aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "referencedb.h"
  19
  20 //**********************************************************************************************************************
  21 vector<string> AlignCommand::setParameters(){
  22         try {
  23                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  24                 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
  25                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  26                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  27                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  28                 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
  29                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  30                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  31                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  32                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  33                 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  34                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  35                 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "AlignCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string AlignCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
  53                 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
  54                 helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
  55                 helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.";
  56                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.";
  57                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
  58                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
  59                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
  60                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
  61                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.";
  62                 helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.";
  63                 helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.";
  64                 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
  65                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  66                 helpString += "The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.";
  67                 helpString += "The align.seqs command should be in the following format:";
  68                 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
  69                 helpString += "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)";
  70                 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
  71                 return helpString;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "AlignCommand", "getHelpString");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 AlignCommand::AlignCommand(){
  80         try {
  81                 abort = true; calledHelp = true;
  82                 setParameters();
  83                 vector<string> tempOutNames;
  84                 outputTypes["fasta"] = tempOutNames;
  85                 outputTypes["alignreport"] = tempOutNames;
  86                 outputTypes["accnos"] = tempOutNames;
  87         }
  88         catch(exception& e) {
  89                 m->errorOut(e, "AlignCommand", "AlignCommand");
  90                 exit(1);
  91         }
  92 }
  93 //**********************************************************************************************************************
  94 AlignCommand::AlignCommand(string option)  {
  95         try {
  96                 abort = false; calledHelp = false;
  97                 ReferenceDB* rdb = ReferenceDB::getInstance();
  98
  99                 //allow user to run help
 100                 if(option == "help") { help(); abort = true; calledHelp = true;}
 101                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 102
 103                 else {
 104                         vector<string> myArray = setParameters();
 105
 106                         OptionParser parser(option);
 107                         map<string, string> parameters = parser.getParameters();
 108
 109                         ValidParameters validParameter("align.seqs");
 110                         map<string, string>::iterator it;
 111
 112                         //check to make sure all parameters are valid for command
 113                         for (it = parameters.begin(); it != parameters.end(); it++) {
 114                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 115                         }
 116
 117                         //initialize outputTypes
 118                         vector<string> tempOutNames;
 119                         outputTypes["fasta"] = tempOutNames;
 120                         outputTypes["alignreport"] = tempOutNames;
 121                         outputTypes["accnos"] = tempOutNames;
 122
 123                         //if the user changes the output directory command factory will send this info to us in the output parameter
 124                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 125
 126
 127                         //if the user changes the input directory command factory will send this info to us in the output parameter
 128                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 129
 130                         if (inputDir == "not found"){   inputDir = "";          }
 131                         else {
 132                                 string path;
 133
 134                                 it = parameters.find("reference");
 135
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 141                                 }
 142                         }
 143
 144                         candidateFileName = validParameter.validFile(parameters, "fasta", false);
 145                         if (candidateFileName == "not found") {
 146                                 //if there is a current fasta file, use it
 147                                 string filename = m->getFastaFile();
 148                                 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 149                                 else {  m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
 150                         }else {
 151                                 m->splitAtDash(candidateFileName, candidateFileNames);
 152
 153                                 //go through files and make sure they are good, if not, then disregard them
 154                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 155                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 156
 157                                         bool ignore = false;
 158                                         if (candidateFileNames[i] == "current") {
 159                                                 candidateFileNames[i] = m->getFastaFile();
 160                                                 if (candidateFileNames[i] != "") {  m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 161                                                 else {
 162                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 163                                                         //erase from file list
 164                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 165                                                         i--;
 166                                                 }
 167                                         }
 168
 169                                         if (!ignore) {
 170
 171                                                 if (inputDir != "") {
 172                                                         string path = m->hasPath(candidateFileNames[i]);
 173                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 174                                                         if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 175                                                 }
 176
 177                                                 int ableToOpen;
 178                                                 ifstream in;
 179                                                 ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 180                                                 in.close();
 181
 182                                                 //if you can't open it, try default location
 183                                                 if (ableToOpen == 1) {
 184                                                         if (m->getDefaultPath() != "") { //default path is set
 185                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 186                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 187                                                                 ifstream in2;
 188                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 189                                                                 in2.close();
 190                                                                 candidateFileNames[i] = tryPath;
 191                                                         }
 192                                                 }
 193
 194                                                 //if you can't open it, try output location
 195                                                 if (ableToOpen == 1) {
 196                                                         if (m->getOutputDir() != "") { //default path is set
 197                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 198                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 199                                                                 ifstream in2;
 200                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 201                                                                 in2.close();
 202                                                                 candidateFileNames[i] = tryPath;
 203                                                         }
 204                                                 }
 205
 206
 207
 208                                                 if (ableToOpen == 1) {
 209                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 210                                                         //erase from file list
 211                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 212                                                         i--;
 213                                                 }else {
 214                                                         m->setFastaFile(candidateFileNames[i]);
 215                                                 }
 216                                         }
 217                                 }
 218
 219                                 //make sure there is at least one valid file left
 220                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 221                         }
 222
 223                         //check for optional parameter and set defaults
 224                         // ...at some point should added some additional type checking...
