distancecommand.cpp

   1 /*
   2  *  distancecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/7/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "distancecommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> DistanceCommand::setParameters(){
  14         try {
  15                 CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
  16                 CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(poutput);
  19                 CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
  20                 CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
  21                 CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "DistanceCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string DistanceCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
  41                 helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors.  \n";
  42                 helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
  43                 helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
  44                 helpString += "The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
  45                 helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n";
  46                 helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
  47                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
  48                 helpString += "The processors parameter allows you to specify number of processors to use.  The default is 1.\n";
  49                 helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n";
  50                 helpString += "The dist.seqs command should be in the following format: \n";
  51                 helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
  52                 helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "DistanceCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string DistanceCommand::getOutputFileNameTag(string type, string inputName=""){
  63         try {
  64         string outputFileName = "";
  65                 map<string, vector<string> >::iterator it;
  66
  67         //is this a type this command creates
  68         it = outputTypes.find(type);
  69         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  70         else {
  71             if (type == "phylip") {  outputFileName =  "dist"; }
  72             else if (type == "column") {  outputFileName =  "dist"; }
  73             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  74         }
  75         return outputFileName;
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "DistanceCommand", "getOutputFileNameTag");
  79                 exit(1);
  80         }
  81 }
  82 //**********************************************************************************************************************
  83 DistanceCommand::DistanceCommand(){
  84         try {
  85                 abort = true; calledHelp = true;
  86                 setParameters();
  87                 vector<string> tempOutNames;
  88                 outputTypes["phylip"] = tempOutNames;
  89                 outputTypes["column"] = tempOutNames;
  90         }
  91         catch(exception& e) {
  92                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
  93                 exit(1);
  94         }
  95 }
  96 //**********************************************************************************************************************
  97 DistanceCommand::DistanceCommand(string option) {
  98         try {
  99                 abort = false; calledHelp = false;
 100                 Estimators.clear();
 101
 102                 //allow user to run help
 103                 if(option == "help") { help(); abort = true; calledHelp = true; }
 104                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 105
 106                 else {
 107                         vector<string> myArray = setParameters();
 108
 109                         OptionParser parser(option);
 110                         map<string, string> parameters = parser.getParameters();
 111
 112                         ValidParameters validParameter("dist.seqs");
 113                         map<string, string>::iterator it2;
 114
 115                         //check to make sure all parameters are valid for command
 116                         for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 117                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 118                         }
 119
 120                         //initialize outputTypes
 121                         vector<string> tempOutNames;
 122                         outputTypes["phylip"] = tempOutNames;
 123                         outputTypes["column"] = tempOutNames;
 124
 125                         //if the user changes the input directory command factory will send this info to us in the output parameter
 126                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 127                         if (inputDir == "not found"){   inputDir = "";          }
 128                         else {
 129                                 string path;
 130                                 it2 = parameters.find("fasta");
 131                                 //user has given a template file
 132                                 if(it2 != parameters.end()){
 133                                         path = m->hasPath(it2->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["fasta"] = inputDir + it2->second;           }
 136                                 }
 137
 138                                 it2 = parameters.find("oldfasta");
 139                                 //user has given a template file
 140                                 if(it2 != parameters.end()){
 141                                         path = m->hasPath(it2->second);
 142                                         //if the user has not given a path then, add inputdir. else leave path alone.
 143                                         if (path == "") {       parameters["oldfasta"] = inputDir + it2->second;                }
 144                                 }
 145
 146                                 it2 = parameters.find("column");
 147                                 //user has given a template file
 148                                 if(it2 != parameters.end()){
 149                                         path = m->hasPath(it2->second);
 150                                         //if the user has not given a path then, add inputdir. else leave path alone.
 151                                         if (path == "") {       parameters["column"] = inputDir + it2->second;          }
 152                                 }
 153                         }
 154
 155                         //check for required parameters
 156                         fastafile = validParameter.validFile(parameters, "fasta", true);
 157                         if (fastafile == "not found") {
 158                                 fastafile = m->getFastaFile();
 159                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
 160                                         ifstream inFASTA;
 161                                         m->openInputFile(fastafile, inFASTA);
 162                                         alignDB = SequenceDB(inFASTA);
 163                                         inFASTA.close();
 164                                 }else {         m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 165                         }else if (fastafile == "not open") { abort = true; }
 166                         else{
 167                                 ifstream inFASTA;
 168                                 m->openInputFile(fastafile, inFASTA);
 169                                 alignDB = SequenceDB(inFASTA);
 170                                 inFASTA.close();
 171                                 m->setFastaFile(fastafile);
 172                         }
 173
 174                         oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
 175                         if (oldfastafile == "not found") { oldfastafile = ""; }
 176                         else if (oldfastafile == "not open") { abort = true; }
 177
 178                         column = validParameter.validFile(parameters, "column", true);
 179                         if (column == "not found") { column = ""; }
 180                         else if (column == "not open") { abort = true; }
 181                         else { m->setColumnFile(column); }
 182
 183                         //if the user changes the output directory command factory will send this info to us in the output parameter
 184                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 185                                 outputDir = "";
 186                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 187                         }
 188
 189                         //check for optional parameter and set defaults
 190                         // ...at some point should added some additional type checking...
