sffinfocommand.cpp

   1 /*
   2  *  sffinfocommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 7/7/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sffinfocommand.h"
  11 #include "endiannessmacros.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SffInfoCommand::setParameters(){
  15         try {
  16                 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
  17                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  18                 CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
  19                 CommandParameter pflow("flow", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pflow);
  20                 CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
  21                 CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
  22                 CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "SffInfoCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string SffInfoCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file.\n";
  40                 helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n";
  41                 helpString += "The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n";
  42                 helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n";
  43                 helpString += "The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n";
  44                 helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=True. \n";
  45                 helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n";
  46                 helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
  47                 helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n";
  48                 helpString += "The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n";
  49                 helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
  50                 helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n";
  51                 return helpString;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "SffInfoCommand", "getHelpString");
  55                 exit(1);
  56         }
  57 }
  58
  59
  60 //**********************************************************************************************************************
  61 SffInfoCommand::SffInfoCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["fasta"] = tempOutNames;
  67                 outputTypes["flow"] = tempOutNames;
  68                 outputTypes["sfftxt"] = tempOutNames;
  69                 outputTypes["qfile"] = tempOutNames;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77
  78 SffInfoCommand::SffInfoCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81                 hasAccnos = false;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         //valid paramters for this command
  89                         vector<string> myArray = setParameters();
  90
  91                         OptionParser parser(option);
  92                         map<string, string> parameters = parser.getParameters();
  93
  94                         ValidParameters validParameter;
  95                         //check to make sure all parameters are valid for command
  96                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["fasta"] = tempOutNames;
 103                         outputTypes["flow"] = tempOutNames;
 104                         outputTypes["sfftxt"] = tempOutNames;
 105                         outputTypes["qfile"] = tempOutNames;
 106
 107                         //if the user changes the output directory command factory will send this info to us in the output parameter
 108                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 109
 110                         //if the user changes the input directory command factory will send this info to us in the output parameter
 111                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
 112
 113                         sffFilename = validParameter.validFile(parameters, "sff", false);
 114                         if (sffFilename == "not found") { sffFilename = "";  }
 115                         else {
 116                                 m->splitAtDash(sffFilename, filenames);
 117
 118                                 //go through files and make sure they are good, if not, then disregard them
 119                                 for (int i = 0; i < filenames.size(); i++) {
 120                                         bool ignore = false;
 121                                         if (filenames[i] == "current") {
 122                                                 filenames[i] = m->getSFFFile();
 123                                                 if (filenames[i] != "") {  m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current."); m->mothurOutEndLine(); }
 124                                                 else {
 125                                                         m->mothurOut("You have no current sfffile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 126                                                         //erase from file list
 127                                                         filenames.erase(filenames.begin()+i);
 128                                                         i--;
 129                                                 }
 130                                         }
 131
 132                                         if (!ignore) {
 133                                                 if (inputDir != "") {
 134                                                         string path = m->hasPath(filenames[i]);
 135                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                                         if (path == "") {       filenames[i] = inputDir + filenames[i];         }
 137                                                 }
 138
 139                                                 ifstream in;
 140                                                 int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
 141
 142                                                 //if you can't open it, try default location
 143                                                 if (ableToOpen == 1) {
 144                                                         if (m->getDefaultPath() != "") { //default path is set
 145                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
 146                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 147                                                                 ifstream in2;
 148                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 149                                                                 in2.close();
 150                                                                 filenames[i] = tryPath;
 151                                                         }
 152                                                 }
 153
 154                                                 //if you can't open it, try default location
 155                                                 if (ableToOpen == 1) {
 156                                                         if (m->getOutputDir() != "") { //default path is set
 157                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
 158                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 159                                                                 ifstream in2;
