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                         CloseHandle(hThreadArray[i]);
 598                         delete pDataArray[i];
 599                 }
 600 #endif
 601
 602                 //append and remove temp files
 603                 for (int i=0;i<processIDS.size();i++) {
 604                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 605                         m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 606                 }
 607
 608         }
 609         catch(exception& e) {
 610                 m->errorOut(e, "DistanceCommand", "createProcesses");
 611                 exit(1);
 612         }
 613 }
 614 /**************************************************************************************************/
 615 /////// need to fix to work with calcs and sequencedb
 616 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 617         try {
 618                 ValidCalculators validCalculator;
 619                 Dist* distCalculator;
 620                 if (m->isTrue(countends) == true) {
 621                         for (int i=0; i<Estimators.size(); i++) {
 622                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 623                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 624                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 625                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 626                                 }
 627                         }
 628                 }else {
 629                         for (int i=0; i<Estimators.size(); i++) {
 630                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 631                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 632                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 633                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 634                                 }
 635                         }
 636                 }
 637
 638                 int startTime = time(NULL);
 639
 640                 //column file
 641                 ofstream outFile(dFileName.c_str(), ios::trunc);
 642                 outFile.setf(ios::fixed, ios::showpoint);
 643                 outFile << setprecision(4);
 644
 645                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 646
 647                 for(int i=startLine;i<endLine;i++){
 648                         if(output == "lt")      {
 649                                 string name = alignDB.get(i).getName();
 650                                 if (name.length() < 10) { //pad with spaces to make compatible
 651                                         while (name.length() < 10) {  name += " ";  }
 652                                 }
 653                                 outFile << name << '\t';
 654                         }
 655                         for(int j=0;j<i;j++){
 656
 657                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 658
 659                                 //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
 660                                 //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
 661                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 662
 663                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 664                                 double dist = distCalculator->getDist();
 665
 666                                 if(dist <= cutoff){
 667                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 668                                 }
 669                                 if (output == "lt") {  outFile << dist << '\t'; }
 670                         }
 671
 672                         if (output == "lt") { outFile << endl; }
 673
 674                         if(i % 100 == 0){
 675                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 676                         }
 677
 678                 }
 679                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 680
 681                 outFile.close();
 682                 delete distCalculator;
 683
 684                 return 1;
 685         }
 686         catch(exception& e) {
 687                 m->errorOut(e, "DistanceCommand", "driver");
 688                 exit(1);
 689         }
 690 }
 691 /**************************************************************************************************/
 692 /////// need to fix to work with calcs and sequencedb
 693 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 694         try {
 695                 ValidCalculators validCalculator;
 696                 Dist* distCalculator;
 697                 if (m->isTrue(countends) == true) {
 698                         for (int i=0; i<Estimators.size(); i++) {
 699                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 700                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 701                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 702                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 703                                 }
 704                         }
 705                 }else {
 706                         for (int i=0; i<Estimators.size(); i++) {
 707                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 708                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 709                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 710                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 711                                 }
 712                         }
 713                 }
 714
 715                 int startTime = time(NULL);
 716
 717                 //column file
 718                 ofstream outFile(dFileName.c_str(), ios::trunc);
 719                 outFile.setf(ios::fixed, ios::showpoint);
 720                 outFile << setprecision(4);
 721
 722                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 723
 724                 for(int i=startLine;i<endLine;i++){
 725
 726                         string name = alignDB.get(i).getName();
 727                         //pad with spaces to make compatible
 728                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 729
 730                         outFile << name << '\t';
 731
 732                         for(int j=0;j<alignDB.getNumSeqs();j++){
 733
 734                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 735
 736                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 737                                 double dist = distCalculator->getDist();
 738
 739                                 outFile << dist << '\t';
 740                         }
 741
 742                         outFile << endl;
 743
 744                         if(i % 100 == 0){
 745                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 746                         }
 747
 748                 }
 749                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 750
 751                 outFile.close();
 752                 delete distCalculator;
 753
 754                 return 1;
 755         }
 756         catch(exception& e) {
 757                 m->errorOut(e, "DistanceCommand", "driver");
 758                 exit(1);
 759         }
 760 }
 761 #ifdef USE_MPI
 762 /**************************************************************************************************/
 763 /////// need to fix to work with calcs and sequencedb
 764 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 765         try {
 766