 191                         calc = validParameter.validFile(parameters, "calc", false);
 192                         if (calc == "not found") { calc = "onegap";  }
 193                         else {
 194                                  if (calc == "default")  {  calc = "onegap";  }
 195                         }
 196                         m->splitAtDash(calc, Estimators);
 197
 198                         string temp;
 199                         temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
 200                         convert(temp, countends);
 201
 202                         temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
 203                         m->mothurConvert(temp, cutoff);
 204
 205                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 206                         m->setProcessors(temp);
 207                         m->mothurConvert(temp, processors);
 208
 209                         temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
 210                         convert(temp, compress);
 211
 212                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "column"; }
 213             if (output == "phylip") { output = "lt";  }
 214
 215                         if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
 216
 217                         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; }
 218
 219                         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"; }
 220
 221                 }
 222
 223         }
 224         catch(exception& e) {
 225                 m->errorOut(e, "DistanceCommand", "DistanceCommand");
 226                 exit(1);
 227         }
 228 }
 229 //**********************************************************************************************************************
 230
 231 int DistanceCommand::execute(){
 232         try {
 233
 234                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 235
 236                 int startTime = time(NULL);
 237
 238                 //save number of new sequence
 239                 numNewFasta = alignDB.getNumSeqs();
 240
 241                 //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
 242                 if ((oldfastafile != "") && (column != ""))  {  if (!(sanityCheck())) { return 0; }  }
 243
 244                 if (m->control_pressed) { return 0; }
 245
 246                 int numSeqs = alignDB.getNumSeqs();
 247                 cutoff += 0.005;
 248
 249                 if (!alignDB.sameLength()) {  m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
 250
 251                 string outputFile;
 252
 253                 if (output == "lt") { //does the user want lower triangle phylip formatted file
 254                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip." + getOutputFileNameTag("phylip");
 255                         m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 256
 257                         //output numSeqs to phylip formatted dist file
 258                 }else if (output == "column") { //user wants column format
 259                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
 260                         outputTypes["column"].push_back(outputFile);
 261
 262                         //so we don't accidentally overwrite
 263                         if (outputFile == column) {
 264                                 string tempcolumn = column + ".old";
 265                                 rename(column.c_str(), tempcolumn.c_str());
 266                         }
 267
 268                         m->mothurRemove(outputFile);
 269                 }else { //assume square
 270                         outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square." + getOutputFileNameTag("phylip");
 271                         m->mothurRemove(outputFile);
 272                         outputTypes["phylip"].push_back(outputFile);
 273                 }
 274
 275
 276 #ifdef USE_MPI
 277
 278                 int pid, start, end;
 279                 int tag = 2001;
 280
 281                 MPI_Status status;
 282                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 283                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 284
 285                 //each process gets where it should start and stop in the file
 286                 if (output != "square") {
 287                         start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 288                         end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 289                 }else{
 290                         start = int ((float(pid)/float(processors)) * numSeqs);
 291                         end = int ((float(pid+1)/float(processors)) * numSeqs);
 292                 }
 293
 294                 if (output == "column") {
 295                         MPI_File outMPI;
 296                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 297
 298                         //char* filename = new char[outputFile.length()];
 299                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 300
 301                         char filename[1024];
 302                         strcpy(filename, outputFile.c_str());
 303
 304                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 305                         //delete filename;
 306
 307                         if (pid == 0) { //you are the root process
 308
 309                                 //do your part
 310                                 string outputMyPart;
 311
 312                                 driverMPI(start, end, outMPI, cutoff);
 313
 314                                 if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);   return 0; }
 315
 316                                 //wait on chidren
 317                                 for(int i = 1; i < processors; i++) {
 318                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);    return 0; }
 319
 320                                         char buf[5];
 321                                         MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 322                                 }
 323                         }else { //you are a child process
 324                                 //do your part
 325                                 driverMPI(start, end, outMPI, cutoff);
 326
 327                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
 328
 329                                 char buf[5];
 330                                 strcpy(buf, "done");
 331                                 //tell parent you are done.
