 517                         outputNames.push_back(outputFile + ".gz");
 518                 }else { outputNames.push_back(outputFile); }
 519
 520                 return 0;
 521
 522         }
 523         catch(exception& e) {
 524                 m->errorOut(e, "DistanceCommand", "execute");
 525                 exit(1);
 526         }
 527 }
 528 /**************************************************************************************************/
 529 void DistanceCommand::createProcesses(string filename) {
 530         try {
 531 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 532                 int process = 1;
 533                 processIDS.clear();
 534
 535                 //loop through and create all the processes you want
 536                 while (process != processors) {
 537                         int pid = fork();
 538
 539                         if (pid > 0) {
 540                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 541                                 process++;
 542                         }else if (pid == 0){
 543                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 544                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 545                                 exit(0);
 546                         }else {
 547                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
 548                                 perror(" : ");
 549                                 for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
 550                                 exit(0);
 551                         }
 552                 }
 553
 554                 //parent does its part
 555                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 556                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 557
 558
 559                 //force parent to wait until all the processes are done
 560                 for (int i=0;i<processIDS.size();i++) {
 561                         int temp = processIDS[i];
 562                         wait(&temp);
 563                 }
 564 #else
 565                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 566                 //Windows version shared memory, so be careful when passing variables through the distanceData struct.
 567                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 568                 //that's why the distance calculator was moved inside of the driver to make separate copies.
 569                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 570
 571                 vector<distanceData*> pDataArray; //[processors-1];
 572                 DWORD   dwThreadIdArray[processors-1];
 573                 HANDLE  hThreadArray[processors-1];
 574
 575                 //Create processor-1 worker threads.
 576                 for( int i=0; i<processors-1; i++ ){
 577
 578                         // Allocate memory for thread data.
 579                         distanceData* tempDist = new distanceData(lines[i+1].start, lines[i+1].end, (filename + toString(i) + ".temp"), cutoff, alignDB, Estimators, m, output, numNewFasta, countends);
 580                         pDataArray.push_back(tempDist);
 581                         processIDS.push_back(i);
 582
 583                         //MyDistThreadFunction is in header. It must be global or static to work with the threads.
 584                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 585                         hThreadArray[i] = CreateThread(NULL, 0, MyDistThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 586                 }
 587
 588                 //do your part
 589                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 590                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 591
 592                 //Wait until all threads have terminated.
 593                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 594
 595                 //Close all thread handles and free memory allocations.
 596                 for(int i=0; i < pDataArray.size(); i++){
 597             if (pDataArray[i]->count != (pDataArray[i]->endLine-pDataArray[i]->startLine)) {
 598                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->endLine-pDataArray[i]->startLine) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
 599             }
 600                         CloseHandle(hThreadArray[i]);
 601                         delete pDataArray[i];
 602                 }
 603 #endif
 604
 605                 //append and remove temp files
 606                 for (int i=0;i<processIDS.size();i++) {
 607                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 608                         m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 609                 }
 610
 611         }
 612         catch(exception& e) {
 613                 m->errorOut(e, "DistanceCommand", "createProcesses");
 614                 exit(1);
 615         }
 616 }
 617 /**************************************************************************************************/
 618 /////// need to fix to work with calcs and sequencedb
 619 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 620         try {
 621                 ValidCalculators validCalculator;
 622                 Dist* distCalculator;
 623                 if (m->isTrue(countends) == true) {
 624                         for (int i=0; i<Estimators.size(); i++) {
 625                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 626                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 627                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 628                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 629                                 }
 630                         }
 631                 }else {
 632                         for (int i=0; i<Estimators.size(); i++) {
 633                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 634                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 635                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 636                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 637                                 }
 638                         }
 639                 }
 640
 641                 int startTime = time(NULL);
 642
 643                 //column file
 644                 ofstream outFile(dFileName.c_str(), ios::trunc);
 645                 outFile.setf(ios::fixed, ios::showpoint);
 646                 outFile << setprecision(4);
 647
 648                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 649
 650                 for(int i=startLine;i<endLine;i++){
 651                         if(output == "lt")      {
 652                                 string name = alignDB.get(i).getName();
 653                                 if (name.length() < 10) { //pad with spaces to make compatible