 160                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 161                                                                 in2.close();
 162                                                                 filenames[i] = tryPath;
 163                                                         }
 164                                                 }
 165
 166                                                 in.close();
 167
 168                                                 if (ableToOpen == 1) {
 169                                                         m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 170                                                         //erase from file list
 171                                                         filenames.erase(filenames.begin()+i);
 172                                                         i--;
 173                                                 }else { m->setSFFFile(filenames[i]); }
 174                                         }
 175                                 }
 176
 177                                 //make sure there is at least one valid file left
 178                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 179                         }
 180
 181                         accnosName = validParameter.validFile(parameters, "accnos", false);
 182                         if (accnosName == "not found") { accnosName = "";  }
 183                         else {
 184                                 hasAccnos = true;
 185                                 m->splitAtDash(accnosName, accnosFileNames);
 186
 187                                 //go through files and make sure they are good, if not, then disregard them
 188                                 for (int i = 0; i < accnosFileNames.size(); i++) {
 189                                         bool ignore = false;
 190                                         if (accnosFileNames[i] == "current") {
 191                                                 accnosFileNames[i] = m->getAccnosFile();
 192                                                 if (accnosFileNames[i] != "") {  m->mothurOut("Using " + accnosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
 193                                                 else {
 194                                                         m->mothurOut("You have no current accnosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 195                                                         //erase from file list
 196                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 197                                                         i--;
 198                                                 }
 199                                         }
 200
 201                                         if (!ignore) {
 202
 203                                                 if (inputDir != "") {
 204                                                         string path = m->hasPath(accnosFileNames[i]);
 205                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                                         if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
 207                                                 }
 208
 209                                                 ifstream in;
 210                                                 int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
 211
 212                                                 //if you can't open it, try default location
 213                                                 if (ableToOpen == 1) {
 214                                                         if (m->getDefaultPath() != "") { //default path is set
 215                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
 216                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 217                                                                 ifstream in2;
 218                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 219                                                                 in2.close();
 220                                                                 accnosFileNames[i] = tryPath;
 221                                                         }
 222                                                 }
 223                                                 //if you can't open it, try default location
 224                                                 if (ableToOpen == 1) {
 225                                                         if (m->getOutputDir() != "") { //default path is set
 226                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
 227                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 228                                                                 ifstream in2;
 229                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 230                                                                 in2.close();
 231                                                                 accnosFileNames[i] = tryPath;
 232                                                         }
 233                                                 }
 234                                                 in.close();
 235
 236                                                 if (ableToOpen == 1) {
 237                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 238                                                         //erase from file list
 239                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 240                                                         i--;
 241                                                 }
 242                                         }
 243                                 }
 244
 245                                 //make sure there is at least one valid file left
 246                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 247                         }
 248
 249                         if (hasAccnos) {
 250                                 if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
 251                         }
 252
 253                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 254                         qual = m->isTrue(temp);
 255
 256                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 257                         fasta = m->isTrue(temp);
 258
 259                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "T";                             }
 260                         flow = m->isTrue(temp);
 261
 262                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 263                         trim = m->isTrue(temp);
 264
 265                         temp = validParameter.validFile(parameters, "sfftxt", false);
 266                         if (temp == "not found")        {       temp = "F";      sfftxt = false; sfftxtFilename = "";           }
 267                         else if (m->isTrue(temp))       {       sfftxt = true;          sfftxtFilename = "";                            }
 268                         else {
 269                                 //you are a filename
 270                                 if (inputDir != "") {
 271                                         map<string,string>::iterator it = parameters.find("sfftxt");