 332                                 MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 333                         }
 334
 335                         MPI_File_close(&outMPI);
 336
 337                 }else { //lower triangle format
 338                         if (pid == 0) { //you are the root process
 339
 340                                 //do your part
 341                                 string outputMyPart;
 342                                 unsigned long long mySize;
 343
 344                                 if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 345                                 else { driverMPI(start, end, outputFile, mySize, output); }
 346
 347                                 if (m->control_pressed) {  outputTypes.clear();   return 0; }
 348
 349                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 350                                 MPI_File outMPI;
 351                                 MPI_File inMPI;
 352
 353                                 //char* filename = new char[outputFile.length()];
 354                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 355
 356                                 char filename[1024];
 357                                 strcpy(filename, outputFile.c_str());
 358
 359                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 360                                 //delete filename;
 361
 362                                 //wait on chidren
 363                                 for(int b = 1; b < processors; b++) {
 364                                         unsigned long long fileSize;
 365
 366                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
 367
 368                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 369
 370                                         string outTemp = outputFile + toString(b) + ".temp";
 371
 372                                         char* buf = new char[outTemp.length()];
 373                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 374
 375                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 376                                         delete buf;
 377
 378                                         int count = 0;
 379                                         while (count < fileSize) {
 380                                                 char buf2[1];
 381                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 382                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 383                                                 count += 1;
 384                                         }
 385
 386                                         MPI_File_close(&inMPI); //deleted on close
 387                                 }
 388
 389                                 MPI_File_close(&outMPI);
 390                         }else { //you are a child process
 391                                 //do your part
 392                                 unsigned long long size;
 393                                 if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 394                                 else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 395
 396                                 if (m->control_pressed) {  return 0; }
 397
 398                                 //tell parent you are done.
 399                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 400                         }
 401                 }
 402                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 403 #else
 404
 405         //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 406                 //if you don't need to fork anything
 407                 if(processors == 1){
 408                         if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 409                         else { driver(0, numSeqs, outputFile, "square");  }
 410                 }else{ //you have multiple processors
 411
 412                         unsigned long long numDists = 0;
 413
 414                         if (output == "square") {
 415                                  numDists = numSeqs * numSeqs;
 416                         }else {
 417                                 for(int i=0;i<numSeqs;i++){
 418                                         for(int j=0;j<i;j++){
 419                                                 numDists++;
 420                                                 if (numDists > processors) { break; }
 421                                         }
 422                                 }
 423                         }
 424
 425                         if (numDists < processors) { processors = numDists; }
 426
 427                         for (int i = 0; i < processors; i++) {
 428                                 distlinePair tempLine;
 429                                 lines.push_back(tempLine);
 430                                 if (output != "square") {
 431                                         lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
 432                                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 433                                 }else{
 434                                         lines[i].start = int ((float(i)/float(processors)) * numSeqs);
 435                                         lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
 436                                 }
 437
 438                         }
 439
 440                         createProcesses(outputFile);
 441                 }
 442         //#else
 443                 //ifstream inFASTA;
 444                 //if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 445                 //else { driver(0, numSeqs, outputFile, "square");  }
 446         //#endif
 447
 448 #endif
 449                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 450
 451                 #ifdef USE_MPI
 452                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 453
 454                         if (pid == 0) { //only one process should output to screen
 455                 #endif
 456
 457                 //if (output == "square") {  convertMatrix(outputFile); }
 458
 459                 ifstream fileHandle;
 460                 fileHandle.open(outputFile.c_str());
 461                 if(fileHandle) {
 462                         m->gobble(fileHandle);
 463                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 464                 }
 465
 466                 //append the old column file to the new one