 654                                         while (name.length() < 10) {  name += " ";  }
 655                                 }
 656                                 outFile << name << '\t';
 657                         }
 658                         for(int j=0;j<i;j++){
 659
 660                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 661
 662                                 //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
 663                                 //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
 664                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 665
 666                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 667                                 double dist = distCalculator->getDist();
 668
 669                                 if(dist <= cutoff){
 670                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 671                                 }
 672                                 if (output == "lt") {  outFile << dist << '\t'; }
 673                         }
 674
 675                         if (output == "lt") { outFile << endl; }
 676
 677                         if(i % 100 == 0){
 678                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 679                         }
 680
 681                 }
 682                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 683
 684                 outFile.close();
 685                 delete distCalculator;
 686
 687                 return 1;
 688         }
 689         catch(exception& e) {
 690                 m->errorOut(e, "DistanceCommand", "driver");
 691                 exit(1);
 692         }
 693 }
 694 /**************************************************************************************************/
 695 /////// need to fix to work with calcs and sequencedb
 696 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 697         try {
 698                 ValidCalculators validCalculator;
 699                 Dist* distCalculator;
 700                 if (m->isTrue(countends) == true) {
 701                         for (int i=0; i<Estimators.size(); i++) {
 702                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 703                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 704                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 705                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 706                                 }
 707                         }
 708                 }else {
 709                         for (int i=0; i<Estimators.size(); i++) {
 710                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 711                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 712                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 713                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 714                                 }
 715                         }
 716                 }
 717
 718                 int startTime = time(NULL);
 719
 720                 //column file
 721                 ofstream outFile(dFileName.c_str(), ios::trunc);
 722                 outFile.setf(ios::fixed, ios::showpoint);
 723                 outFile << setprecision(4);
 724
 725                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 726
 727                 for(int i=startLine;i<endLine;i++){
 728
 729                         string name = alignDB.get(i).getName();
 730                         //pad with spaces to make compatible
 731                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 732
 733                         outFile << name << '\t';
 734
 735                         for(int j=0;j<alignDB.getNumSeqs();j++){
 736
 737                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 738
 739                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 740                                 double dist = distCalculator->getDist();
 741
 742                                 outFile << dist << '\t';
 743                         }
 744
 745                         outFile << endl;
 746
 747                         if(i % 100 == 0){
 748                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 749                         }
 750
 751                 }
 752                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 753
 754                 outFile.close();
 755                 delete distCalculator;
 756
 757                 return 1;
 758         }
 759         catch(exception& e) {
 760                 m->errorOut(e, "DistanceCommand", "driver");
 761                 exit(1);
 762         }
 763 }
 764 #ifdef USE_MPI
 765 /**************************************************************************************************/
 766 /////// need to fix to work with calcs and sequencedb
 767 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 768         try {
 769
 770                 ValidCalculators validCalculator;
 771                 Dist* distCalculator;
 772                 if (m->isTrue(countends) == true) {
 773                         for (int i=0; i<Estimators.size(); i++) {
 774                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 775                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 776                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 777                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 778                                 }
 779                         }
 780                 }else {
 781                         for (int i=0; i<Estimators.size(); i++) {
 782                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 783                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 784                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 785                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 786                                 }
 787                         }
 788                 }
 789
 790
 791                 MPI_Status status;
 792                 int startTime = time(NULL);
 793
 794                 string outputString = "";
 795
 796                 for(int i=startLine;i<endLine;i++){
 797
 798                         for(int j=0;j<i;j++){
 799
 800                                 if (m->control_pressed) {  delete distCalculator; return 0;  }
 801
 802                                 //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
 803                                 //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
 804                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 805
 806                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 807                                 double dist = distCalculator->getDist();
 808
 809                                 if(dist <= cutoff){