 272                                         //user has given a template file
 273                                         if(it != parameters.end()){
 274                                                 string path = m->hasPath(it->second);
 275                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 276                                                 if (path == "") {       parameters["sfftxt"] = inputDir + it->second;           }
 277                                         }
 278                                 }
 279
 280                                 sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
 281                                 if (sfftxtFilename == "not found") { sfftxtFilename = "";  }
 282                                 else if (sfftxtFilename == "not open") { sfftxtFilename = "";  }
 283                         }
 284
 285                         if ((sfftxtFilename == "") && (filenames.size() == 0)) {
 286                                 //if there is a current sff file, use it
 287                                 string filename = m->getSFFFile();
 288                                 if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
 289                                 else {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
 290                         }
 291                 }
 292         }
 293         catch(exception& e) {
 294                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 295                 exit(1);
 296         }
 297 }
 298 //**********************************************************************************************************************
 299 int SffInfoCommand::execute(){
 300         try {
 301                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 302
 303                 for (int s = 0; s < filenames.size(); s++) {
 304
 305                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 306
 307                         int start = time(NULL);
 308
 309                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 310
 311                         string accnos = "";
 312                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 313
 314                         int numReads = extractSffInfo(filenames[s], accnos);
 315
 316                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 317                 }
 318
 319                 if (sfftxtFilename != "") {  parseSffTxt(); }
 320
 321                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 322
 323                 //set fasta file as new current fastafile
 324                 string current = "";
 325                 itTypes = outputTypes.find("fasta");
 326                 if (itTypes != outputTypes.end()) {
 327                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 328                 }
 329
 330                 itTypes = outputTypes.find("qfile");
 331                 if (itTypes != outputTypes.end()) {
 332                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 333                 }
 334
 335                 itTypes = outputTypes.find("flow");
 336                 if (itTypes != outputTypes.end()) {
 337                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
 338                 }
 339
 340                 //report output filenames
 341                 m->mothurOutEndLine();
 342                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 343                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 344                 m->mothurOutEndLine();
 345
 346                 return 0;
 347         }
 348         catch(exception& e) {
 349                 m->errorOut(e, "SffInfoCommand", "execute");
 350                 exit(1);
 351         }
 352 }
 353 //**********************************************************************************************************************
 354 int SffInfoCommand::extractSffInfo(string input, string accnos){
 355         try {
 356
 357                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 358
 359                 if (accnos != "")       {  readAccnosFile(accnos);  }
 360                 else                            {       seqNames.clear();               }
 361
 362                 ofstream outSfftxt, outFasta, outQual, outFlow;
 363                 string outFastaFileName, outQualFileName;
 364         string rootName = outputDir + m->getRootName(m->getSimpleName(input));
 365         if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
 366
 367                 string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 368                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 369                 if (trim) {
 370                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 371                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 372                 }else{
 373                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 374                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 375                 }
 376
 377                 if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
 378                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 379                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
 380                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
 381
 382                 ifstream in;
 383                 in.open(input.c_str(), ios::binary);
 384
 385                 CommonHeader header;
 386                 readCommonHeader(in, header);
 387
 388                 int count = 0;
 389                 mycount = 0;
 390
 391                 //check magic number and version
 392                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 393                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 394
 395                 //print common header
 396                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 397                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 398
 399                 //read through the sff file
 400                 while (!in.eof()) {
 401
 402                         bool print = true;
 403
 404                         //read header
 405                         Header readheader;
 406                         readHeader(in, readheader);
 407
 408                         //read data
 409                         seqRead read;
 410                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 411             bool okay = sanityCheck(readheader, read);
 412             if (!okay) { break; }
 413
 414                         //if you have provided an accosfile and this seq is not in it, then dont print
 415                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 416
 417                         //print
 418                         if (print) {
 419                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 420                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 421                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 422                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 423                         }
 424
 425                         count++;
 426                         mycount++;
 427
 428                         //report progress
 429                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 430