 467                 if ((oldfastafile != "") && (column != ""))  {
 468                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 469                         if (outputFile == column) {
 470                                 string tempcolumn = column + ".old";
 471                                 m->appendFiles(tempcolumn, outputFile);
 472                                 m->mothurRemove(tempcolumn);
 473                         }else{
 474                                 m->appendFiles(outputFile, column);
 475                                 m->mothurRemove(outputFile);
 476                                 outputFile = column;
 477                         }
 478
 479                         if (outputDir != "") {
 480                                 string newOutputName = outputDir + m->getSimpleName(outputFile);
 481                                 rename(outputFile.c_str(), newOutputName.c_str());
 482                                 m->mothurRemove(outputFile);
 483                                 outputFile = newOutputName;
 484                         }
 485                 }
 486
 487
 488                 #ifdef USE_MPI
 489                         }
 490                 #endif
 491
 492                 if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 493
 494                 //set phylip file as new current phylipfile
 495                 string current = "";
 496                 itTypes = outputTypes.find("phylip");
 497                 if (itTypes != outputTypes.end()) {
 498                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 499                 }
 500
 501                 //set column file as new current columnfile
 502                 itTypes = outputTypes.find("column");
 503                 if (itTypes != outputTypes.end()) {
 504                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
 505                 }
 506
 507                 m->mothurOutEndLine();
 508                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 509                 m->mothurOut(outputFile); m->mothurOutEndLine();
 510                 m->mothurOutEndLine();
 511                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 512
 513
 514                 if (m->isTrue(compress)) {
 515                         m->mothurOut("Compressing..."); m->mothurOutEndLine();
 516                         m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
 517                         system(("gzip -v " + outputFile).c_str());
 518                         outputNames.push_back(outputFile + ".gz");
 519                 }else { outputNames.push_back(outputFile); }
 520
 521                 return 0;
 522
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "DistanceCommand", "execute");
 526                 exit(1);
 527         }
 528 }
 529 /**************************************************************************************************/
 530 void DistanceCommand::createProcesses(string filename) {
 531         try {
 532 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 533                 int process = 1;
 534                 processIDS.clear();
 535
 536                 //loop through and create all the processes you want
 537                 while (process != processors) {
 538                         int pid = fork();
 539
 540                         if (pid > 0) {
 541                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 542                                 process++;
 543                         }else if (pid == 0){
 544                                 if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
 545                                 else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
 546                                 exit(0);
 547                         }else {
 548                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
 549                                 perror(" : ");
 550                                 for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
 551                                 exit(0);
 552                         }
 553                 }
 554
 555                 //parent does its part
 556                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 557                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 558
 559
 560                 //force parent to wait until all the processes are done
 561                 for (int i=0;i<processIDS.size();i++) {
 562                         int temp = processIDS[i];
 563                         wait(&temp);
 564                 }
 565 #else
 566                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 567                 //Windows version shared memory, so be careful when passing variables through the distanceData struct.
 568                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 569                 //that's why the distance calculator was moved inside of the driver to make separate copies.
 570                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 571
 572                 vector<distanceData*> pDataArray; //[processors-1];
 573                 DWORD   dwThreadIdArray[processors-1];
 574                 HANDLE  hThreadArray[processors-1];
 575
 576                 //Create processor-1 worker threads.
 577                 for( int i=0; i<processors-1; i++ ){
 578
 579                         // Allocate memory for thread data.
 580                         distanceData* tempDist = new distanceData(lines[i+1].start, lines[i+1].end, (filename + toString(i) + ".temp"), cutoff, alignDB, Estimators, m, output, numNewFasta, countends);
 581                         pDataArray.push_back(tempDist);
 582                         processIDS.push_back(i);
 583
 584                         //MyDistThreadFunction is in header. It must be global or static to work with the threads.
 585                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 586                         hThreadArray[i] = CreateThread(NULL, 0, MyDistThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 587                 }
 588
 589                 //do your part
 590                 if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
 591                 else { driver(lines[0].start, lines[0].end, filename, "square"); }
 592
 593                 //Wait until all threads have terminated.
 594                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 595
 596                 //Close all thread handles and free memory allocations.
