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 sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 365                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 366                 if (trim) {
 367                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 368                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 369                 }else{
 370                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 371                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 372                 }
 373
 374                 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); }
 375                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 376                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
 377                 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);  }
 378
 379                 ifstream in;
 380                 in.open(input.c_str(), ios::binary);
 381
 382                 CommonHeader header;
 383                 readCommonHeader(in, header);
 384
 385                 int count = 0;
 386                 mycount = 0;
 387
 388                 //check magic number and version
 389                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 390                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 391
 392                 //print common header
 393                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 394                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 395
 396                 //read through the sff file
 397                 while (!in.eof()) {
 398
 399                         bool print = true;
 400
 401                         //read header
 402                         Header readheader;
 403                         readHeader(in, readheader);
 404
 405                         //read data
 406                         seqRead read;
 407                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 408             bool okay = sanityCheck(readheader, read);
 409             if (!okay) { break; }
 410
 411                         //if you have provided an accosfile and this seq is not in it, then dont print
 412                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 413
 414                         //print
 415                         if (print) {
 416                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 417                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 418                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 419                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 420                         }
 421
 422                         count++;
 423                         mycount++;
 424
 425                         //report progress
 426                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 427
 428                         if (m->control_pressed) { count = 0; break;   }
 429
 430                         if (count >= header.numReads) { break; }
 431                 }
 432
 433                 //report progress
 434                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 435
 436                 in.close();
 437
 438                 if (sfftxt) {  outSfftxt.close();       }
 439                 if (fasta)      {  outFasta.close();    }
 440                 if (qual)       {  outQual.close();             }
 441                 if (flow)       {  outFlow.close();             }
 442
 443                 return count;
 444         }
 445         catch(exception& e) {
 446                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 447                 exit(1);
 448         }
 449 }
 450 //**********************************************************************************************************************
 451 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 452         try {
 453
 454                 if (!in.eof()) {
 455
 456                         //read magic number
 457                         char buffer[4];
 458                         in.read(buffer, 4);
 459                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 460
 461                         //read version
 462                         char buffer9[4];
 463                         in.read(buffer9, 4);
 464                         header.version = "";
 465                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 466
 467                         //read offset
 468                         char buffer2 [8];
 469                         in.read(buffer2, 8);
 470                         header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 471
 472                         //read index length
 473                         char buffer3 [4];
 474                         in.read(buffer3, 4);
 475                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 476
 477                         //read num reads
 478                         char buffer4 [4];
 479                         in.read(buffer4, 4);
 480                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 481
 482                         //read header length
 483                         char buffer5 [2];
 484                         in.read(buffer5, 2);
 485                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 486
 487                         //read key length
 488                         char buffer6 [2];
 489                         in.read(buffer6, 2);
 490                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 491
 492                         //read number of flow reads
 493                         char buffer7 [2];
 494                         in.read(buffer7, 2);
 495                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 496
 497                         //read format code
 498                         char buffer8 [1];
 499                         in.read(buffer8, 1);
 500                         header.flogramFormatCode = (int)(buffer8[0]);
 501
 502                         //read flow chars
 503                         char* tempBuffer = new char[header.numFlowsPerRead];
 504                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 505                         header.flowChars = tempBuffer;
 506                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 507                         delete[] tempBuffer;
 508
 509                         //read key
 510                         char* tempBuffer2 = new char[header.keyLength];
 511                         in.read(&(*tempBuffer2), header.keyLength);
 512                         header.keySequence = tempBuffer2;
 513                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 514                         delete[] tempBuffer2;
 515
 516                         /* Pad to 8 chars */
 517                         unsigned long long spotInFile = in.tellg();
 518                         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 519                         in.seekg(spot);
 520
 521                 }else{
 522                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 523                 }
 524
 525                 return 0;
 526         }
 527         catch(exception& e) {
 528                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 529                 exit(1);
 530         }
 531 }
 532 //**********************************************************************************************************************
 533 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 534         try {
 535
 536                 if (!in.eof()) {
 537
 538                         //read header length
 539                         char buffer [2];
 540                         in.read(buffer, 2);
 541                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 542
 543                         //read name length
 544                         char buffer2 [2];
 545                         in.read(buffer2, 2);
 546                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 547
 548                         //read num bases
 549                         char buffer3 [4];
 550                         in.read(buffer3, 4);
 551                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 552
 553                         //read clip qual left
 554                         char buffer4 [2];