 810                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 811                                 }
 812                         }
 813
 814                         if(i % 100 == 0){
 815                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 816                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 817                         }
 818
 819
 820                         //send results to parent
 821                         int length = outputString.length();
 822
 823                         char* buf = new char[length];
 824                         memcpy(buf, outputString.c_str(), length);
 825
 826                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 827                         outputString = "";
 828                         delete buf;
 829
 830                 }
 831
 832                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 833                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 834                 delete distCalculator;
 835                 return 1;
 836         }
 837         catch(exception& e) {
 838                 m->errorOut(e, "DistanceCommand", "driverMPI");
 839                 exit(1);
 840         }
 841 }
 842 /**************************************************************************************************/
 843 /////// need to fix to work with calcs and sequencedb
 844 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 845         try {
 846                 ValidCalculators validCalculator;
 847                 Dist* distCalculator;
 848                 if (m->isTrue(countends) == true) {
 849                         for (int i=0; i<Estimators.size(); i++) {
 850                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 851                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 852                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 853                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 854                                 }
 855                         }
 856                 }else {
 857                         for (int i=0; i<Estimators.size(); i++) {
 858                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 859                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 860                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 861                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 862                                 }
 863                         }
 864                 }
 865
 866
 867                 MPI_Status status;
 868
 869                 MPI_File outMPI;
 870                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 871
 872                 //char* filename = new char[file.length()];
 873                 //memcpy(filename, file.c_str(), file.length());
 874
 875                 char filename[1024];
 876                 strcpy(filename, file.c_str());
 877
 878                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 879                 //delete filename;
 880
 881                 int startTime = time(NULL);
 882
 883                 string outputString = "";
 884                 size = 0;
 885
 886                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 887
 888                 for(int i=startLine;i<endLine;i++){
 889
 890                         string name = alignDB.get(i).getName();
 891                         if (name.length() < 10) { //pad with spaces to make compatible
 892                                 while (name.length() < 10) {  name += " ";  }
 893                         }
 894                         outputString += name + "\t";
 895
 896                         for(int j=0;j<i;j++){
 897
 898                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 899
 900                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 901                                 double dist = distCalculator->getDist();
 902
 903                                 outputString += toString(dist) + "\t";
 904                         }
 905
 906                         outputString += "\n";
 907
 908
 909                         if(i % 100 == 0){
 910                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 911                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 912                         }
 913
 914
 915                         //send results to parent
 916                         int length = outputString.length();
 917                         char* buf = new char[length];
 918                         memcpy(buf, outputString.c_str(), length);
 919
 920                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 921                         size += outputString.length();
 922                         outputString = "";
 923                         delete buf;
 924                 }
 925
 926                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 927                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 928                 MPI_File_close(&outMPI);
 929                 delete distCalculator;
 930
 931                 return 1;
 932         }
 933         catch(exception& e) {
 934                 m->errorOut(e, "DistanceCommand", "driverMPI");
 935                 exit(1);
 936         }
 937 }
 938 /**************************************************************************************************/
 939 /////// need to fix to work with calcs and sequencedb
 940 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 941         try {
 942                 ValidCalculators validCalculator;
 943                 Dist* distCalculator;
 944                 if (m->isTrue(countends) == true) {
 945                         for (int i=0; i<Estimators.size(); i++) {
 946                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 947                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 948                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 949                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 950                                 }
 951                         }
 952                 }else {
 953                         for (int i=0; i<Estimators.size(); i++) {
 954                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 955                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 956                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 957                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 958                                 }
 959                         }
 960                 }
 961
 962                 MPI_Status status;
 963
 964                 MPI_File outMPI;
 965                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 966
 967                 //char* filename = new char[file.length()];
 968                 //memcpy(filename, file.c_str(), file.length());
 969
 970                 char filename[1024];