 597                 for(int i=0; i < pDataArray.size(); i++){
 598                         CloseHandle(hThreadArray[i]);
 599                         delete pDataArray[i];
 600                 }
 601 #endif
 602
 603                 //append and remove temp files
 604                 for (int i=0;i<processIDS.size();i++) {
 605                         m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
 606                         m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 607                 }
 608
 609         }
 610         catch(exception& e) {
 611                 m->errorOut(e, "DistanceCommand", "createProcesses");
 612                 exit(1);
 613         }
 614 }
 615 /**************************************************************************************************/
 616 /////// need to fix to work with calcs and sequencedb
 617 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 618         try {
 619                 ValidCalculators validCalculator;
 620                 Dist* distCalculator;
 621                 if (m->isTrue(countends) == true) {
 622                         for (int i=0; i<Estimators.size(); i++) {
 623                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 624                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 625                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 626                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 627                                 }
 628                         }
 629                 }else {
 630                         for (int i=0; i<Estimators.size(); i++) {
 631                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 632                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 633                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 634                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 635                                 }
 636                         }
 637                 }
 638
 639                 int startTime = time(NULL);
 640
 641                 //column file
 642                 ofstream outFile(dFileName.c_str(), ios::trunc);
 643                 outFile.setf(ios::fixed, ios::showpoint);
 644                 outFile << setprecision(4);
 645
 646                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 647
 648                 for(int i=startLine;i<endLine;i++){
 649                         if(output == "lt")      {
 650                                 string name = alignDB.get(i).getName();
 651                                 if (name.length() < 10) { //pad with spaces to make compatible
 652                                         while (name.length() < 10) {  name += " ";  }
 653                                 }
 654                                 outFile << name << '\t';
 655                         }
 656                         for(int j=0;j<i;j++){
 657
 658                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 659
 660                                 //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
 661                                 //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
 662                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 663
 664                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 665                                 double dist = distCalculator->getDist();
 666
 667                                 if(dist <= cutoff){
 668                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 669                                 }
 670                                 if (output == "lt") {  outFile << dist << '\t'; }
 671                         }
 672
 673                         if (output == "lt") { outFile << endl; }
 674
 675                         if(i % 100 == 0){
 676                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 677                         }
 678
 679                 }
 680                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 681
 682                 outFile.close();
 683                 delete distCalculator;
 684
 685                 return 1;
 686         }
 687         catch(exception& e) {
 688                 m->errorOut(e, "DistanceCommand", "driver");
 689                 exit(1);
 690         }
 691 }
 692 /**************************************************************************************************/
 693 /////// need to fix to work with calcs and sequencedb
 694 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 695         try {
 696                 ValidCalculators validCalculator;
 697                 Dist* distCalculator;
 698                 if (m->isTrue(countends) == true) {
 699                         for (int i=0; i<Estimators.size(); i++) {
 700                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 701                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 702                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 703                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 704                                 }
 705                         }
 706                 }else {
 707                         for (int i=0; i<Estimators.size(); i++) {
 708                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 709                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 710                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 711                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 712                                 }
 713                         }
 714                 }
 715
 716                 int startTime = time(NULL);
 717
 718                 //column file
 719                 ofstream outFile(dFileName.c_str(), ios::trunc);
 720                 outFile.setf(ios::fixed, ios::showpoint);
 721                 outFile << setprecision(4);
 722
 723                 if(startLine == 0){     outFile << alignDB.getNumSeqs() << endl;        }
 724
 725                 for(int i=startLine;i<endLine;i++){
 726
 727                         string name = alignDB.get(i).getName();
 728                         //pad with spaces to make compatible
 729                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 730
 731                         outFile << name << '\t';
 732
 733                         for(int j=0;j<alignDB.getNumSeqs();j++){
 734
 735                                 if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 736
 737                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 738                                 double dist = distCalculator->getDist();
 739
 740                                 outFile << dist << '\t';
 741                         }
 742
 743                         outFile << endl;
 744
 745                         if(i % 100 == 0){
 746                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 747                         }
 748
 749                 }
 750                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 751
 752                 outFile.close();
 753                 delete distCalculator;
 754
 755                 return 1;
 756         }
 757         catch(exception& e) {
 758                 m->errorOut(e, "DistanceCommand", "driver");
 759                 exit(1);
 760         }
 761 }
 762 #ifdef USE_MPI
 763 /**************************************************************************************************/
 764 /////// need to fix to work with calcs and sequencedb
 765 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 766         try {
 767
 768                 ValidCalculators validCalculator;
 769                 Dist* distCalculator;
