filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 /**************************************************************************************/
  14
  15 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  16         try {
  17                 abort = false;
  18                 filterFileName = "";
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         map<string,string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("fasta");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  50                                 }
  51
  52                                 it = parameters.find("hard");
  53                                 //user has given a template file
  54                                 if(it != parameters.end()){
  55                                         path = hasPath(it->second);
  56                                         //if the user has not given a path then, add inputdir. else leave path alone.
  57                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
  58                                 }
  59                         }
  60
  61                         //check for required parameters
  62                         fasta = validParameter.validFile(parameters, "fasta", false);
  63                         if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true;  }
  64                         else {
  65                                 splitAtDash(fasta, fastafileNames);
  66
  67                                 //go through files and make sure they are good, if not, then disregard them
  68                                 for (int i = 0; i < fastafileNames.size(); i++) {
  69                                         if (inputDir != "") {
  70                                                 string path = hasPath(fastafileNames[i]);
  71                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  72                                                 if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
  73                                         }
  74
  75                                         int ableToOpen;
  76                                         ifstream in;
  77                                         ableToOpen = openInputFile(fastafileNames[i], in);
  78                                         if (ableToOpen == 1) {
  79                                                 m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  80                                                 //erase from file list
  81                                                 fastafileNames.erase(fastafileNames.begin()+i);
  82                                                 i--;
  83                                         }else{
  84                                                 string simpleName = getSimpleName(fastafileNames[i]);
  85                                                 filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
  86                                         }
  87                                         in.close();
  88                                 }
  89
  90                                 //make sure there is at least one valid file left
  91                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  92                         }
  93
  94                         if (!abort) {
  95                                 //if the user changes the output directory command factory will send this info to us in the output parameter
  96                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  97                                         outputDir = "";
  98                                         outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
  99                                 }
 100                         }
 101                         //check for optional parameter and set defaults
 102                         // ...at some point should added some additional type checking...
 103
 104                         string temp;
 105                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 106                         trump = temp[0];
 107
 108                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 109                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 110
 111                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 112                         convert(temp, processors);
 113
 114                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 115                         else if (hard == "not open") { abort = true; }
 116
 117                         vertical = validParameter.validFile(parameters, "vertical", false);             if (vertical == "not found") { vertical = "T"; }
 118
 119                         numSeqs = 0;
 120
 121                 }
 122
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 126                 exit(1);
 127         }
 128 }
 129
 130 //**********************************************************************************************************************
 131
 132 void FilterSeqsCommand::help(){
 133         try {
 134
 135                 m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
 136                 m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
 137                 m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
 138                 m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
 139                 m->mothurOut("The trump parameter .... The default is ...\n");
 140                 m->mothurOut("The soft parameter .... The default is ....\n");
 141                 m->mothurOut("The hard parameter .... The default is ....\n");
 142                 m->mothurOut("The vertical parameter .... The default is T.\n");
 143                 m->mothurOut("The filter.seqs command should be in the following format: \n");
 144                 m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
 145                 m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
 146                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 147
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "FilterSeqsCommand", "help");
 151                 exit(1);
 152         }
 153 }
 154
 155 /**************************************************************************************/
 156
 157 int FilterSeqsCommand::execute() {
 158         try {
 159
 160                 if (abort == true) { return 0; }
 161                 vector<string> outputNames;
 162
 163                 ifstream inFASTA;
 164                 openInputFile(fastafileNames[0], inFASTA);
 165
 166                 Sequence testSeq(inFASTA);
 167                 alignmentLength = testSeq.getAlignLength();
 168                 inFASTA.close();
 169
 170                 ////////////create filter/////////////////
 171
 172                 filter = createFilter();
 173
 174                 ofstream outFilter;
