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                 start = int (sqrt(float(pid)/float(processors)) * numSeqs);
 241                 end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
 242
 243                 if (output != "lt") {
 244                         MPI_File outMPI;
 245                         int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 246
 247                         //char* filename = new char[outputFile.length()];
 248                         //memcpy(filename, outputFile.c_str(), outputFile.length());
 249
 250                         char filename[1024];
 251                         strcpy(filename, outputFile.c_str());
 252
 253                         MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
 254                         //delete filename;
 255
 256                         if (pid == 0) { //you are the root process
 257
 258                                 //do your part
 259                                 string outputMyPart;
 260                                 driverMPI(start, end, outMPI, cutoff);
 261
 262                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 263
 264                                 //wait on chidren
 265                                 for(int i = 1; i < processors; i++) {
 266                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 267
 268                                         char buf[4];
 269                                         MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 270                                 }
 271                         }else { //you are a child process
 272                                 //do your part
 273                                 driverMPI(start, end, outMPI, cutoff);
 274
 275                                 if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 276
 277                                 char buf[4];
 278                                 strcpy(buf, "done");
 279                                 //tell parent you are done.
 280                                 MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 281                         }
 282
 283                         MPI_File_close(&outMPI);
 284
 285                 }else { //lower triangle format
 286                         if (pid == 0) { //you are the root process
 287
 288                                 //do your part
 289                                 string outputMyPart;
 290                                 long mySize;
 291                                 driverMPI(start, end, outputFile, mySize);
 292
 293                                 if (m->control_pressed) {  delete distCalculator;  return 0; }
 294
 295                                 int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
 296                                 MPI_File outMPI;
 297                                 MPI_File inMPI;
 298
 299                                 //char* filename = new char[outputFile.length()];
 300                                 //memcpy(filename, outputFile.c_str(), outputFile.length());
 301
 302                                 char filename[1024];
 303                                 strcpy(filename, outputFile.c_str());
 304
 305                                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 306                                 //delete filename;
 307
 308                                 //wait on chidren
 309                                 for(int b = 1; b < processors; b++) {
 310                                         long fileSize;
 311
 312                                         if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 313
 314                                         MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
 315
 316                                         string outTemp = outputFile + toString(b) + ".temp";
 317
 318                                         char* buf = new char[outTemp.length()];
 319                                         memcpy(buf, outTemp.c_str(), outTemp.length());
 320
 321                                         MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 322                                         delete buf;
 323
 324                                         int count = 0;
 325                                         while (count < fileSize) {
 326                                                 char buf2[1];
 327                                                 MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
 328                                                 MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
 329                                                 count += 1;
 330                                         }
 331
 332                                         MPI_File_close(&inMPI); //deleted on close
 333                                 }
 334
 335                                 MPI_File_close(&outMPI);
 336                         }else { //you are a child process
 337                                 //do your part
 338                                 long size;
 339                                 driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
 340
 341                                 if (m->control_pressed) { delete distCalculator;  return 0; }
 342
 343                                 //tell parent you are done.