 225                         string temp;
 226                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 227                         m->mothurConvert(temp, kmerSize);
 228
 229                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 230                         m->mothurConvert(temp, match);
 231
 232                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 233                         m->mothurConvert(temp, misMatch);
 234
 235                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 236                         m->mothurConvert(temp, gapOpen);
 237
 238                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 239                         m->mothurConvert(temp, gapExtend);
 240
 241                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 242                         m->setProcessors(temp);
 243                         m->mothurConvert(temp, processors);
 244
 245                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 246                         flip = m->isTrue(temp);
 247
 248                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 249                         save = m->isTrue(temp);
 250                         rdb->save = save;
 251                         if (save) { //clear out old references
 252                                 rdb->clearMemory();
 253                         }
 254
 255                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 256                         templateFileName = validParameter.validFile(parameters, "reference", true);
 257                         if (templateFileName == "not found") {
 258                                 //check for saved reference sequences
 259                                 if (rdb->referenceSeqs.size() != 0) {
 260                                         templateFileName = "saved";
 261                                 }else {
 262                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
 263                                         m->mothurOutEndLine();
 264                                         abort = true;
 265                                 }
 266                         }else if (templateFileName == "not open") { abort = true; }
 267                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 268
 269                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 270                         m->mothurConvert(temp, threshold);
 271
 272                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 273                         if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
 274
 275                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 276                         if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
 277
 278                 }
 279
 280         }
 281         catch(exception& e) {
 282                 m->errorOut(e, "AlignCommand", "AlignCommand");
 283                 exit(1);
 284         }
 285 }
 286 //**********************************************************************************************************************
 287 AlignCommand::~AlignCommand(){
 288
 289         if (abort == false) {
 290                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 291                 delete templateDB;
 292         }
 293 }
 294 //**********************************************************************************************************************
 295
 296 int AlignCommand::execute(){
 297         try {
 298                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 299
 300                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
 301
 302                 for (int s = 0; s < candidateFileNames.size(); s++) {
 303                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 304
 305                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 306
 307                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 308                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 309                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 310                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 311                         bool hasAccnos = true;
 312
 313                         int numFastaSeqs = 0;
 314                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 315                         int start = time(NULL);
 316
 317 #ifdef USE_MPI
 318                                 int pid, numSeqsPerProcessor;
 319                                 int tag = 2001;
 320                                 vector<unsigned long long> MPIPos;
 321                                 MPIWroteAccnos = false;
 322
 323                                 MPI_Status status;
 324                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 325                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 326
 327                                 MPI_File inMPI;
 328                                 MPI_File outMPIAlign;
 329                                 MPI_File outMPIReport;
 330                                 MPI_File outMPIAccnos;
 331
 332                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 333                                 int inMode=MPI_MODE_RDONLY;
 334
 335                                 char outAlignFilename[1024];
 336                                 strcpy(outAlignFilename, alignFileName.c_str());
 337
 338                                 char outReportFilename[1024];
 339                                 strcpy(outReportFilename, reportFileName.c_str());
 340
 341                                 char outAccnosFilename[1024];
 342                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 343
 344                                 char inFileName[1024];
 345                                 strcpy(inFileName, candidateFileNames[s].c_str());
 346
 347                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 348                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 349                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 350                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 351
 352                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 353
 354                                 if (pid == 0) { //you are the root process
 355
 356                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 357
 358                                         //send file positions to all processes
 359                                         for(int i = 1; i < processors; i++) {
 360                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 361                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 362                                         }
 363
 364                                         //figure out how many sequences you have to align
 365                                         numSeqsPerProcessor = numFastaSeqs / processors;
 366                                         int startIndex =  pid * numSeqsPerProcessor;
 367                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 368
 369                                         //align your part
 370                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 371
 372                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 373
 374                                         for (int i = 1; i < processors; i++) {
 375                                                 bool tempResult;
 376                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 377                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 378                                         }
 379                                 }else{ //you are a child process
 380                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 381                                         MPIPos.resize(numFastaSeqs+1);
 382                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 383
 384
 385                                         //figure out how many sequences you have to align
 386                                         numSeqsPerProcessor = numFastaSeqs / processors;
 387                                         int startIndex =  pid * numSeqsPerProcessor;
 388                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 389
 390
 391                                         //align your part