 175
 176                 string filterFile = outputDir + filterFileName + ".filter";
 177                 openOutputFile(filterFile, outFilter);
 178                 outFilter << filter << endl;
 179                 outFilter.close();
 180                 outputNames.push_back(filterFile);
 181
 182
 183                 ////////////run filter/////////////////
 184
 185                 numSeqs = 0;
 186                 for (int i = 0; i < fastafileNames.size(); i++) {
 187                         ifstream in;
 188                         openInputFile(fastafileNames[i], in);
 189                         string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta";
 190                         ofstream outFASTA;
 191                         openOutputFile(filteredFasta, outFASTA);
 192                         outputNames.push_back(filteredFasta);
 193
 194
 195                         while(!in.eof()){
 196                                 if (m->control_pressed) { in.close(); outFASTA.close(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 197
 198                                 Sequence seq(in);
 199                                 if (seq.getName() != "") {
 200                                         string align = seq.getAligned();
 201                                         string filterSeq = "";
 202
 203                                         for(int j=0;j<alignmentLength;j++){
 204                                                 if(filter[j] == '1'){
 205                                                         filterSeq += align[j];
 206                                                 }
 207                                         }
 208
 209                                         outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
 210                                         numSeqs++;
 211                                 }
 212                                 gobble(in);
 213                         }
 214                         outFASTA.close();
 215                         in.close();
 216                 }
 217
 218                 int filteredLength = 0;
 219                 for(int i=0;i<alignmentLength;i++){
 220                         if(filter[i] == '1'){   filteredLength++;       }
 221                 }
 222
 223                 if (m->control_pressed) {  for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }  return 0; }
 224
 225
 226                 m->mothurOutEndLine();
 227                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 228                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 229                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 230                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 231
 232
 233                 m->mothurOutEndLine();
 234                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 235                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 236                 m->mothurOutEndLine();
 237
 238                 return 0;
 239
 240         }
 241         catch(exception& e) {
 242                 m->errorOut(e, "FilterSeqsCommand", "execute");
 243                 exit(1);
 244         }
 245 }
 246 /**************************************************************************************/
 247 string FilterSeqsCommand::createFilter() {
 248         try {
 249                 string filterString = "";
 250
 251                 Filters F;
 252
 253                 if (soft != 0)                  {  F.setSoft(soft);             }
 254                 if (trump != '*')               {  F.setTrump(trump);   }
 255
 256                 F.setLength(alignmentLength);
 257
 258                 if(soft != 0 || isTrue(vertical)){
 259                         F.initialize();
 260                 }
 261
 262                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 263                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 264
 265                 numSeqs = 0;
 266
 267                 if(trump != '*' || isTrue(vertical) || soft != 0){
 268                         for (int s = 0; s < fastafileNames.size(); s++) {
 269
 270                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 271
 272 #ifdef USE_MPI
 273                                 int pid, rc, ierr;
 274                                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 275                                 int tag = 2001;
 276
 277                                 MPI_Status status;
 278                                 MPI_File in;
 279                                 rc = MPI_Comm_size(MPI_COMM_WORLD, &processors);
 280                                 rc = MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 281
 282
 283                                 char* tempFileName = new char(fastafileNames[s].length());
 284                                 tempFileName = &(fastafileNames[s][0]);
 285
 286                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &in);  //comm, filename, mode, info, filepointer
 287
 288                                 if (pid == 0) { //you are the root process
 289                                                 setLines(fastafileNames[s]);
 290
 291                                                 for (int j = 0; j < lines.size(); j++) { //each process
 292                                                         if (j != 0) { //don't send to yourself
 293                                                                 MPI_Send(&lines[j]->start, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //start position in file
 294                                                                 MPI_Send(&lines[j]->numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how many sequences we are sending
 295                                                                 MPI_Send(&bufferSizes[j], 1, MPI_INT, j, tag, MPI_COMM_WORLD); //how bytes for the read
 296                                                         }
 297                                                 }
 298
 299                                                 char buf[bufferSizes[0]];
 300                                                 MPI_File_read_at(in, 0, buf, bufferSizes[0], MPI_CHAR, &status);
 301
 302                                                 MPICreateFilter(F, buf);
 303
 304                                                 vector<int> temp; temp.resize(alignmentLength+1);
 305
 306                                                 //get the frequencies from the child processes
 307                                                 for(int i = 0; i < ((processors-1)*5); i++) {
 308                                 cout << "i = " << i << endl;
 309                                 //vector<int> trial; trial.resize(10);
 310                                 //cout << "trials size = " << trial.size() << endl;