 344                                 MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
 345                         }
 346                 }
 347                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 348 #else
 349
 350         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 351                 //if you don't need to fork anything
 352                 if(processors == 1){
 353                         driver(0, numSeqs, outputFile, cutoff);
 354                 }else{ //you have multiple processors
 355
 356                         for (int i = 0; i < processors; i++) {
 357                                 lines.push_back(new linePair());
 358                                 lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
 359                                 lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
 360                         }
 361
 362                         createProcesses(outputFile);
 363
 364                         map<int, int>::iterator it = processIDS.begin();
 365                         rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
 366                         it++;
 367
 368                         //append and remove temp files
 369                         for (; it != processIDS.end(); it++) {
 370                                 m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
 371                                 remove((outputFile + toString(it->second) + ".temp").c_str());
 372                         }
 373                 }
 374         #else
 375                 ifstream inFASTA;
 376                 driver(0, numSeqs, outputFile, cutoff);
 377         #endif
 378
 379 #endif
 380                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 381
 382                 #ifdef USE_MPI
 383                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 384
 385                         if (pid == 0) { //only one process should output to screen
 386                 #endif
 387
 388                 if (output == "square") {  convertMatrix(outputFile); }
 389
 390                 ifstream fileHandle;
 391                 fileHandle.open(outputFile.c_str());
 392                 if(fileHandle) {
 393                         m->gobble(fileHandle);
 394                         if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
 395                 }
 396
 397                 //append the old column file to the new one
 398                 if ((oldfastafile != "") && (column != ""))  {
 399                         //we had to rename the column file so we didnt overwrite above, but we want to keep old name
 400                         if (outputFile == column) {
 401                                 string tempcolumn = column + ".old";
 402                                 m->appendFiles(tempcolumn, outputFile);
 403                                 remove(tempcolumn.c_str());
 404                         }else{
 405                                 m->appendFiles(outputFile, column);
 406                                 remove(outputFile.c_str());
 407                                 outputFile = column;
 408                         }
 409                 }
 410
 411
 412                 #ifdef USE_MPI
 413                         }
 414                 #endif
 415
 416                 if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
 417
 418                 delete distCalculator;
 419
 420                 m->mothurOutEndLine();
 421                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 422                 m->mothurOut(outputFile); m->mothurOutEndLine();
 423                 m->mothurOutEndLine();
 424                 m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 425                 return 0;
 426
 427         }
 428         catch(exception& e) {
 429                 m->errorOut(e, "DistanceCommand", "execute");
 430                 exit(1);
 431         }
 432 }
 433 /**************************************************************************************************/
 434 void DistanceCommand::createProcesses(string filename) {
 435         try {
 436 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 437                 int process = 0;
 438                 processIDS.clear();
 439
 440                 //loop through and create all the processes you want
 441                 while (process != processors) {
 442                         int pid = fork();
 443
 444                         if (pid > 0) {
 445                                 processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
 446                                 process++;
 447                         }else if (pid == 0){
 448                                 driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
 449                                 exit(0);
 450                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 451                 }
 452
 453                 //force parent to wait until all the processes are done
 454                 for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
 455                         int temp = it->second;
 456                         wait(&temp);
 457                 }
 458 #endif
 459         }
 460         catch(exception& e) {
 461                 m->errorOut(e, "DistanceCommand", "createProcesses");
 462                 exit(1);
 463         }
 464 }
 465
 466 /**************************************************************************************************/
 467 /////// need to fix to work with calcs and sequencedb
 468 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 469         try {
 470
 471                 int startTime = time(NULL);
 472
 473                 //column file
 474                 ofstream outFile(dFileName.c_str(), ios::trunc);
 475                 outFile.setf(ios::fixed, ios::showpoint);
 476                 outFile << setprecision(4);
 477
 478                 if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl;        }
 479
 480                 for(int i=startLine;i<endLine;i++){
 481                         if(output == "lt")      {
 482                                 string name = alignDB.get(i).getName();
 483                                 if (name.length() < 10) { //pad with spaces to make compatible
 484                                         while (name.length() < 10) {  name += " ";  }
 485                                 }
 486                                 outFile << name << '\t';
 487                         }
 488                         for(int j=0;j<i;j++){
 489
 490                                 if (m->control_pressed) { outFile.close(); return 0;  }
 491
 492                                 //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
 493                                 //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
 494                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 495
 496                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 497                                 double dist = distCalculator->getDist();
 498
 499                                 if(dist <= cutoff){
 500                                         if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
 501                                 }
 502                                 if (output == "lt") {  outFile << dist << '\t'; }