 971                 strcpy(filename, file.c_str());
 972
 973                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 974                 //delete filename;
 975
 976                 int startTime = time(NULL);
 977
 978                 string outputString = "";
 979                 size = 0;
 980
 981                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 982
 983                 for(int i=startLine;i<endLine;i++){
 984
 985                         string name = alignDB.get(i).getName();
 986                         if (name.length() < 10) { //pad with spaces to make compatible
 987                                 while (name.length() < 10) {  name += " ";  }
 988                         }
 989                         outputString += name + "\t";
 990
 991                         for(int j=0;j<alignDB.getNumSeqs();j++){
 992
 993                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 994
 995                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 996                                 double dist = distCalculator->getDist();
 997
 998                                 outputString += toString(dist) + "\t";
 999                         }
1000
1001                         outputString += "\n";
1002
1003
1004                         if(i % 100 == 0){
1005                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
1006                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
1007                         }
1008
1009
1010                         //send results to parent
1011                         int length = outputString.length();
1012                         char* buf = new char[length];
1013                         memcpy(buf, outputString.c_str(), length);
1014
1015                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
1016                         size += outputString.length();
1017                         outputString = "";
1018                         delete buf;
1019                 }
1020
1021                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
1022                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
1023                 MPI_File_close(&outMPI);
1024                 delete distCalculator;
1025                 return 1;
1026         }
1027         catch(exception& e) {
1028                 m->errorOut(e, "DistanceCommand", "driverMPI");
1029                 exit(1);
1030         }
1031 }
1032 #endif
1033 /**************************************************************************************************
1034 int DistanceCommand::convertMatrix(string outputFile) {
1035         try{
1036
1037                 //sort file by first column so the distances for each row are together
1038                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1039
1040                 //use the unix sort
1041                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1042                         string command = "sort -n " + outputFile + " -o " + outfile;
1043                         system(command.c_str());
1044                 #else //sort using windows sort
1045                         string command = "sort " + outputFile + " /O " + outfile;
1046                         system(command.c_str());
1047                 #endif
1048
1049
1050                 //output to new file distance for each row and save positions in file where new row begins
1051                 ifstream in;
1052                 m->openInputFile(outfile, in);
1053
1054                 ofstream out;
1055                 m->openOutputFile(outputFile, out);
1056
1057                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1058
1059                 out << alignDB.getNumSeqs() << endl;
1060
1061                 //get first currentRow
1062                 string first, currentRow, second;
1063                 float dist;
1064                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1065                 map<string, float>::iterator it;
1066
1067                 in >> first;
1068                 currentRow = first;
1069
1070                 rowDists[first] = 0.00; //distance to yourself is 0.0
1071
1072                 in.seekg(0);
1073                 //m->openInputFile(outfile, in);
1074
1075                 while(!in.eof()) {
1076                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1077
1078                         in >> first >> second >> dist; m->gobble(in);
1079
1080                         if (first != currentRow) {
1081                                 //print out last row
1082                                 out << currentRow << '\t'; //print name
1083
1084                                 //print dists
1085                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1086                                         out << it->second << '\t';
1087                                 }
1088                                 out << endl;
1089
1090                                 //start new row
1091                                 currentRow = first;
1092                                 rowDists.clear();
1093                                 rowDists[first] = 0.00;
1094                                 rowDists[second] = dist;
1095                         }else{
1096                                 rowDists[second] = dist;
1097                         }
1098                 }
1099                 //print out last row
1100                 out << currentRow << '\t'; //print name
1101
1102                 //print dists
1103                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1104                         out << it->second << '\t';
1105                 }
1106                 out << endl;
1107
1108                 in.close();
1109                 out.close();
1110
1111                 m->mothurRemove(outfile);
1112
1113                 return 1;
1114
1115         }
1116         catch(exception& e) {
1117                 m->errorOut(e, "DistanceCommand", "convertMatrix");
1118                 exit(1);
1119         }
1120 }
1121 **************************************************************************************************
1122 int DistanceCommand::convertToLowerTriangle(string outputFile) {
1123         try{
1124
1125                 //sort file by first column so the distances for each row are together
1126                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1127
1128                 //use the unix sort
1129                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1130                         string command = "sort -n " + outputFile + " -o " + outfile;
1131                         system(command.c_str());
1132                 #else //sort using windows sort
1133                         string command = "sort " + outputFile + " /O " + outfile;
1134                         system(command.c_str());
1135                 #endif
1136
1137