 770                 if (m->isTrue(countends) == true) {
 771                         for (int i=0; i<Estimators.size(); i++) {
 772                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 773                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 774                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 775                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 776                                 }
 777                         }
 778                 }else {
 779                         for (int i=0; i<Estimators.size(); i++) {
 780                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 781                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 782                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 783                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 784                                 }
 785                         }
 786                 }
 787
 788
 789                 MPI_Status status;
 790                 int startTime = time(NULL);
 791
 792                 string outputString = "";
 793
 794                 for(int i=startLine;i<endLine;i++){
 795
 796                         for(int j=0;j<i;j++){
 797
 798                                 if (m->control_pressed) {  delete distCalculator; return 0;  }
 799
 800                                 //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
 801                                 //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
 802                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 803
 804                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 805                                 double dist = distCalculator->getDist();
 806
 807                                 if(dist <= cutoff){
 808                                          outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 809                                 }
 810                         }
 811
 812                         if(i % 100 == 0){
 813                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 814                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 815                         }
 816
 817
 818                         //send results to parent
 819                         int length = outputString.length();
 820
 821                         char* buf = new char[length];
 822                         memcpy(buf, outputString.c_str(), length);
 823
 824                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 825                         outputString = "";
 826                         delete buf;
 827
 828                 }
 829
 830                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 831                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 832                 delete distCalculator;
 833                 return 1;
 834         }
 835         catch(exception& e) {
 836                 m->errorOut(e, "DistanceCommand", "driverMPI");
 837                 exit(1);
 838         }
 839 }
 840 /**************************************************************************************************/
 841 /////// need to fix to work with calcs and sequencedb
 842 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 843         try {
 844                 ValidCalculators validCalculator;
 845                 Dist* distCalculator;
 846                 if (m->isTrue(countends) == true) {
 847                         for (int i=0; i<Estimators.size(); i++) {
 848                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 849                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 850                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 851                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 852                                 }
 853                         }
 854                 }else {
 855                         for (int i=0; i<Estimators.size(); i++) {
 856                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 857                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 858                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 859                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 860                                 }
 861                         }
 862                 }
 863
 864
 865                 MPI_Status status;
 866
 867                 MPI_File outMPI;
 868                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 869
 870                 //char* filename = new char[file.length()];
 871                 //memcpy(filename, file.c_str(), file.length());
 872
 873                 char filename[1024];
 874                 strcpy(filename, file.c_str());
 875
 876                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 877                 //delete filename;
 878
 879                 int startTime = time(NULL);
 880
 881                 string outputString = "";
 882                 size = 0;
 883
 884                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 885
 886                 for(int i=startLine;i<endLine;i++){
 887
 888                         string name = alignDB.get(i).getName();
 889                         if (name.length() < 10) { //pad with spaces to make compatible
 890                                 while (name.length() < 10) {  name += " ";  }
 891                         }
 892                         outputString += name + "\t";
 893
 894                         for(int j=0;j<i;j++){
 895
 896                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 897
 898                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 899                                 double dist = distCalculator->getDist();
 900
 901                                 outputString += toString(dist) + "\t";
 902                         }
 903
 904                         outputString += "\n";
 905
 906
 907                         if(i % 100 == 0){
 908                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 909                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 910                         }
 911
 912
 913                         //send results to parent
 914                         int length = outputString.length();
 915                         char* buf = new char[length];
 916                         memcpy(buf, outputString.c_str(), length);
 917
 918                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 919                         size += outputString.length();
 920                         outputString = "";
 921                         delete buf;
 922                 }
 923
 924                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 925                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 926                 MPI_File_close(&outMPI);
 927                 delete distCalculator;
 928
 929                 return 1;
 930         }
 931         catch(exception& e) {
 932                 m->errorOut(e, "DistanceCommand", "driverMPI");
 933                 exit(1);
 934         }
 935 }
 936 /**************************************************************************************************/
 937 /////// need to fix to work with calcs and sequencedb
 938 int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 939         try {
 940                 ValidCalculators validCalculator;
 941                 Dist* distCalculator;
 942                 if (m->isTrue(countends) == true) {
 943                         for (int i=0; i<Estimators.size(); i++) {