 555                         in.read(buffer4, 2);
 556                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 557                         header.clipQualLeft = 5;
 558
 559                         //read clip qual right
 560                         char buffer5 [2];
 561                         in.read(buffer5, 2);
 562                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 563
 564                         //read clipAdapterLeft
 565                         char buffer6 [2];
 566                         in.read(buffer6, 2);
 567                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 568
 569                         //read clipAdapterRight
 570                         char buffer7 [2];
 571                         in.read(buffer7, 2);
 572                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 573
 574                         //read name
 575                         char* tempBuffer = new char[header.nameLength];
 576                         in.read(&(*tempBuffer), header.nameLength);
 577                         header.name = tempBuffer;
 578                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 579                         delete[] tempBuffer;
 580
 581                         //extract info from name
 582                         decodeName(header.timestamp, header.region, header.xy, header.name);
 583
 584                         /* Pad to 8 chars */
 585                         unsigned long long spotInFile = in.tellg();
 586                         unsigned long long spot = (spotInFile + 7)& ~7;
 587                         in.seekg(spot);
 588
 589                 }else{
 590                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 591                 }
 592
 593                 return 0;
 594         }
 595         catch(exception& e) {
 596                 m->errorOut(e, "SffInfoCommand", "readHeader");
 597                 exit(1);
 598         }
 599 }
 600 //**********************************************************************************************************************
 601 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 602         try {
 603
 604                 if (!in.eof()) {
 605
 606                         //read flowgram
 607                         read.flowgram.resize(numFlowReads);
 608                         for (int i = 0; i < numFlowReads; i++) {
 609                                 char buffer [2];
 610                                 in.read(buffer, 2);
 611                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 612                         }
 613
 614                         //read flowIndex
 615                         read.flowIndex.resize(numBases);
 616                         for (int i = 0; i < numBases; i++) {
 617                                 char temp[1];
 618                                 in.read(temp, 1);
 619                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 620                         }
 621
 622                         //read bases
 623                         char* tempBuffer = new char[numBases];
 624                         in.read(&(*tempBuffer), numBases);
 625                         read.bases = tempBuffer;
 626                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 627                         delete[] tempBuffer;
 628
 629                         //read qual scores
 630                         read.qualScores.resize(numBases);
 631                         for (int i = 0; i < numBases; i++) {
 632                                 char temp[1];
 633                                 in.read(temp, 1);
 634                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 635                         }
 636
 637                         /* Pad to 8 chars */
 638                         unsigned long long spotInFile = in.tellg();
 639                         unsigned long long spot = (spotInFile + 7)& ~7;
 640                         in.seekg(spot);
 641
 642                 }else{
 643                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 644                 }
 645
 646                 return 0;
 647         }
 648         catch(exception& e) {
 649                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 650                 exit(1);
 651         }
 652 }
 653 //**********************************************************************************************************************
 654 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 655         try {
 656
 657                 if (name.length() >= 6) {
 658                         string time = name.substr(0, 6);
 659                         unsigned int timeNum = m->fromBase36(time);
 660
 661                         int q1 = timeNum / 60;
 662                         int sec = timeNum - 60 * q1;
 663                         int q2 = q1 / 60;
 664                         int minute = q1 - 60 * q2;
 665                         int q3 = q2 / 24;
 666                         int hr = q2 - 24 * q3;
 667                         int q4 = q3 / 32;
 668                         int day = q3 - 32 * q4;
 669                         int q5 = q4 / 13;
 670                         int mon = q4 - 13 * q5;
 671                         int year = 2000 + q5;
 672
 673                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
 674                 }
 675
 676                 if (name.length() >= 9) {
 677                         region = name.substr(7, 2);
 678
 679                         string xyNum = name.substr(9);
 680                         unsigned int myXy = m->fromBase36(xyNum);
 681                         int x = myXy >> 12;
 682                         int y = myXy & 4095;
 683
 684                         xy = toString(x) + "_" + toString(y);
 685                 }
 686
 687                 return 0;
 688         }
 689         catch(exception& e) {
 690                 m->errorOut(e, "SffInfoCommand", "decodeName");
 691                 exit(1);
 692         }
 693 }
 694 //**********************************************************************************************************************
 695 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 696         try {
 697
 698                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 699                 out << "Version: " << header.version << endl;
 700                 out << "Index Offset: " << header.indexOffset << endl;
 701                 out << "Index Length: " << header.indexLength << endl;
 702                 out << "Number of Reads: " << header.numReads << endl;
 703                 out << "Header Length: " << header.headerLength << endl;
 704                 out << "Key Length: " << header.keyLength << endl;
 705                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 706                 out << "Format Code: " << header.flogramFormatCode << endl;
 707                 out << "Flow Chars: " << header.flowChars << endl;
 708                 out << "Key Sequence: " << header.keySequence << endl << endl;
 709
 710                 return 0;
 711         }
 712         catch(exception& e) {
 713                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 714                 exit(1);
 715         }
 716 }
 717 //**********************************************************************************************************************
 718 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 719         try {
 720
 721                 out << ">" << header.name << endl;
 722                 out << "Run Prefix: " << header.timestamp << endl;
 723                 out << "Region #:  " << header.region << endl;
 724                 out << "XY Location: " << header.xy << endl << endl;
 725
 726                 out << "Run Name:  " << endl;
 727                 out << "Analysis Name:  " << endl;
 728                 out << "Full Path: " << endl << endl;
 729
 730                 out << "Read Header Len: " << header.headerLength << endl;
 731                 out << "Name Length: " << header.nameLength << endl;
 732                 out << "# of Bases: " << header.numBases << endl;
 733                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 734                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 735                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 736                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 737