 431                         if (m->control_pressed) { count = 0; break;   }
 432
 433                         if (count >= header.numReads) { break; }
 434                 }
 435
 436                 //report progress
 437                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 438
 439                 in.close();
 440
 441                 if (sfftxt) {  outSfftxt.close();       }
 442                 if (fasta)      {  outFasta.close();    }
 443                 if (qual)       {  outQual.close();             }
 444                 if (flow)       {  outFlow.close();             }
 445
 446                 return count;
 447         }
 448         catch(exception& e) {
 449                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 450                 exit(1);
 451         }
 452 }
 453 //**********************************************************************************************************************
 454 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 455         try {
 456
 457                 if (!in.eof()) {
 458
 459                         //read magic number
 460                         char buffer[4];
 461                         in.read(buffer, 4);
 462                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 463
 464                         //read version
 465                         char buffer9[4];
 466                         in.read(buffer9, 4);
 467                         header.version = "";
 468                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 469
 470                         //read offset
 471                         char buffer2 [8];
 472                         in.read(buffer2, 8);
 473                         header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 474
 475                         //read index length
 476                         char buffer3 [4];
 477                         in.read(buffer3, 4);
 478                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 479
 480                         //read num reads
 481                         char buffer4 [4];
 482                         in.read(buffer4, 4);
 483                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 484
 485                         //read header length
 486                         char buffer5 [2];
 487                         in.read(buffer5, 2);
 488                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 489
 490                         //read key length
 491                         char buffer6 [2];
 492                         in.read(buffer6, 2);
 493                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 494
 495                         //read number of flow reads
 496                         char buffer7 [2];
 497                         in.read(buffer7, 2);
 498                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 499
 500                         //read format code
 501                         char buffer8 [1];
 502                         in.read(buffer8, 1);
 503                         header.flogramFormatCode = (int)(buffer8[0]);
 504
 505                         //read flow chars
 506                         char* tempBuffer = new char[header.numFlowsPerRead];
 507                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 508                         header.flowChars = tempBuffer;
 509                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 510                         delete[] tempBuffer;
 511
 512                         //read key
 513                         char* tempBuffer2 = new char[header.keyLength];
 514                         in.read(&(*tempBuffer2), header.keyLength);
 515                         header.keySequence = tempBuffer2;
 516                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 517                         delete[] tempBuffer2;
 518
 519                         /* Pad to 8 chars */
 520                         unsigned long long spotInFile = in.tellg();
 521                         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 522                         in.seekg(spot);
 523
 524                 }else{
 525                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 526                 }
 527
 528                 return 0;
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 532                 exit(1);
 533         }
 534 }
 535 //**********************************************************************************************************************
 536 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 537         try {
 538
 539                 if (!in.eof()) {
 540
 541                         //read header length
 542                         char buffer [2];
 543                         in.read(buffer, 2);
 544                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 545
 546                         //read name length
 547                         char buffer2 [2];
 548                         in.read(buffer2, 2);
 549                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 550
 551                         //read num bases
 552                         char buffer3 [4];
 553                         in.read(buffer3, 4);
 554                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 555
 556                         //read clip qual left
 557                         char buffer4 [2];
 558                         in.read(buffer4, 2);
 559                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 560                         header.clipQualLeft = 5;
 561
 562                         //read clip qual right
 563                         char buffer5 [2];
 564                         in.read(buffer5, 2);
 565                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 566
 567                         //read clipAdapterLeft
 568                         char buffer6 [2];
 569                         in.read(buffer6, 2);
 570                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 571
 572                         //read clipAdapterRight
 573                         char buffer7 [2];
 574                         in.read(buffer7, 2);
 575                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 576
 577                         //read name
 578                         char* tempBuffer = new char[header.nameLength];
 579                         in.read(&(*tempBuffer), header.nameLength);
 580                         header.name = tempBuffer;
 581                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 582                         delete[] tempBuffer;
 583
 584                         //extract info from name
 585                         decodeName(header.timestamp, header.region, header.xy, header.name);
 586
 587                         /* Pad to 8 chars */
 588                         unsigned long long spotInFile = in.tellg();
 589                         unsigned long long spot = (spotInFile + 7)& ~7;
 590                         in.seekg(spot);
 591
 592                 }else{
 593                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 594                 }
 595
 596                 return 0;
 597         }
 598         catch(exception& e) {
 599                 m->errorOut(e, "SffInfoCommand", "readHeader");