 944                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 945                                         if (Estimators[i] == "nogaps")                  {       distCalculator = new ignoreGaps();      }
 946                                         else if (Estimators[i] == "eachgap")    {       distCalculator = new eachGapDist();     }
 947                                         else if (Estimators[i] == "onegap")             {       distCalculator = new oneGapDist();      }
 948                                 }
 949                         }
 950                 }else {
 951                         for (int i=0; i<Estimators.size(); i++) {
 952                                 if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
 953                                         if (Estimators[i] == "nogaps")          {       distCalculator = new ignoreGaps();                                      }
 954                                         else if (Estimators[i] == "eachgap"){   distCalculator = new eachGapIgnoreTermGapDist();        }
 955                                         else if (Estimators[i] == "onegap")     {       distCalculator = new oneGapIgnoreTermGapDist();         }
 956                                 }
 957                         }
 958                 }
 959
 960                 MPI_Status status;
 961
 962                 MPI_File outMPI;
 963                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 964
 965                 //char* filename = new char[file.length()];
 966                 //memcpy(filename, file.c_str(), file.length());
 967
 968                 char filename[1024];
 969                 strcpy(filename, file.c_str());
 970
 971                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 972                 //delete filename;
 973
 974                 int startTime = time(NULL);
 975
 976                 string outputString = "";
 977                 size = 0;
 978
 979                 if(startLine == 0){     outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 980
 981                 for(int i=startLine;i<endLine;i++){
 982
 983                         string name = alignDB.get(i).getName();
 984                         if (name.length() < 10) { //pad with spaces to make compatible
 985                                 while (name.length() < 10) {  name += " ";  }
 986                         }
 987                         outputString += name + "\t";
 988
 989                         for(int j=0;j<alignDB.getNumSeqs();j++){
 990
 991                                 if (m->control_pressed) { delete distCalculator; return 0;  }
 992
 993                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 994                                 double dist = distCalculator->getDist();
 995
 996                                 outputString += toString(dist) + "\t";
 997                         }
 998
 999                         outputString += "\n";
1000
1001
1002                         if(i % 100 == 0){
1003                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
1004                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
1005                         }
1006
1007
1008                         //send results to parent
1009                         int length = outputString.length();
1010                         char* buf = new char[length];
1011                         memcpy(buf, outputString.c_str(), length);
1012
1013                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
1014                         size += outputString.length();
1015                         outputString = "";
1016                         delete buf;
1017                 }
1018
1019                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
1020                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
1021                 MPI_File_close(&outMPI);
1022                 delete distCalculator;
1023                 return 1;
1024         }
1025         catch(exception& e) {
1026                 m->errorOut(e, "DistanceCommand", "driverMPI");
1027                 exit(1);
1028         }
1029 }
1030 #endif
1031 /**************************************************************************************************
1032 int DistanceCommand::convertMatrix(string outputFile) {
1033         try{
1034
1035                 //sort file by first column so the distances for each row are together
1036                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1037
1038                 //use the unix sort
1039                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1040                         string command = "sort -n " + outputFile + " -o " + outfile;
1041                         system(command.c_str());
1042                 #else //sort using windows sort
1043                         string command = "sort " + outputFile + " /O " + outfile;
1044                         system(command.c_str());
1045                 #endif
1046
1047
1048                 //output to new file distance for each row and save positions in file where new row begins
1049                 ifstream in;
1050                 m->openInputFile(outfile, in);
1051
1052                 ofstream out;
1053                 m->openOutputFile(outputFile, out);
1054
1055                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1056
1057                 out << alignDB.getNumSeqs() << endl;
1058
1059                 //get first currentRow
1060                 string first, currentRow, second;
1061                 float dist;
1062                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1063                 map<string, float>::iterator it;
1064
1065                 in >> first;
1066                 currentRow = first;
1067
1068                 rowDists[first] = 0.00; //distance to yourself is 0.0
1069
1070                 in.seekg(0);
1071                 //m->openInputFile(outfile, in);
1072
1073                 while(!in.eof()) {
1074                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1075
1076                         in >> first >> second >> dist; m->gobble(in);
1077
1078                         if (first != currentRow) {
1079                                 //print out last row
1080                                 out << currentRow << '\t'; //print name
1081
1082                                 //print dists
1083                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1084                                         out << it->second << '\t';
1085                                 }
1086                                 out << endl;
1087
1088                                 //start new row
1089                                 currentRow = first;
1090                                 rowDists.clear();
1091                                 rowDists[first] = 0.00;
1092                                 rowDists[second] = dist;
1093                         }else{
1094                                 rowDists[second] = dist;
1095                         }
1096                 }
1097                 //print out last row
1098                 out << currentRow << '\t'; //print name
1099
1100                 //print dists
1101                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1102                         out << it->second << '\t';
1103                 }
1104                 out << endl;
1105
1106                 in.close();
1107                 out.close();
1108
1109                 m->mothurRemove(outfile);
1110
1111                 return 1;
1112
1113         }
1114         catch(exception& e) {
1115                 m->errorOut(e, "DistanceCommand", "convertMatrix");
1116                 exit(1);
1117         }
1118 }
1119 **************************************************************************************************