 738                 return 0;
 739         }
 740         catch(exception& e) {
 741                 m->errorOut(e, "SffInfoCommand", "printHeader");
 742                 exit(1);
 743         }
 744 }
 745 //**********************************************************************************************************************
 746 bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
 747         try {
 748         bool okay = true;
 749         string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
 750
 751         if (header.clipQualLeft > read.bases.length()) {
 752             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
 753         }
 754         if (header.clipQualRight > read.bases.length()) {
 755             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
 756         }
 757         if (header.clipQualLeft > read.qualScores.size()) {
 758             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
 759         }
 760         if (header.clipQualRight > read.qualScores.size()) {
 761             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
 762         }
 763
 764         if (okay == false) {
 765             m->mothurOut(message); m->mothurOutEndLine();
 766         }
 767
 768                 return okay;
 769         }
 770         catch(exception& e) {
 771                 m->errorOut(e, "SffInfoCommand", "sanityCheck");
 772                 exit(1);
 773         }
 774 }
 775 //**********************************************************************************************************************
 776 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 777         try {
 778                 out << "Flowgram: ";
 779                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 780
 781                 out << endl <<  "Flow Indexes: ";
 782                 int sum = 0;
 783                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 784
 785                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 786                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 787                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 788                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 789                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 790
 791                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 792                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 793
 794
 795                 out << endl << endl;
 796
 797                 return 0;
 798         }
 799         catch(exception& e) {
 800                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 801                 exit(1);
 802         }
 803 }
 804 //**********************************************************************************************************************
 805 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 806         try {
 807                 string seq = read.bases;
 808
 809         if (trim) {
 810                         if(header.clipQualRight < header.clipQualLeft){
 811                                 seq = "NNNN";
 812                         }
 813                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 814                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 815                         }
 816                         else {
 817                                 seq = seq.substr(header.clipQualLeft-1);
 818                         }
 819                 }else{
 820                         //if you wanted the sfftxt then you already converted the bases to the right case
 821                         if (!sfftxt) {
 822                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 823                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 824                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 825                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 826                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 827                         }
 828                 }
 829
 830                 out << ">" << header.name  << " xy=" << header.xy << endl;
 831                 out << seq << endl;
 832
 833                 return 0;
 834         }
 835         catch(exception& e) {
 836                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 837                 exit(1);
 838         }
 839 }
 840
 841 //**********************************************************************************************************************
 842 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 843         try {
 844
 845                 if (trim) {
 846                         if(header.clipQualRight < header.clipQualLeft){
 847                                 out << ">" << header.name << " xy=" << header.xy << endl;
 848                                 out << "0\t0\t0\t0";
 849                         }
 850                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 851                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 852                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 853                         }
 854                         else{
 855                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 856                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 857                         }
 858                 }else{
 859                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
 860                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 861                 }
 862
 863                 out << endl;
 864
 865                 return 0;
 866         }
 867         catch(exception& e) {
 868                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 869                 exit(1);
 870         }
 871 }
 872
 873 //**********************************************************************************************************************
 874 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 875         try {
 876                 if(header.clipQualRight > header.clipQualLeft){
 877
 878                         int rightIndex = 0;
 879                         for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
 880
 881                         out << header.name << ' ' << rightIndex;
 882                         for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
 883                         out << endl;
 884                 }
 885
 886
 887                 return 0;
 888         }
 889         catch(exception& e) {
 890                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 891                 exit(1);
 892         }
 893 }
 894 //**********************************************************************************************************************
 895 int SffInfoCommand::readAccnosFile(string filename) {
 896         try {
 897                 //remove old names
 898                 seqNames.clear();
 899
 900                 ifstream in;
 901                 m->openInputFile(filename, in);
 902                 string name;
 903
 904                 while(!in.eof()){
 905                         in >> name; m->gobble(in);
 906
 907                         seqNames.insert(name);
 908
 909                         if (m->control_pressed) { seqNames.clear(); break; }
 910                 }
 911                 in.close();
 912
 913                 return 0;
 914         }
 915         catch(exception& e) {
 916                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 917                 exit(1);
 918         }
 919 }
 920 //**********************************************************************************************************************
 921 int SffInfoCommand::parseSffTxt() {
 922         try {
 923
 924                 ifstream inSFF;
 925                 m->openInputFile(sfftxtFilename, inSFF);
 926
 927                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
 928
 929                 //output file names
 930                 ofstream outFasta, outQual, outFlow;
 931                 string outFastaFileName, outQualFileName;
 932                 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
 933                 if (fileRoot.length() > 0) {
 934                         //rip off last .