 600                 exit(1);
 601         }
 602 }
 603 //**********************************************************************************************************************
 604 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 605         try {
 606
 607                 if (!in.eof()) {
 608
 609                         //read flowgram
 610                         read.flowgram.resize(numFlowReads);
 611                         for (int i = 0; i < numFlowReads; i++) {
 612                                 char buffer [2];
 613                                 in.read(buffer, 2);
 614                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 615                         }
 616
 617                         //read flowIndex
 618                         read.flowIndex.resize(numBases);
 619                         for (int i = 0; i < numBases; i++) {
 620                                 char temp[1];
 621                                 in.read(temp, 1);
 622                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 623                         }
 624
 625                         //read bases
 626                         char* tempBuffer = new char[numBases];
 627                         in.read(&(*tempBuffer), numBases);
 628                         read.bases = tempBuffer;
 629                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 630                         delete[] tempBuffer;
 631
 632                         //read qual scores
 633                         read.qualScores.resize(numBases);
 634                         for (int i = 0; i < numBases; i++) {
 635                                 char temp[1];
 636                                 in.read(temp, 1);
 637                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 638                         }
 639
 640                         /* Pad to 8 chars */
 641                         unsigned long long spotInFile = in.tellg();
 642                         unsigned long long spot = (spotInFile + 7)& ~7;
 643                         in.seekg(spot);
 644
 645                 }else{
 646                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 647                 }
 648
 649                 return 0;
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 653                 exit(1);
 654         }
 655 }
 656 //**********************************************************************************************************************
 657 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 658         try {
 659
 660                 if (name.length() >= 6) {
 661                         string time = name.substr(0, 6);
 662                         unsigned int timeNum = m->fromBase36(time);
 663
 664                         int q1 = timeNum / 60;
 665                         int sec = timeNum - 60 * q1;
 666                         int q2 = q1 / 60;
 667                         int minute = q1 - 60 * q2;
 668                         int q3 = q2 / 24;
 669                         int hr = q2 - 24 * q3;
 670                         int q4 = q3 / 32;
 671                         int day = q3 - 32 * q4;
 672                         int q5 = q4 / 13;
 673                         int mon = q4 - 13 * q5;
 674                         int year = 2000 + q5;
 675
 676                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
 677                 }
 678
 679                 if (name.length() >= 9) {
 680                         region = name.substr(7, 2);
 681
 682                         string xyNum = name.substr(9);
 683                         unsigned int myXy = m->fromBase36(xyNum);
 684                         int x = myXy >> 12;
 685                         int y = myXy & 4095;
 686
 687                         xy = toString(x) + "_" + toString(y);
 688                 }
 689
 690                 return 0;
 691         }
 692         catch(exception& e) {
 693                 m->errorOut(e, "SffInfoCommand", "decodeName");
 694                 exit(1);
 695         }
 696 }
 697 //**********************************************************************************************************************
 698 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 699         try {
 700
 701                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 702                 out << "Version: " << header.version << endl;
 703                 out << "Index Offset: " << header.indexOffset << endl;
 704                 out << "Index Length: " << header.indexLength << endl;
 705                 out << "Number of Reads: " << header.numReads << endl;
 706                 out << "Header Length: " << header.headerLength << endl;
 707                 out << "Key Length: " << header.keyLength << endl;
 708                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 709                 out << "Format Code: " << header.flogramFormatCode << endl;
 710                 out << "Flow Chars: " << header.flowChars << endl;
 711                 out << "Key Sequence: " << header.keySequence << endl << endl;
 712
 713                 return 0;
 714         }
 715         catch(exception& e) {
 716                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 717                 exit(1);
 718         }
 719 }
 720 //**********************************************************************************************************************
 721 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 722         try {
 723
 724                 out << ">" << header.name << endl;
 725                 out << "Run Prefix: " << header.timestamp << endl;
 726                 out << "Region #:  " << header.region << endl;
 727                 out << "XY Location: " << header.xy << endl << endl;
 728
 729                 out << "Run Name:  " << endl;
 730                 out << "Analysis Name:  " << endl;
 731                 out << "Full Path: " << endl << endl;
 732
 733                 out << "Read Header Len: " << header.headerLength << endl;
 734                 out << "Name Length: " << header.nameLength << endl;
 735                 out << "# of Bases: " << header.numBases << endl;
 736                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 737                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 738                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 739                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 740
 741                 return 0;
 742         }
 743         catch(exception& e) {
 744                 m->errorOut(e, "SffInfoCommand", "printHeader");
 745                 exit(1);
 746         }
 747 }
 748 //**********************************************************************************************************************
 749 bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
 750         try {
 751         bool okay = true;
 752         string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
 753
 754         if (header.clipQualLeft > read.bases.length()) {
 755             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
 756         }
 757         if (header.clipQualRight > read.bases.length()) {
 758             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
 759         }
 760         if (header.clipQualLeft > read.qualScores.size()) {
 761             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