 503
 504                                 if (output == "square") { //make a square column you can convert to square phylip
 505                                         outFile << alignDB.get(i).getName() << '\t' << alignDB.get(j).getName() << '\t' << dist << endl;
 506                                         outFile << alignDB.get(j).getName() << '\t' << alignDB.get(i).getName() << '\t' << dist << endl;
 507                                 }
 508
 509                         }
 510
 511                         if (output == "lt") { outFile << endl; }
 512
 513                         if(i % 100 == 0){
 514                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 515                         }
 516
 517                 }
 518                 m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 519
 520                 outFile.close();
 521
 522                 return 1;
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "DistanceCommand", "driver");
 526                 exit(1);
 527         }
 528 }
 529 #ifdef USE_MPI
 530 /**************************************************************************************************/
 531 /////// need to fix to work with calcs and sequencedb
 532 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 533         try {
 534                 MPI_Status status;
 535                 int startTime = time(NULL);
 536
 537                 string outputString = "";
 538
 539                 for(int i=startLine;i<endLine;i++){
 540
 541                         for(int j=0;j<i;j++){
 542
 543                                 if (m->control_pressed) {  return 0;  }
 544
 545                                 //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
 546                                 //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
 547                                 if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
 548
 549                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 550                                 double dist = distCalculator->getDist();
 551
 552                                 if(dist <= cutoff){
 553                                         if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
 554                                 }
 555
 556                                 if (output == "square") { //make a square column you can convert to square phylip
 557                                         outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
 558                                         outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
 559                                 }
 560                         }
 561
 562                         if(i % 100 == 0){
 563                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 564                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 565                         }
 566
 567
 568                         //send results to parent
 569                         int length = outputString.length();
 570
 571                         char* buf = new char[length];
 572                         memcpy(buf, outputString.c_str(), length);
 573
 574                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 575                         outputString = "";
 576                         delete buf;
 577
 578                 }
 579
 580                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 581                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 582                 return 1;
 583         }
 584         catch(exception& e) {
 585                 m->errorOut(e, "DistanceCommand", "driverMPI");
 586                 exit(1);
 587         }
 588 }
 589 /**************************************************************************************************/
 590 /////// need to fix to work with calcs and sequencedb
 591 int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
 592         try {
 593                 MPI_Status status;
 594
 595                 MPI_File outMPI;
 596                 int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 597
 598                 //char* filename = new char[file.length()];
 599                 //memcpy(filename, file.c_str(), file.length());
 600
 601                 char filename[1024];
 602                 strcpy(filename, file.c_str());
 603
 604                 MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 605                 //delete filename;
 606
 607                 int startTime = time(NULL);
 608
 609                 string outputString = "";
 610                 size = 0;
 611
 612                 if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n";  }
 613
 614                 for(int i=startLine;i<endLine;i++){
 615                         if(output == "lt")      {
 616                                 string name = alignDB.get(i).getName();
 617                                 if (name.length() < 10) { //pad with spaces to make compatible
 618                                         while (name.length() < 10) {  name += " ";  }
 619                                 }
 620                                 outputString += name + "\t";
 621                         }
 622                         for(int j=0;j<i;j++){
 623
 624                                 if (m->control_pressed) {  return 0;  }
 625
 626                                 distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 627                                 double dist = distCalculator->getDist();
 628
 629                                 if (output == "lt") {  outputString += toString(dist) + "\t"; }
 630                         }
 631
 632                         if (output == "lt") { outputString += "\n"; }
 633
 634
 635                         if(i % 100 == 0){
 636                                 //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 637                                 cout << i << '\t' << (time(NULL) - startTime) << endl;
 638                         }
 639
 640
 641                         //send results to parent
 642                         int length = outputString.length();
 643                         char* buf = new char[length];
 644                         memcpy(buf, outputString.c_str(), length);
 645
 646                         MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
 647                         size += outputString.length();
 648                         outputString = "";
 649                         delete buf;
 650                 }
 651
 652                 //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 653                 cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 654                 MPI_File_close(&outMPI);
 655
 656                 return 1;
 657         }
 658         catch(exception& e) {
 659                 m->errorOut(e, "DistanceCommand", "driverMPI");
 660                 exit(1);
 661         }
 662 }
 663 #endif
 664 /**************************************************************************************************/
 665 int DistanceCommand::convertMatrix(string outputFile) {
 666         try{
 667
 668                 //sort file by first column so the distances for each row are together
 669                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 670
 671                 //use the unix sort