 392                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 393
 394                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 395
 396                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 397                                 }
 398
 399                                 //close files
 400                                 MPI_File_close(&inMPI);
 401                                 MPI_File_close(&outMPIAlign);
 402                                 MPI_File_close(&outMPIReport);
 403                                 MPI_File_close(&outMPIAccnos);
 404
 405                                 //delete accnos file if blank
 406                                 if (pid == 0) {
 407                                         //delete accnos file if its blank else report to user
 408                                         if (MPIWroteAccnos) {
 409                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 410                                                 if (!flip) {
 411                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 412                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 413                                                 m->mothurOutEndLine();
 414                                         }else {
 415                                                 //MPI_Info info;
 416                                                 //MPI_File_delete(outAccnosFilename, info);
 417                                                 hasAccnos = false;
 418                                                 m->mothurRemove(accnosFileName);
 419                                         }
 420                                 }
 421
 422 #else
 423
 424                         vector<unsigned long long> positions;
 425                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 426                         positions = m->divideFile(candidateFileNames[s], processors);
 427                         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 428                 #else
 429                         if (processors == 1) {
 430                                 lines.push_back(new linePair(0, 1000));
 431                         }else {
 432                                 positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs);
 433
 434                                 //figure out how many sequences you have to process
 435                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 436                                 for (int i = 0; i < processors; i++) {
 437                                         int startIndex =  i * numSeqsPerProcessor;
 438                                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 439                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 440                                 }
 441                         }
 442                 #endif
 443
 444                         if(processors == 1){
 445                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 446                         }else{
 447                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 448                         }
 449
 450                         if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear();  return 0; }
 451
 452                         //delete accnos file if its blank else report to user
 453                         if (m->isBlank(accnosFileName)) {  m->mothurRemove(accnosFileName);  hasAccnos = false; }
 454                         else {
 455                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 456                                 if (!flip) {
 457                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 458                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 459                                 m->mothurOutEndLine();
 460                         }
 461
 462 #endif
 463
 464
 465                 #ifdef USE_MPI
 466                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 467
 468                         if (pid == 0) { //only one process should output to screen
 469                 #endif
 470
 471                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 472                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 473                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 474
 475                 #ifdef USE_MPI
 476                         }
 477                 #endif
 478
 479                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 480                         m->mothurOutEndLine();
 481                         m->mothurOutEndLine();
 482                 }
 483
 484                 //set align file as new current fastafile
 485                 string currentFasta = "";
 486                 itTypes = outputTypes.find("fasta");
 487                 if (itTypes != outputTypes.end()) {
 488                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 489                 }
 490
 491                 m->mothurOutEndLine();
 492                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 493                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 494                 m->mothurOutEndLine();
 495
 496                 return 0;
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "AlignCommand", "execute");
 500                 exit(1);
 501         }
 502 }
 503
 504 //**********************************************************************************************************************
 505 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 506         try {
 507                 ofstream alignmentFile;
 508                 m->openOutputFile(alignFName, alignmentFile);
 509
 510                 ofstream accnosFile;
 511                 m->openOutputFile(accnosFName, accnosFile);
 512
 513                 NastReport report(reportFName);
 514
 515                 ifstream inFASTA;
 516                 m->openInputFile(filename, inFASTA);
 517
 518                 inFASTA.seekg(filePos->start);
 519
 520                 bool done = false;
 521                 int count = 0;
 522
 523                 //moved this into driver to avoid deep copies in windows paralellized version
 524                 Alignment* alignment;
 525                 int longestBase = templateDB->getLongestBase();
 526                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 527                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 528                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 529                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 530                 else {
 531                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 532                         m->mothurOutEndLine();
 533                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 534                 }
 535
 536                 while (!done) {
 537
 538                         if (m->control_pressed) {  break; }
 539
 540                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 541                         report.setCandidate(candidateSeq);
 542
 543                         int origNumBases = candidateSeq->getNumBases();
 544                         string originalUnaligned = candidateSeq->getUnaligned();
 545                         int numBasesNeeded = origNumBases * threshold;
 546
 547                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 548                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 549                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 550                                 }
 551
 552                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 553                                 Sequence* templateSeq = &temp;
 554
 555                                 float searchScore = templateDB->getSearchScore();
 556
 557                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 558
 559                                 Sequence* copy;
 560
 561                                 Nast* nast2;
 562                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 563                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 564                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 565                                                                                                 //so this bool tells you if you need to delete it