 311                                 //int ierr = MPI_Recv(&trial[0], 10, MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
 312                                                         int ierr = MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, tag, MPI_COMM_WORLD, &status);
 313                                         cout << "recieved something" << endl;
 314                         //for (int g = 0; g < trial.size(); g++) {  cout << trial[g] << '\t';  } cout << endl;
 315                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 316                                         cout << "reciveve tag = " << receiveTag << endl;
 317                                         for (int k = 0; k < alignmentLength; k++) {             cout << k << '\t' << temp[k] << endl;   }
 318                                         cout << "done " << endl << endl;
 319
 320                                                         int sender = status.MPI_SOURCE;
 321
 322                                                         if (receiveTag == Atag) { //you are recieveing the A frequencies
 323                                                                 for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 324                                                         }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 325                                                                 for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 326                                                         }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 327                                                                 for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 328                                                         }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 329                                                                 for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 330                                                         }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 331                                                                 for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 332                                                         }
 333
 334                                                         m->mothurOut("receive tag = " + toString(receiveTag) + " " + toString(sender) + " is complete."); m->mothurOutEndLine();
 335                                                 }
 336
 337
 338                                 }else { //i am the child process
 339                                         int startPos, numLines, bufferSize;
 340                                         ierr = MPI_Recv(&startPos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 341                                         ierr = MPI_Recv(&numLines, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 342                                         ierr = MPI_Recv(&bufferSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 343
 344                                         //send freqs
 345                                         char buf2[bufferSize];
 346                                         MPI_File_read_at( in, startPos, buf2, bufferSize, MPI_CHAR, &status);
 347
 348                                         MPICreateFilter(F, buf2);
 349
 350                                         //send my fequency counts
 351                                         F.a.push_back(Atag);
 352                                         int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 353                                         F.t.push_back(Ttag);
 354                                         ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 355                                         F.c.push_back(Ctag);
 356                                         ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 357                                         F.g.push_back(Gtag);
 358                                         ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 359                                         F.gap.push_back(Gaptag);
 360                                         ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, tag, MPI_COMM_WORLD);
 361                                 }
 362
 363                                 MPI_Barrier(MPI_COMM_WORLD);
 364
 365 #else
 366                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 367                                 if(processors == 1){
 368                                         ifstream inFASTA;
 369                                         openInputFile(fastafileNames[s], inFASTA);
 370                                         int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 371                                         inFASTA.close();
 372
 373                                         numSeqs += numFastaSeqs;
 374
 375                                         lines.push_back(new linePair(0, numFastaSeqs));
 376
 377                                         driverCreateFilter(F, fastafileNames[s], lines[0]);
 378                                 }else{
 379
 380                                         setLines(fastafileNames[s]);
 381                                         createProcessesCreateFilter(F, fastafileNames[s]);
 382                                 }
 383                 #else
 384                                 ifstream inFASTA;
 385                                 openInputFile(fastafileNames[s], inFASTA);
 386                                 int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 387                                 inFASTA.close();
 388
 389                                 numSeqs += numFastaSeqs;
 390
 391                                 lines.push_back(new linePair(0, numFastaSeqs));
 392
 393                                 driverCreateFilter(F, lines[0], fastafileNames[s]);
 394                 #endif
 395 #endif
 396
 397                         }
 398                 }
 399
 400
 401         cout << "made it here, numSeqs = " << numSeqs << endl;
 402                 F.setNumSeqs(numSeqs);
 403
 404                 if(isTrue(vertical) == 1)       {       F.doVertical(); }
 405                 if(soft != 0)                           {       F.doSoft();             }
 406 //cout << "Filter String = " << F.getFilter() << endl;
 407                 filterString = F.getFilter();
 408
 409                 return filterString;
 410         }
 411         catch(exception& e) {
 412                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 413                 exit(1);
 414         }
 415 }
 416 /**************************************************************************************/
 417 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
 418         try {
 419
 420                 ifstream in;
 421                 openInputFile(filename, in);