 767                 ValidCalculators validCalculator;
 768                 Dist* distCalculator;
 769                 if (m->isTrue(countends) == true) {
 770                         for (int i=0; i<Estimators.size(); i++) {
 771                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 772                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 773                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 774                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 775                                 }
 776                         }
 777                 }else {
 778                         for (int i=0; i<Estimators.size(); i++) {
 779                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 780                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 781                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 782                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 783                                 }
 784                         }
 785                 }
 786
 787
 788                 MPI_Status status;
 789                 int startTime = time(NULL);
 790
 791                 string outputString = "";
 792
 793                 for(int i=startLine;i<endLine;i++){
 794
 795                         for(int j=0;j<i;j++){
 796
 797                                 if (m->control_pressed) {  delete distCalculator; return 0;  }
 798
 799                                 //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
 800                                 //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
 801                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 802
 803                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 804                                 double dist = distCalculator->getDist();
 805
 806                                 if(dist <= cutoff){
 807                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 808                                 }
 809                         }
 810
 811                         if(i % 100 == 0){
 812                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 813                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 814                         }
 815
 816
 817                         //send results to parent
 818                         int length = outputString.length();
 819
 820                         char* buf = new char[length];
 821                         memcpy(buf, outputString.c_str(), length);
 822
 823                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 824                         outputString = "";
 825                         delete buf;
 826
 827                 }
 828
 829                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 830                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 831                 delete distCalculator;
 832                 return 1;
 833         }
 834         catch(exception& e) {
 835                 m->errorOut(e, "DistanceCommand", "driverMPI");
 836                 exit(1);
 837         }
 838 }
 839 /**************************************************************************************************/
 840 /////// need to fix to work with calcs and sequencedb
 841 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 842         try {
 843                 ValidCalculators validCalculator;
 844                 Dist* distCalculator;
 845                 if (m->isTrue(countends) == true) {
 846                         for (int i=0; i<Estimators.size(); i++) {
 847                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 848                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 849                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 850                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 851                                 }
 852                         }
 853                 }else {
 854                         for (int i=0; i<Estimators.size(); i++) {
 855                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 856                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 857                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 858                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 859                                 }
 860                         }
 861                 }
 862
 863
 864                 MPI_Status status;
 865
 866                 MPI_File outMPI;
 867                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 868
 869                 //char* filename = new char[file.length()];
 870                 //memcpy(filename, file.c_str(), file.length());
 871
 872                 char filename[1024];
 873                 strcpy(filename, file.c_str());
 874
 875                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 876                 //delete filename;
 877
 878                 int startTime = time(NULL);
 879
 880                 string outputString = "";
 881                 size = 0;
 882
 883                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 884
 885                 for(int i=startLine;i<endLine;i++){
 886
 887                         string name = alignDB.get(i).getName();
 888                         if (name.length() < 10) { //pad with spaces to make compatible
 889                                 while (name.length() < 10) {  name += " ";  }
 890                         }
 891                         outputString += name + "\t";
 892
 893                         for(int j=0;j<i;j++){
 894
 895                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 896
 897                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 898                                 double dist = distCalculator->getDist();
 899
 900                                 outputString += toString(dist) + "\t";
 901                         }
 902
 903                         outputString += "\n";
 904
 905
 906                         if(i % 100 == 0){
 907                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 908                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 909                         }
 910
 911
 912                         //send results to parent
 913                         int length = outputString.length();
 914                         char* buf = new char[length];
 915                         memcpy(buf, outputString.c_str(), length);
 916
 917                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 918                         size += outputString.length();
 919                         outputString = "";
 920                         delete buf;
 921                 }
 922
 923                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 924                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 925                 MPI_File_close(&outMPI);
 926                 delete distCalculator;
 927
 928                 return 1;
 929         }
 930         catch(exception& e) {
 931                 m->errorOut(e, "DistanceCommand", "driverMPI");
 932                 exit(1);
 933         }
 934 }
 935 /**************************************************************************************************/
 936 /////// need to fix to work with calcs and sequencedb
 937 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 938         try {
 939                 ValidCalculators validCalculator;
 940                 Dist* distCalculator;