 566
 567                                 //if there is a possibility that this sequence should be reversed
 568                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 569
 570                                         string wasBetter =  "";
 571                                         //if the user wants you to try the reverse
 572                                         if (flip) {
 573
 574                                                 //get reverse compliment
 575                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 576                                                 copy->reverseComplement();
 577
 578                                                 //rerun alignment
 579                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 580                                                 Sequence* templateSeq2 = &temp2;
 581
 582                                                 searchScore = templateDB->getSearchScore();
 583
 584                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 585
 586                                                 //check if any better
 587                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 588                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 589                                                         templateSeq = templateSeq2;
 590                                                         delete nast;
 591                                                         nast = nast2;
 592                                                         needToDeleteCopy = true;
 593                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 594                                                 }else{
 595                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 596                                                         delete nast2;
 597                                                         delete copy;
 598                                                 }
 599                                         }
 600
 601                                         //create accnos file with names
 602                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 603                                 }
 604
 605                                 report.setTemplate(templateSeq);
 606                                 report.setSearchParameters(search, searchScore);
 607                                 report.setAlignmentParameters(align, alignment);
 608                                 report.setNastParameters(*nast);
 609
 610                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 611
 612                                 report.print();
 613                                 delete nast;
 614                                 if (needToDeleteCopy) {   delete copy;   }
 615
 616                                 count++;
 617                         }
 618                         delete candidateSeq;
 619
 620                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 621                                 unsigned long long pos = inFASTA.tellg();
 622                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 623                         #else
 624                                 if (inFASTA.eof()) { break; }
 625                         #endif
 626
 627                         //report progress
 628                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 629
 630                 }
 631                 //report progress
 632                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 633
 634                 delete alignment;
 635                 alignmentFile.close();
 636                 inFASTA.close();
 637                 accnosFile.close();
 638
 639                 return count;
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "AlignCommand", "driver");
 643                 exit(1);
 644         }
 645 }
 646 //**********************************************************************************************************************
 647 #ifdef USE_MPI
 648 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& MPIPos){
 649         try {
 650                 string outputString = "";
 651                 MPI_Status statusReport;
 652                 MPI_Status statusAlign;
 653                 MPI_Status statusAccnos;
 654                 MPI_Status status;
 655                 int pid;
 656                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 657
 658                 NastReport report;
 659
 660                 if (pid == 0) {
 661                         outputString = report.getHeaders();
 662                         int length = outputString.length();
 663
 664                         char* buf = new char[length];
 665                         memcpy(buf, outputString.c_str(), length);
 666
 667                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 668
 669             delete buf;
 670                 }
 671
 672                 Alignment* alignment;
 673                 int longestBase = templateDB->getLongestBase();
 674                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 675                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 676                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 677                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 678                 else {
 679                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 680                         m->mothurOutEndLine();
 681                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 682                 }
 683
 684
 685                 for(int i=0;i<num;i++){
 686
 687                         if (m->control_pressed) { delete alignment; return 0; }
 688
 689                         //read next sequence
 690                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 691
 692                         char* buf4 = new char[length];
 693                         //memcpy(buf4, outputString.c_str(), length);
 694
 695                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 696
 697                         string tempBuf = buf4;
 698
 699                         delete buf4;
 700
 701                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 702
 703                         istringstream iss (tempBuf,istringstream::in);
 704
 705                         Sequence* candidateSeq = new Sequence(iss);
 706                         report.setCandidate(candidateSeq);
 707
 708                         int origNumBases = candidateSeq->getNumBases();
 709                         string originalUnaligned = candidateSeq->getUnaligned();
 710                         int numBasesNeeded = origNumBases * threshold;
 711
 712                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 713                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 714                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 715                                 }
 716
 717                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 718                                 Sequence* templateSeq = &temp;
 719
 720                                 float searchScore = templateDB->getSearchScore();
 721
 722                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 723                                 Sequence* copy;
 724
 725                                 Nast* nast2;
 726                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 727                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 728                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 729                                                                                                 //so this bool tells you if you need to delete it
 730
 731                                 //if there is a possibility that this sequence should be reversed
 732                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 733
 734                                         string wasBetter = "";
 735                                         //if the user wants you to try the reverse
 736                                         if (flip) {
 737                                                 //get reverse compliment
 738                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 739                                                 copy->reverseComplement();