 422
 423                 in.seekg(line->start);
 424
 425                 for(int i=0;i<line->numSeqs;i++){
 426
 427                         if (m->control_pressed) { in.close(); return 1; }
 428
 429                         Sequence seq(in);
 430                         if (seq.getName() != "") {
 431                                         if(trump != '*'){       F.doTrump(seq); }
 432                                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 433                                         cout.flush();
 434                         }
 435
 436                         //report progress
 437                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 438                 }
 439
 440                 //report progress
 441                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 442
 443                 in.close();
 444
 445                 return 0;
 446         }
 447         catch(exception& e) {
 448                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 449                 exit(1);
 450         }
 451 }
 452 /**************************************************************************************/
 453 int FilterSeqsCommand::MPICreateFilter(Filters& F, string input) {
 454         try {
 455
 456                 vector<string> seqStrings;
 457                 parseBuffer(input, seqStrings);
 458
 459                 for(int i=0;i<seqStrings.size();i++){
 460
 461                         if (m->control_pressed) { return 1; }
 462
 463                         Sequence seq("", seqStrings[i]);
 464
 465                         if(trump != '*'){       F.doTrump(seq); }
 466                         if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
 467                         cout.flush();
 468
 469                         //report progress
 470                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 471                 }
 472
 473                 //report progress
 474                 if((seqStrings.size()) % 100 != 0){     m->mothurOut(toString(seqStrings.size())); m->mothurOutEndLine();               }
 475
 476                 return 0;
 477         }
 478         catch(exception& e) {
 479                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
 480                 exit(1);
 481         }
 482 }
 483
 484 /**************************************************************************************************/
 485
 486 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
 487         try {
 488 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 489                 int process = 0;
 490                 int exitCommand = 1;
 491                 vector<int> processIDS;
 492
 493                 //loop through and create all the processes you want
 494                 while (process != processors) {
 495                         int pid = vfork();
 496
 497                         if (pid > 0) {
 498                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 499                                 process++;
 500                         }else if (pid == 0){
 501                                 driverCreateFilter(F, filename, lines[process]);
 502                                 exit(0);
 503                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 504                 }
 505
 506                 //force parent to wait until all the processes are done
 507                 for (int i=0;i<processors;i++) {
 508                         int temp = processIDS[i];
 509                         wait(&temp);
 510                 }
 511
 512                 return exitCommand;
 513 #endif
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
 517                 exit(1);
 518         }
 519 }
 520 /**************************************************************************************************/
 521
 522 int FilterSeqsCommand::setLines(string filename) {
 523         try {
 524                 vector<int> positions;
 525                 map<int, int> buf;
 526                 bufferSizes.clear();
 527
 528                 int pid;
 529                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 530
 531                 ifstream inFASTA;
 532                 openInputFile(filename, inFASTA);
 533
 534                 string input;
 535                 int numbuf = 0;
 536                 while(!inFASTA.eof()){
 537                         input = getline(inFASTA);
 538
 539                         if (input.length() != 0) {
 540                                 numbuf += input.length();
 541                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  buf[(pos - input.length() - 1)] = numbuf; }
 542                         }
 543                 }
 544
 545                 inFASTA.close();
 546
 547                 int numFastaSeqs = positions.size();
 548
 549                 numSeqs += numFastaSeqs;
 550
 551                 int numSeqsPerProcessor = numFastaSeqs / processors;
 552
 553                 for (int i = 0; i < processors; i++) {
 554
 555                         long int startPos = positions[ i * numSeqsPerProcessor ];
 556                         if(i == processors - 1){
 557                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 558                                 bufferSizes.push_back(numbuf-buf[startPos]);
 559                         }else{
 560                                 int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 561                                 bufferSizes.push_back(buf[myEnd]-buf[startPos]);
 562                         }
 563                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 564                 }
 565
 566                 return 0;
 567         }
 568         catch(exception& e) {
 569                 m->errorOut(e, "FilterSeqsCommand", "setLines");
 570                 exit(1);
 571         }
 572 }
 573 /**************************************************************************************************/
 574 int FilterSeqsCommand::parseBuffer(string file, vector<string>& seqs) {
 575         try {
 576
 577                 istringstream iss (file,istringstream::in);
 578                 string name, seqstring;
 579
 580                 while (iss) {
 581
 582                         if (m->control_pressed) { return 0; }
 583
 584                         Sequence seq(iss); gobble(iss);
 585
 586                         if (seq.getName() != "") {
 587                                 seqs.push_back(seq.getAligned());
 588                         }
 589                 }
 590
 591                 return 0;
 592         }
 593         catch(exception& e) {
 594                 m->errorOut(e, "FilterSeqsCommand", "parseBuffer");
 595                 exit(1);
 596         }
 597 }
 598 /**************************************************************************************/