 672                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 673                         string command = "sort -n " + outputFile + " -o " + outfile;
 674                         system(command.c_str());
 675                 #else //sort using windows sort
 676                         string command = "sort " + outputFile + " /O " + outfile;
 677                         system(command.c_str());
 678                 #endif
 679
 680
 681                 //output to new file distance for each row and save positions in file where new row begins
 682                 ifstream in;
 683                 m->openInputFile(outfile, in);
 684
 685                 ofstream out;
 686                 m->openOutputFile(outputFile, out);
 687
 688                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 689
 690                 out << alignDB.getNumSeqs() << endl;
 691
 692                 //get first currentRow
 693                 string first, currentRow, second;
 694                 float dist;
 695                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 696                 map<string, float>::iterator it;
 697
 698                 in >> first;
 699                 currentRow = first;
 700
 701                 rowDists[first] = 0.00; //distance to yourself is 0.0
 702
 703                 in.seekg(0);
 704                 //m->openInputFile(outfile, in);
 705
 706                 while(!in.eof()) {
 707                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 708
 709                         in >> first >> second >> dist; m->gobble(in);
 710
 711                         if (first != currentRow) {
 712                                 //print out last row
 713                                 out << currentRow << '\t'; //print name
 714
 715                                 //print dists
 716                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 717                                         out << it->second << '\t';
 718                                 }
 719                                 out << endl;
 720
 721                                 //start new row
 722                                 currentRow = first;
 723                                 rowDists.clear();
 724                                 rowDists[first] = 0.00;
 725                                 rowDists[second] = dist;
 726                         }else{
 727                                 rowDists[second] = dist;
 728                         }
 729                 }
 730                 //print out last row
 731                 out << currentRow << '\t'; //print name
 732
 733                 //print dists
 734                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 735                         out << it->second << '\t';
 736                 }
 737                 out << endl;
 738
 739                 in.close();
 740                 out.close();
 741
 742                 remove(outfile.c_str());
 743
 744                 return 1;
 745
 746         }
 747         catch(exception& e) {
 748                 m->errorOut(e, "DistanceCommand", "convertMatrix");
 749                 exit(1);
 750         }
 751 }
 752 /**************************************************************************************************/
 753 int DistanceCommand::convertToLowerTriangle(string outputFile) {
 754         try{
 755
 756                 //sort file by first column so the distances for each row are together
 757                 string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
 758
 759                 //use the unix sort
 760                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 761                         string command = "sort -n " + outputFile + " -o " + outfile;
 762                         system(command.c_str());
 763                 #else //sort using windows sort
 764                         string command = "sort " + outputFile + " /O " + outfile;
 765                         system(command.c_str());
 766                 #endif
 767
 768
 769                 //output to new file distance for each row and save positions in file where new row begins
 770                 ifstream in;
 771                 m->openInputFile(outfile, in);
 772
 773                 ofstream out;
 774                 m->openOutputFile(outputFile, out);
 775
 776                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 777
 778                 out << alignDB.getNumSeqs() << endl;
 779
 780                 //get first currentRow
 781                 string first, currentRow, second;
 782                 float dist;
 783                 int i, j;
 784                 i = 0; j = 0;
 785                 map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
 786                 map<string, float>::iterator it;
 787
 788                 in >> first;
 789                 currentRow = first;
 790
 791                 rowDists[first] = 0.00; //distance to yourself is 0.0
 792
 793                 in.seekg(0);
 794                 //m->openInputFile(outfile, in);
 795
 796                 while(!in.eof()) {
 797                         if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
 798
 799                         in >> first >> second >> dist; m->gobble(in);
 800
 801                         if (first != currentRow) {
 802                                 //print out last row
 803                                 out << currentRow << '\t'; //print name
 804
 805                                 //print dists
 806                                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 807                                         if (j >= i) { break; }
 808                                         out << it->second << '\t';
 809                                         j++;
 810                                 }
 811                                 out << endl;
 812
 813                                 //start new row
 814                                 currentRow = first;
 815                                 rowDists.clear();
 816                                 rowDists[first] = 0.00;
 817                                 rowDists[second] = dist;
 818                                 j = 0;
 819                                 i++;
 820                         }else{
 821                                 rowDists[second] = dist;
 822                         }
 823                 }
 824                 //print out last row
 825                 out << currentRow << '\t'; //print name
 826
 827                 //print dists
 828                 for (it = rowDists.begin(); it != rowDists.end(); it++) {
 829                         out << it->second << '\t';
 830                 }
 831                 out << endl;
 832
 833                 in.close();
 834                 out.close();
 835
 836                 remove(outfile.c_str());
 837
 838                 return 1;
 839
 840         }
 841         catch(exception& e) {
 842                 m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
 843                 exit(1);
 844         }
 845 }
 846 /**************************************************************************************************/
 847 //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,
 848 //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.