1120 int DistanceCommand::convertToLowerTriangle(string outputFile) {
1121         try{
1122
1123                 //sort file by first column so the distances for each row are together
1124                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
1125
1126                 //use the unix sort
1127                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1128                         string command = "sort -n " + outputFile + " -o " + outfile;
1129                         system(command.c_str());
1130                 #else //sort using windows sort
1131                         string command = "sort " + outputFile + " /O " + outfile;
1132                         system(command.c_str());
1133                 #endif
1134
1135
1136                 //output to new file distance for each row and save positions in file where new row begins
1137                 ifstream in;
1138                 m->openInputFile(outfile, in);
1139
1140                 ofstream out;
1141                 m->openOutputFile(outputFile, out);
1142
1143                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1144
1145                 out << alignDB.getNumSeqs() << endl;
1146
1147                 //get first currentRow
1148                 string first, currentRow, second;
1149                 float dist;
1150                 int i, j;
1151                 i = 0; j = 0;
1152                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
1153                 map<string, float>::iterator it;
1154
1155                 in >> first;
1156                 currentRow = first;
1157
1158                 rowDists[first] = 0.00; //distance to yourself is 0.0
1159
1160                 in.seekg(0);
1161                 //m->openInputFile(outfile, in);
1162
1163                 while(!in.eof()) {
1164                         if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
1165
1166                         in >> first >> second >> dist; m->gobble(in);
1167
1168                         if (first != currentRow) {
1169                                 //print out last row
1170                                 out << currentRow << '\t'; //print name
1171
1172                                 //print dists
1173                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1174                                         if (j >= i) { break; }
1175                                         out << it->second << '\t';
1176                                         j++;
1177                                 }
1178                                 out << endl;
1179
1180                                 //start new row
1181                                 currentRow = first;
1182                                 rowDists.clear();
1183                                 rowDists[first] = 0.00;
1184                                 rowDists[second] = dist;
1185                                 j = 0;
1186                                 i++;
1187                         }else{
1188                                 rowDists[second] = dist;
1189                         }
1190                 }
1191                 //print out last row
1192                 out << currentRow << '\t'; //print name
1193
1194                 //print dists
1195                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
1196                         out << it->second << '\t';
1197                 }
1198                 out << endl;
1199
1200                 in.close();
1201                 out.close();
1202
1203                 m->mothurRemove(outfile);
1204
1205                 return 1;
1206
1207         }
1208         catch(exception& e) {
1209                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
1210                 exit(1);
1211         }
1212 }
1213 **************************************************************************************************/
1214 //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,
1215 //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.
1216 //also check to make sure the 2 files have the same alignment length.
1217 bool DistanceCommand::sanityCheck() {
1218         try{
1219                 bool good = true;
1220
1221                 //make sure the 2 fasta files have the same alignment length
1222                 ifstream in;
1223                 m->openInputFile(fastafile, in);
1224                 int fastaAlignLength = 0;
1225                 if (in) {
1226                         Sequence tempIn(in);
1227                         fastaAlignLength = tempIn.getAligned().length();
1228                 }
1229                 in.close();
1230
1231                 ifstream in2;
1232                 m->openInputFile(oldfastafile, in2);
1233                 int oldfastaAlignLength = 0;
1234                 if (in2) {
1235                         Sequence tempIn2(in2);
1236                         oldfastaAlignLength = tempIn2.getAligned().length();
1237                 }
1238                 in2.close();
1239
1240                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
1241
1242                 //read fasta file and save names as well as adding them to the alignDB
1243                 set<string> namesOldFasta;
1244
1245                 ifstream inFasta;
1246                 m->openInputFile(oldfastafile, inFasta);
1247
1248                 while (!inFasta.eof()) {
1249                         if (m->control_pressed) {  inFasta.close(); return good;  }
1250
1251                         Sequence temp(inFasta);
1252
1253                         if (temp.getName() != "") {
1254                                 namesOldFasta.insert(temp.getName());  //save name
1255                                 alignDB.push_back(temp);  //add to DB
1256                         }
1257
1258                         m->gobble(inFasta);
1259                 }
1260
1261                 inFasta.close();
1262
1263                 //read through the column file checking names and removing distances above the cutoff
1264                 ifstream inDist;
1265                 m->openInputFile(column, inDist);
1266
1267                 ofstream outDist;
1268                 string outputFile = column + ".temp";
1269                 m->openOutputFile(outputFile, outDist);
1270
1271                 string name1, name2;
1272                 float dist;
1273                 while (!inDist.eof()) {
1274                         if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
1275
1276                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
1277
1278                         //both names are in fasta file and distance is below cutoff
1279                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
1280                         else{
1281                                 if (dist <= cutoff) {
1282                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
1283                                 }
1284                         }
1285                 }
1286
1287                 inDist.close();
1288                 outDist.close();
1289
1290                 if (good) {
1291                         m->mothurRemove(column);
1292                         rename(outputFile.c_str(), column.c_str());
1293                 }else{
1294                         m->mothurRemove(outputFile); //temp file is bad because file mismatch above
1295                 }
1296
1297                 return good;
1298
1299         }
1300         catch(exception& e) {
1301                 m->errorOut(e, "DistanceCommand", "sanityCheck");
1302                 exit(1);
1303         }
1304 }
1305 /**************************************************************************************************/
1306
1307
1308
1309