1138                 //output to new file distance for each row and save positions in file where new row begins
1139                 ifstream in;
1140                 m->openInputFile(outfile, in);
1141
1142                 ofstream out;
1143                 m->openOutputFile(outputFile, out);
1144
1145                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1146
1147                 out << alignDB.getNumSeqs() << endl;
1148
1149                 //get first currentRow
1150                 string first, currentRow, second;
1151                 float dist;
1152                 int i, j;
1153                 i = 0; j = 0;
1154                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1155                 map<string, float>::iterator it;
1156
1157                 in >> first;
1158                 currentRow = first;
1159
1160                 rowDists[first] = 0.00; //distance to yourself is 0.0
1161
1162                 in.seekg(0);
1163                 //m->openInputFile(outfile, in);
1164
1165                 while(!in.eof()) {
1166                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1167
1168                         in >> first >> second >> dist; m->gobble(in);
1169
1170                         if (first != currentRow) {
1171                                 //print out last row
1172                                 out << currentRow << '\t'; //print name
1173
1174                                 //print dists
1175                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1176                                         if (j >= i) { break; }
1177                                         out << it->second << '\t';
1178                                         j++;
1179                                 }
1180                                 out << endl;
1181
1182                                 //start new row
1183                                 currentRow = first;
1184                                 rowDists.clear();
1185                                 rowDists[first] = 0.00;
1186                                 rowDists[second] = dist;
1187                                 j = 0;
1188                                 i++;
1189                         }else{
1190                                 rowDists[second] = dist;
1191                         }
1192                 }
1193                 //print out last row
1194                 out << currentRow << '\t'; //print name
1195
1196                 //print dists
1197                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1198                         out << it->second << '\t';
1199                 }
1200                 out << endl;
1201
1202                 in.close();
1203                 out.close();
1204
1205                 m->mothurRemove(outfile);
1206
1207                 return 1;
1208
1209         }
1210         catch(exception& e) {
1211                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
1212                 exit(1);
1213         }
1214 }
1215 **************************************************************************************************/
1216 //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,
1217 //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.
1218 //also check to make sure the 2 files have the same alignment length.
1219 bool DistanceCommand::sanityCheck() {
1220         try{
1221                 bool good = true;
1222
1223                 //make sure the 2 fasta files have the same alignment length
1224                 ifstream in;
1225                 m->openInputFile(fastafile, in);
1226                 int fastaAlignLength = 0;
1227                 if (in) {
1228                         Sequence tempIn(in);
1229                         fastaAlignLength = tempIn.getAligned().length();
1230                 }
1231                 in.close();
1232
1233                 ifstream in2;
1234                 m->openInputFile(oldfastafile, in2);
1235                 int oldfastaAlignLength = 0;
1236                 if (in2) {
1237                         Sequence tempIn2(in2);
1238                         oldfastaAlignLength = tempIn2.getAligned().length();
1239                 }
1240                 in2.close();
1241
1242                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1243
1244                 //read fasta file and save names as well as adding them to the alignDB
1245                 set<string> namesOldFasta;
1246
1247                 ifstream inFasta;
1248                 m->openInputFile(oldfastafile, inFasta);
1249
1250                 while (!inFasta.eof()) {
1251                         if (m->control_pressed) {  inFasta.close(); return good;  }
1252
1253                         Sequence temp(inFasta);
1254
1255                         if (temp.getName() != "") {
1256                                 namesOldFasta.insert(temp.getName());  //save name
1257                                 alignDB.push_back(temp);  //add to DB
1258                         }
1259
1260                         m->gobble(inFasta);
1261                 }
1262
1263                 inFasta.close();
1264
1265                 //read through the column file checking names and removing distances above the cutoff
1266                 ifstream inDist;
1267                 m->openInputFile(column, inDist);
1268
1269                 ofstream outDist;
1270                 string outputFile = column + ".temp";
1271                 m->openOutputFile(outputFile, outDist);
1272
1273                 string name1, name2;
1274                 float dist;
1275                 while (!inDist.eof()) {
1276                         if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
1277
1278                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1279
1280                         //both names are in fasta file and distance is below cutoff
1281                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1282                         else{
1283                                 if (dist <= cutoff) {
1284                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1285                                 }
1286                         }
1287                 }
1288
1289                 inDist.close();
1290                 outDist.close();
1291
1292                 if (good) {
1293                         m->mothurRemove(column);
1294                         rename(outputFile.c_str(), column.c_str());
1295                 }else{
1296                         m->mothurRemove(outputFile); //temp file is bad because file mismatch above
1297                 }
1298
1299                 return good;
1300
1301         }
1302         catch(exception& e) {
1303                 m->errorOut(e, "DistanceCommand", "sanityCheck");
1304                 exit(1);
1305         }
1306 }
1307 /**************************************************************************************************/
1308
1309
1310
1311