 740
 741                                                 //rerun alignment
 742                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 743                                                 Sequence* templateSeq2 = &temp2;
 744
 745                                                 searchScore = templateDB->getSearchScore();
 746
 747                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 748
 749                                                 //check if any better
 750                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 751                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 752                                                         templateSeq = templateSeq2;
 753                                                         delete nast;
 754                                                         nast = nast2;
 755                                                         needToDeleteCopy = true;
 756                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 757                                                 }else{
 758                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 759                                                         delete nast2;
 760                                                         delete copy;
 761                                                 }
 762                                         }
 763
 764                                         //create accnos file with names
 765                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 766
 767                                         //send results to parent
 768                                         int length = outputString.length();
 769
 770                                         char* buf = new char[length];
 771                                         memcpy(buf, outputString.c_str(), length);
 772
 773                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 774                                         delete buf;
 775                                         MPIWroteAccnos = true;
 776                                 }
 777
 778                                 report.setTemplate(templateSeq);
 779                                 report.setSearchParameters(search, searchScore);
 780                                 report.setAlignmentParameters(align, alignment);
 781                                 report.setNastParameters(*nast);
 782
 783                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 784
 785                                 //send results to parent
 786                                 int length = outputString.length();
 787                                 char* buf2 = new char[length];
 788                                 memcpy(buf2, outputString.c_str(), length);
 789
 790                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 791
 792                                 delete buf2;
 793
 794                                 outputString = report.getReport();
 795
 796                                 //send results to parent
 797                                 length = outputString.length();
 798                                 char* buf3 = new char[length];
 799                                 memcpy(buf3, outputString.c_str(), length);
 800
 801                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 802
 803                                 delete buf3;
 804                                 delete nast;
 805                                 if (needToDeleteCopy) {   delete copy;   }
 806                         }
 807                         delete candidateSeq;
 808
 809                         //report progress
 810                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 811                 }
 812                 //report progress
 813                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 814
 815                 return 1;
 816         }
 817         catch(exception& e) {
 818                 m->errorOut(e, "AlignCommand", "driverMPI");
 819                 exit(1);
 820         }
 821 }
 822 #endif
 823 /**************************************************************************************************/
 824
 825 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 826         try {
 827                 int num = 0;
 828                 processIDS.resize(0);
 829 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 830                 int process = 1;
 831
 832                 //loop through and create all the processes you want
 833                 while (process != processors) {
 834                         int pid = fork();
 835
 836                         if (pid > 0) {
 837                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 838                                 process++;
 839                         }else if (pid == 0){
 840                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 841
 842                                 //pass numSeqs to parent
 843                                 ofstream out;
 844                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 845                                 m->openOutputFile(tempFile, out);
 846                                 out << num << endl;
 847                                 out.close();
 848
 849                                 exit(0);
 850                         }else {
 851                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 852                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 853                                 exit(0);
 854                         }
 855                 }
 856
 857                 //do my part
 858                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 859
 860                 //force parent to wait until all the processes are done
 861                 for (int i=0;i<processIDS.size();i++) {
 862                         int temp = processIDS[i];
 863                         wait(&temp);
 864                 }
 865
 866                 vector<string> nonBlankAccnosFiles;
 867                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 868                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 869
 870                 for (int i = 0; i < processIDS.size(); i++) {
 871                         ifstream in;
 872                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 873                         m->openInputFile(tempFile, in);
 874                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 875                         in.close(); m->mothurRemove(tempFile);
 876
 877                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 878                         m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
 879
 880                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 881                         m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
 882
 883                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 884                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 885                         }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp"));  }
 886
 887                 }
 888
 889                 //append accnos files
 890                 if (nonBlankAccnosFiles.size() != 0) {
 891                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 892
 893                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 894                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
 895                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 896                         }
 897                 }else { //recreate the accnosfile if needed
 898                         ofstream out;
 899                         m->openOutputFile(accnosFName, out);
 900                         out.close();
 901                 }
 902 #else
 903                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 904                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
 905                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 906                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 907
 908                 vector<alignData*> pDataArray;
 909                 DWORD   dwThreadIdArray[processors-1];
 910                 HANDLE  hThreadArray[processors-1];
 911
 912                 //Create processor worker threads.