 941                 if (m->isTrue(countends) == true) {
 942                         for (int i=0; i<Estimators.size(); i++) {
 943                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 944                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 945                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 946                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 947                                 }
 948                         }
 949                 }else {
 950                         for (int i=0; i<Estimators.size(); i++) {
 951                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 952                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 953                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 954                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 955                                 }
 956                         }
 957                 }
 958
 959                 MPI_Status status;
 960
 961                 MPI_File outMPI;
 962                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 963
 964                 //char* filename = new char[file.length()];
 965                 //memcpy(filename, file.c_str(), file.length());
 966
 967                 char filename[1024];
 968                 strcpy(filename, file.c_str());
 969
 970                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 971                 //delete filename;
 972
 973                 int startTime = time(NULL);
 974
 975                 string outputString = "";
 976                 size = 0;
 977
 978                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 979
 980                 for(int i=startLine;i<endLine;i++){
 981
 982                         string name = alignDB.get(i).getName();
 983                         if (name.length() < 10) { //pad with spaces to make compatible
 984                                 while (name.length() < 10) {  name += " ";  }
 985                         }
 986                         outputString += name + "\t";
 987
 988                         for(int j=0;j<alignDB.getNumSeqs();j++){
 989
 990                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 991
 992                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 993                                 double dist = distCalculator->getDist();
 994
 995                                 outputString += toString(dist) + "\t";
 996                         }
 997
 998                         outputString += "\n";
 999
1000
1001                         if(i % 100 == 0){
1002                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
1003                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
1004                         }
1005
1006
1007                         //send results to parent
1008                         int length = outputString.length();
1009                         char* buf = new char[length];
1010                         memcpy(buf, outputString.c_str(), length);
1011
1012                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
1013                         size += outputString.length();
1014                         outputString = "";
1015                         delete buf;
1016                 }
1017
1018                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
1019                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
1020                 MPI_File_close(&outMPI);
1021                 delete distCalculator;
1022                 return 1;
1023         }
1024         catch(exception& e) {
1025                 m->errorOut(e, "DistanceCommand", "driverMPI");
1026                 exit(1);
1027         }
1028 }
1029 #endif
1030 /**************************************************************************************************
1031 int DistanceCommand::convertMatrix(string outputFile) {
1032         try{
1033
1034                 //sort file by first column so the distances for each row are together
1035                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1036
1037                 //use the unix sort
1038                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1039                         string command = "sort -n " + outputFile + " -o " + outfile;
1040                         system(command.c_str());
1041                 #else //sort using windows sort
1042                         string command = "sort " + outputFile + " /O " + outfile;
1043                         system(command.c_str());
1044                 #endif
1045
1046
1047                 //output to new file distance for each row and save positions in file where new row begins
1048                 ifstream in;
1049                 m->openInputFile(outfile, in);
1050
1051                 ofstream out;
1052                 m->openOutputFile(outputFile, out);
1053
1054                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1055
1056                 out << alignDB.getNumSeqs() << endl;
1057
1058                 //get first currentRow
1059                 string first, currentRow, second;
1060                 float dist;
1061                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1062                 map<string, float>::iterator it;
1063
1064                 in >> first;
1065                 currentRow = first;
1066
1067                 rowDists[first] = 0.00; //distance to yourself is 0.0
1068
1069                 in.seekg(0);
1070                 //m->openInputFile(outfile, in);
1071
1072                 while(!in.eof()) {
1073                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1074
1075                         in >> first >> second >> dist; m->gobble(in);
1076
1077                         if (first != currentRow) {
1078                                 //print out last row
1079                                 out << currentRow << '\t'; //print name
1080
1081                                 //print dists
1082                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1083                                         out << it->second << '\t';
1084                                 }
1085                                 out << endl;
1086
1087                                 //start new row
1088                                 currentRow = first;
1089                                 rowDists.clear();
1090                                 rowDists[first] = 0.00;
1091                                 rowDists[second] = dist;
1092                         }else{
1093                                 rowDists[second] = dist;
1094                         }
1095                 }
1096                 //print out last row
1097                 out << currentRow << '\t'; //print name
1098
1099                 //print dists
1100                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1101                         out << it->second << '\t';
1102                 }
1103                 out << endl;
1104
1105                 in.close();
1106                 out.close();
1107
1108                 m->mothurRemove(outfile);
1109
1110                 return 1;
1111
1112         }
1113         catch(exception& e) {
1114                 m->errorOut(e, "DistanceCommand", "convertMatrix");
1115                 exit(1);
1116         }
1117 }
1118 **************************************************************************************************
1119 int DistanceCommand::convertToLowerTriangle(string outputFile) {
1120         try{
1121