 849 //also check to make sure the 2 files have the same alignment length.
 850 bool DistanceCommand::sanityCheck() {
 851         try{
 852                 bool good = true;
 853
 854                 //make sure the 2 fasta files have the same alignment length
 855                 ifstream in;
 856                 m->openInputFile(fastafile, in);
 857                 int fastaAlignLength = 0;
 858                 if (in) {
 859                         Sequence tempIn(in);
 860                         fastaAlignLength = tempIn.getAligned().length();
 861                 }
 862                 in.close();
 863
 864                 ifstream in2;
 865                 m->openInputFile(oldfastafile, in2);
 866                 int oldfastaAlignLength = 0;
 867                 if (in2) {
 868                         Sequence tempIn2(in2);
 869                         oldfastaAlignLength = tempIn2.getAligned().length();
 870                 }
 871                 in2.close();
 872
 873                 if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false;  }
 874
 875                 //read fasta file and save names as well as adding them to the alignDB
 876                 set<string> namesOldFasta;
 877
 878                 ifstream inFasta;
 879                 m->openInputFile(oldfastafile, inFasta);
 880
 881                 while (!inFasta.eof()) {
 882                         if (m->control_pressed) {  inFasta.close(); return good;  }
 883
 884                         Sequence temp(inFasta);
 885
 886                         if (temp.getName() != "") {
 887                                 namesOldFasta.insert(temp.getName());  //save name
 888                                 alignDB.push_back(temp);  //add to DB
 889                         }
 890
 891                         m->gobble(inFasta);
 892                 }
 893
 894                 inFasta.close();
 895
 896                 //read through the column file checking names and removing distances above the cutoff
 897                 ifstream inDist;
 898                 m->openInputFile(column, inDist);
 899
 900                 ofstream outDist;
 901                 string outputFile = column + ".temp";
 902                 m->openOutputFile(outputFile, outDist);
 903
 904                 string name1, name2;
 905                 float dist;
 906                 while (!inDist.eof()) {
 907                         if (m->control_pressed) {  inDist.close(); outDist.close(); remove(outputFile.c_str()); return good;  }
 908
 909                         inDist >> name1 >> name2 >> dist; m->gobble(inDist);
 910
 911                         //both names are in fasta file and distance is below cutoff
 912                         if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) {  good = false; break;  }
 913                         else{
 914                                 if (dist <= cutoff) {
 915                                         outDist << name1 << '\t' << name2 << '\t' << dist << endl;
 916                                 }
 917                         }
 918                 }
 919
 920                 inDist.close();
 921                 outDist.close();
 922
 923                 if (good) {
 924                         remove(column.c_str());
 925                         rename(outputFile.c_str(), column.c_str());
 926                 }else{
 927                         remove(outputFile.c_str()); //temp file is bad because file mismatch above
 928                 }
 929
 930         }
 931         catch(exception& e) {
 932                 m->errorOut(e, "DistanceCommand", "m->appendFiles");
 933                 exit(1);
 934         }
 935 }
 936
 937 /**************************************************************************************************
 938 void DistanceCommand::m->appendFiles(string temp, string filename) {
 939         try{
 940                 ofstream output;
 941                 ifstream input;
 942
 943                 //open output file in append mode
 944                 m->openOutputFileAppend(filename, output);
 945                 m->openInputFile(temp, input);
 946
 947                 while(char c = input.get()){
 948                         if(input.eof())         {       break;                  }
 949                         else                            {       output << c;    }
 950                 }
 951
 952                 input.close();
 953                 output.close();
 954         }
 955         catch(exception& e) {
 956                 m->errorOut(e, "DistanceCommand", "m->appendFiles");
 957                 exit(1);
 958         }
 959 }
 960 /**************************************************************************************************/
 961
 962