 762         }
 763         if (header.clipQualRight > read.qualScores.size()) {
 764             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
 765         }
 766
 767         if (okay == false) {
 768             m->mothurOut(message); m->mothurOutEndLine();
 769         }
 770
 771                 return okay;
 772         }
 773         catch(exception& e) {
 774                 m->errorOut(e, "SffInfoCommand", "sanityCheck");
 775                 exit(1);
 776         }
 777 }
 778 //**********************************************************************************************************************
 779 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 780         try {
 781                 out << "Flowgram: ";
 782                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 783
 784                 out << endl <<  "Flow Indexes: ";
 785                 int sum = 0;
 786                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 787
 788                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 789                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 790                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 791                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 792                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 793
 794                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 795                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 796
 797
 798                 out << endl << endl;
 799
 800                 return 0;
 801         }
 802         catch(exception& e) {
 803                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 804                 exit(1);
 805         }
 806 }
 807 //**********************************************************************************************************************
 808 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 809         try {
 810                 string seq = read.bases;
 811
 812         if (trim) {
 813                         if(header.clipQualRight < header.clipQualLeft){
 814                                 seq = "NNNN";
 815                         }
 816                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 817                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 818                         }
 819                         else {
 820                                 seq = seq.substr(header.clipQualLeft-1);
 821                         }
 822                 }else{
 823                         //if you wanted the sfftxt then you already converted the bases to the right case
 824                         if (!sfftxt) {
 825                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 826                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 827                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 828                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 829                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 830                         }
 831                 }
 832
 833                 out << ">" << header.name  << " xy=" << header.xy << endl;
 834                 out << seq << endl;
 835
 836                 return 0;
 837         }
 838         catch(exception& e) {
 839                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 840                 exit(1);
 841         }
 842 }
 843
 844 //**********************************************************************************************************************
 845 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 846         try {
 847
 848                 if (trim) {
 849                         if(header.clipQualRight < header.clipQualLeft){
 850                                 out << ">" << header.name << " xy=" << header.xy << endl;
 851                                 out << "0\t0\t0\t0";
 852                         }
 853                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 854                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 855                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 856                         }
 857                         else{
 858                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 859                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 860                         }
 861                 }else{
 862                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
 863                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 864                 }
 865
 866                 out << endl;
 867
 868                 return 0;
 869         }
 870         catch(exception& e) {
 871                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 872                 exit(1);
 873         }
 874 }
 875
 876 //**********************************************************************************************************************
 877 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 878         try {
 879                 if(header.clipQualRight > header.clipQualLeft){
 880
 881                         int rightIndex = 0;
 882                         for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
 883
 884                         out << header.name << ' ' << rightIndex;
 885                         for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
 886                         out << endl;
 887                 }
 888
 889
 890                 return 0;
 891         }
 892         catch(exception& e) {
 893                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 894                 exit(1);
 895         }
 896 }
 897 //**********************************************************************************************************************
 898 int SffInfoCommand::readAccnosFile(string filename) {
 899         try {
 900                 //remove old names
 901                 seqNames.clear();
 902
 903                 ifstream in;
 904                 m->openInputFile(filename, in);
 905                 string name;
 906
 907                 while(!in.eof()){
 908                         in >> name; m->gobble(in);
 909
 910                         seqNames.insert(name);
 911
 912                         if (m->control_pressed) { seqNames.clear(); break; }
 913                 }
 914                 in.close();
 915
 916                 return 0;
 917         }
 918         catch(exception& e) {
 919                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 920                 exit(1);
 921         }
 922 }
 923 //**********************************************************************************************************************
 924 int SffInfoCommand::parseSffTxt() {
 925         try {
 926
 927                 ifstream inSFF;
 928                 m->openInputFile(sfftxtFilename, inSFF);
 929
 930                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
 931
 932                 //output file names
 933                 ofstream outFasta, outQual, outFlow;
 934                 string outFastaFileName, outQualFileName;
 935                 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
 936                 if (fileRoot.length() > 0) {
 937                         //rip off last .