1122                 //sort file by first column so the distances for each row are together
1123                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1124
1125                 //use the unix sort
1126                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1127                         string command = "sort -n " + outputFile + " -o " + outfile;
1128                         system(command.c_str());
1129                 #else //sort using windows sort
1130                         string command = "sort " + outputFile + " /O " + outfile;
1131                         system(command.c_str());
1132                 #endif
1133
1134
1135                 //output to new file distance for each row and save positions in file where new row begins
1136                 ifstream in;
1137                 m->openInputFile(outfile, in);
1138
1139                 ofstream out;
1140                 m->openOutputFile(outputFile, out);
1141
1142                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1143
1144                 out << alignDB.getNumSeqs() << endl;
1145
1146                 //get first currentRow
1147                 string first, currentRow, second;
1148                 float dist;
1149                 int i, j;
1150                 i = 0; j = 0;
1151                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1152                 map<string, float>::iterator it;
1153
1154                 in >> first;
1155                 currentRow = first;
1156
1157                 rowDists[first] = 0.00; //distance to yourself is 0.0
1158
1159                 in.seekg(0);
1160                 //m->openInputFile(outfile, in);
1161
1162                 while(!in.eof()) {
1163                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1164
1165                         in >> first >> second >> dist; m->gobble(in);
1166
1167                         if (first != currentRow) {
1168                                 //print out last row
1169                                 out << currentRow << '\t'; //print name
1170
1171                                 //print dists
1172                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1173                                         if (j >= i) { break; }
1174                                         out << it->second << '\t';
1175                                         j++;
1176                                 }
1177                                 out << endl;
1178
1179                                 //start new row
1180                                 currentRow = first;
1181                                 rowDists.clear();
1182                                 rowDists[first] = 0.00;
1183                                 rowDists[second] = dist;
1184                                 j = 0;
1185                                 i++;
1186                         }else{
1187                                 rowDists[second] = dist;
1188                         }
1189                 }
1190                 //print out last row
1191                 out << currentRow << '\t'; //print name
1192
1193                 //print dists
1194                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1195                         out << it->second << '\t';
1196                 }
1197                 out << endl;
1198
1199                 in.close();
1200                 out.close();
1201
1202                 m->mothurRemove(outfile);
1203
1204                 return 1;
1205
1206         }
1207         catch(exception& e) {
1208                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
1209                 exit(1);
1210         }
1211 }
1212 **************************************************************************************************/
1213 //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,
1214 //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.
1215 //also check to make sure the 2 files have the same alignment length.
1216 bool DistanceCommand::sanityCheck() {
1217         try{
1218                 bool good = true;
1219
1220                 //make sure the 2 fasta files have the same alignment length
1221                 ifstream in;
1222                 m->openInputFile(fastafile, in);
1223                 int fastaAlignLength = 0;
1224                 if (in) {
1225                         Sequence tempIn(in);
1226                         fastaAlignLength = tempIn.getAligned().length();
1227                 }
1228                 in.close();
1229
1230                 ifstream in2;
1231                 m->openInputFile(oldfastafile, in2);
1232                 int oldfastaAlignLength = 0;
1233                 if (in2) {
1234                         Sequence tempIn2(in2);
1235                         oldfastaAlignLength = tempIn2.getAligned().length();
1236                 }
1237                 in2.close();
1238
1239                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1240
1241                 //read fasta file and save names as well as adding them to the alignDB
1242                 set<string> namesOldFasta;
1243
1244                 ifstream inFasta;
1245                 m->openInputFile(oldfastafile, inFasta);
1246
1247                 while (!inFasta.eof()) {
1248                         if (m->control_pressed) {  inFasta.close(); return good;  }
1249
1250                         Sequence temp(inFasta);
1251
1252                         if (temp.getName() != "") {
1253                                 namesOldFasta.insert(temp.getName());  //save name
1254                                 alignDB.push_back(temp);  //add to DB
1255                         }
1256
1257                         m->gobble(inFasta);
1258                 }
1259
1260                 inFasta.close();
1261
1262                 //read through the column file checking names and removing distances above the cutoff
1263                 ifstream inDist;
1264                 m->openInputFile(column, inDist);
1265
1266                 ofstream outDist;
1267                 string outputFile = column + ".temp";
1268                 m->openOutputFile(outputFile, outDist);
1269
1270                 string name1, name2;
1271                 float dist;
1272                 while (!inDist.eof()) {
1273                         if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
1274
1275                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1276
1277                         //both names are in fasta file and distance is below cutoff
1278                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1279                         else{
1280                                 if (dist <= cutoff) {
1281                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1282                                 }
1283                         }
1284                 }
1285
1286                 inDist.close();
1287                 outDist.close();
1288
1289                 if (good) {
1290                         m->mothurRemove(column);
1291                         rename(outputFile.c_str(), column.c_str());
1292                 }else{
1293                         m->mothurRemove(outputFile); //temp file is bad because file mismatch above
1294                 }
1295
1296                 return good;
1297
1298         }
1299         catch(exception& e) {
1300                 m->errorOut(e, "DistanceCommand", "sanityCheck");
1301                 exit(1);
1302         }
1303 }
1304 /**************************************************************************************************/
1305
1306
1307
1308