distancecommand.cpp

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