 938                         fileRoot = fileRoot.substr(0, fileRoot.length()-1);
 939                         fileRoot = m->getRootName(fileRoot);
 940                 }
 941
 942                 string outFlowFileName = outputDir + fileRoot + "flow";
 943                 if (trim) {
 944                         outFastaFileName = outputDir + fileRoot + "fasta";
 945                         outQualFileName = outputDir + fileRoot + "qual";
 946                 }else{
 947                         outFastaFileName = outputDir + fileRoot + "raw.fasta";
 948                         outQualFileName = outputDir + fileRoot + "raw.qual";
 949                 }
 950
 951                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 952                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 953                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
 954
 955                 //read common header
 956                 string commonHeader = m->getline(inSFF);
 957                 string magicNumber = m->getline(inSFF);
 958                 string version = m->getline(inSFF);
 959                 string indexOffset = m->getline(inSFF);
 960                 string indexLength = m->getline(inSFF);
 961                 int numReads = parseHeaderLineToInt(inSFF);
 962                 string headerLength = m->getline(inSFF);
 963                 string keyLength = m->getline(inSFF);
 964                 int numFlows = parseHeaderLineToInt(inSFF);
 965                 string flowgramCode = m->getline(inSFF);
 966                 string flowChars = m->getline(inSFF);
 967                 string keySequence = m->getline(inSFF);
 968                 m->gobble(inSFF);
 969
 970                 string seqName;
 971
 972                 if (flow)       {       outFlow << numFlows << endl;    }
 973
 974                 for(int i=0;i<numReads;i++){
 975
 976                         //sanity check
 977                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
 978
 979                         Header header;
 980
 981                         //parse read header
 982                         inSFF >> seqName;
 983                         seqName = seqName.substr(1);
 984                         m->gobble(inSFF);
 985                         header.name = seqName;
 986
 987                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
 988                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
 989                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
 990                         m->gobble(inSFF);
 991
 992                         string runName = parseHeaderLineToString(inSFF);
 993                         string analysisName = parseHeaderLineToString(inSFF);
 994                         string fullPath = parseHeaderLineToString(inSFF);
 995                         m->gobble(inSFF);
 996
 997                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
 998                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
 999                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
1000                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
1001                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
1002                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
1003                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
1004                         m->gobble(inSFF);
1005
1006                         seqRead read;
1007
1008                         //parse read
1009                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
1010                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
1011
1012                         //adjust for print
1013                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
1014                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
1015                         read.flowIndex = flowIndicesAdjusted;
1016
1017                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
1018                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
1019                         m->gobble(inSFF);
1020
1021                         //if you have provided an accosfile and this seq is not in it, then dont print
1022                         bool print = true;
1023                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
1024
1025                         //print
1026                         if (print) {
1027                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
1028                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
1029                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
1030                         }
1031
1032                         //report progress
1033                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
1034
1035                         if (m->control_pressed) {  break;  }
1036                 }
1037
1038                 //report progress
1039                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1040
1041                 inSFF.close();
1042
1043                 if (fasta)      {  outFasta.close();    }
1044                 if (qual)       {  outQual.close();             }
1045                 if (flow)       {  outFlow.close();             }
1046
1047                 return 0;
1048         }
1049         catch(exception& e) {
1050                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1051                 exit(1);
1052         }
1053 }
1054 //**********************************************************************************************************************
1055
1056 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1057         try {
1058                 int number;
1059
1060                 while (!file.eof())     {
1061
1062                         char c = file.get();
1063                         if (c == ':'){
1064                                 file >> number;
1065                                 break;
1066                         }
1067
1068                 }
1069                 m->gobble(file);
1070                 return number;
1071         }
1072         catch(exception& e) {
1073                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1074                 exit(1);
1075         }
1076
1077 }
1078
1079 //**********************************************************************************************************************
1080
1081 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1082         try {
1083                 string text;
1084
1085                 while (!file.eof())     {
1086                         char c = file.get();
1087
1088                         if (c == ':'){
1089                                 //m->gobble(file);
1090                                 //text = m->getline(file);
1091                                 file >> text;
1092                                 break;
1093                         }
1094                 }
1095                 m->gobble(file);
1096
1097                 return text;
1098         }
1099         catch(exception& e) {
1100                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1101                 exit(1);
1102         }
1103 }
1104
1105 //**********************************************************************************************************************
1106
1107 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1108         try {
1109                 vector<unsigned short> floatVector(length);
1110
1111                 while (!file.eof())     {
1112                         char c = file.get();
1113                         if (c == ':'){
1114                                 float temp;
1115                                 for(int i=0;i<length;i++){
1116                                         file >> temp;
1117                                         floatVector[i] = temp * 100;
1118                                 }
1119                                 break;
1120                         }
1121                 }
1122                 m->gobble(file);
1123                 return floatVector;
1124         }
1125         catch(exception& e) {
1126                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1127                 exit(1);
1128         }
1129 }
1130
1131 //**********************************************************************************************************************
1132
1133 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1134         try {
1135                 vector<unsigned int> intVector(length);
1136
1137                 while (!file.eof())     {
1138                         char c = file.get();
1139                         if (c == ':'){
1140                                 for(int i=0;i<length;i++){
1141                                         file >> intVector[i];
1142                                 }
1143                                 break;
1144                         }
1145                 }
1146                 m->gobble(file);
1147                 return intVector;
1148         }
1149         catch(exception& e) {
1150                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1151                 exit(1);
1152         }
1153 }
1154
1155 //**********************************************************************************************************************
1156
1157
1158
1159