 913                 for( int i=0; i<processors-1; i++ ){
 914                         //copy templateDb
 915                         //AlignmentDB* tempDB = new AlignmentDB(*templateDB);
 916
 917                         // Allocate memory for thread data.
 918                         string extension = "";
 919                         if (i != 0) { extension = toString(i) + ".temp"; }
 920
 921                         alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
 922                         pDataArray.push_back(tempalign);
 923                         processIDS.push_back(i);
 924
 925                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 926                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 927                         hThreadArray[i] = CreateThread(NULL, 0, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 928                 }
 929
 930                 //need to check for line ending error
 931                 ifstream inFASTA;
 932                 m->openInputFile(filename, inFASTA);
 933                 inFASTA.seekg(lines[processors-1]->start-1);
 934                 char c = inFASTA.peek();
 935
 936                 if (c != '>') { //we need to move back
 937                         lines[processors-1]->start--;
 938                 }
 939
 940                 //using the main process as a worker saves time and memory
 941                 //do my part - do last piece because windows is looking for eof
 942                 num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
 943
 944                 //Wait until all threads have terminated.
 945                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 946
 947                 //Close all thread handles and free memory allocations.
 948                 for(int i=0; i < pDataArray.size(); i++){
 949                         num += pDataArray[i]->count;
 950                         CloseHandle(hThreadArray[i]);
 951                         delete pDataArray[i];
 952                 }
 953
 954                 vector<string> nonBlankAccnosFiles;
 955                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 956                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 957
 958                 for (int i = 1; i < processors; i++) {
 959                         appendAlignFiles((alignFileName + toString(i) + ".temp"), alignFileName);
 960                         m->mothurRemove((alignFileName + toString(i) + ".temp"));
 961
 962                         appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
 963                         m->mothurRemove((reportFileName + toString(i) + ".temp"));
 964
 965                         if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
 966                                 nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
 967                         }else { m->mothurRemove((accnosFName + toString(i) + ".temp"));  }
 968                 }
 969
 970                 //append accnos files
 971                 if (nonBlankAccnosFiles.size() != 0) {
 972                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 973
 974                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 975                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
 976                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 977                         }
 978                 }else { //recreate the accnosfile if needed
 979                         ofstream out;
 980                         m->openOutputFile(accnosFName, out);
 981                         out.close();
 982                 }
 983 #endif
 984
 985                 return num;
 986         }
 987         catch(exception& e) {
 988                 m->errorOut(e, "AlignCommand", "createProcesses");
 989                 exit(1);
 990         }
 991 }
 992 /**************************************************************************************************/
 993
 994 void AlignCommand::appendAlignFiles(string temp, string filename) {
 995         try{
 996
 997                 ofstream output;
 998                 ifstream input;
 999                 m->openOutputFileAppend(filename, output);
1000                 m->openInputFile(temp, input);
1001
1002                 while(char c = input.get()){
1003                         if(input.eof())         {       break;                  }
1004                         else                            {       output << c;    }
1005                 }
1006
1007                 input.close();
1008                 output.close();
1009         }
1010         catch(exception& e) {
1011                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
1012                 exit(1);
1013         }
1014 }
1015 //**********************************************************************************************************************
1016
1017 void AlignCommand::appendReportFiles(string temp, string filename) {
1018         try{
1019
1020                 ofstream output;
1021                 ifstream input;
1022                 m->openOutputFileAppend(filename, output);
1023                 m->openInputFile(temp, input);
1024
1025                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
1026
1027                 while(char c = input.get()){
1028                         if(input.eof())         {       break;                  }
1029                         else                            {       output << c;    }
1030                 }
1031
1032                 input.close();
1033                 output.close();
1034         }
1035         catch(exception& e) {
1036                 m->errorOut(e, "AlignCommand", "appendReportFiles");
1037                 exit(1);
1038         }
1039 }
1040 //**********************************************************************************************************************