 935                         fileRoot = fileRoot.substr(0, fileRoot.length()-1);
 936                         fileRoot = m->getRootName(fileRoot);
 937                 }
 938
 939                 string outFlowFileName = outputDir + fileRoot + "flow";
 940                 if (trim) {
 941                         outFastaFileName = outputDir + fileRoot + "fasta";
 942                         outQualFileName = outputDir + fileRoot + "qual";
 943                 }else{
 944                         outFastaFileName = outputDir + fileRoot + "raw.fasta";
 945                         outQualFileName = outputDir + fileRoot + "raw.qual";
 946                 }
 947
 948                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 949                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 950                 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);  }
 951
 952                 //read common header
 953                 string commonHeader = m->getline(inSFF);
 954                 string magicNumber = m->getline(inSFF);
 955                 string version = m->getline(inSFF);
 956                 string indexOffset = m->getline(inSFF);
 957                 string indexLength = m->getline(inSFF);
 958                 int numReads = parseHeaderLineToInt(inSFF);
 959                 string headerLength = m->getline(inSFF);
 960                 string keyLength = m->getline(inSFF);
 961                 int numFlows = parseHeaderLineToInt(inSFF);
 962                 string flowgramCode = m->getline(inSFF);
 963                 string flowChars = m->getline(inSFF);
 964                 string keySequence = m->getline(inSFF);
 965                 m->gobble(inSFF);
 966
 967                 string seqName;
 968
 969                 if (flow)       {       outFlow << numFlows << endl;    }
 970
 971                 for(int i=0;i<numReads;i++){
 972
 973                         //sanity check
 974                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
 975
 976                         Header header;
 977
 978                         //parse read header
 979                         inSFF >> seqName;
 980                         seqName = seqName.substr(1);
 981                         m->gobble(inSFF);
 982                         header.name = seqName;
 983
 984                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
 985                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
 986                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
 987                         m->gobble(inSFF);
 988
 989                         string runName = parseHeaderLineToString(inSFF);
 990                         string analysisName = parseHeaderLineToString(inSFF);
 991                         string fullPath = parseHeaderLineToString(inSFF);
 992                         m->gobble(inSFF);
 993
 994                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
 995                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
 996                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
 997                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
 998                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
 999                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
1000                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
1001                         m->gobble(inSFF);
1002
1003                         seqRead read;
1004
1005                         //parse read
1006                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
1007                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
1008
1009                         //adjust for print
1010                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
1011                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
1012                         read.flowIndex = flowIndicesAdjusted;
1013
1014                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
1015                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
1016                         m->gobble(inSFF);
1017
1018                         //if you have provided an accosfile and this seq is not in it, then dont print
1019                         bool print = true;
1020                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
1021
1022                         //print
1023                         if (print) {
1024                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
1025                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
1026                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
1027                         }
1028
1029                         //report progress
1030                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
1031
1032                         if (m->control_pressed) {  break;  }
1033                 }
1034
1035                 //report progress
1036                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1037
1038                 inSFF.close();
1039
1040                 if (fasta)      {  outFasta.close();    }
1041                 if (qual)       {  outQual.close();             }
1042                 if (flow)       {  outFlow.close();             }
1043
1044                 return 0;
1045         }
1046         catch(exception& e) {
1047                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1048                 exit(1);
1049         }
1050 }
1051 //**********************************************************************************************************************
1052
1053 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1054         try {
1055                 int number;
1056
1057                 while (!file.eof())     {
1058
1059                         char c = file.get();
1060                         if (c == ':'){
1061                                 file >> number;
1062                                 break;
1063                         }
1064
1065                 }
1066                 m->gobble(file);
1067                 return number;
1068         }
1069         catch(exception& e) {
1070                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1071                 exit(1);
1072         }
1073
1074 }
1075
1076 //**********************************************************************************************************************
1077
1078 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1079         try {
1080                 string text;
1081
1082                 while (!file.eof())     {
1083                         char c = file.get();
1084
1085                         if (c == ':'){
1086                                 //m->gobble(file);
1087                                 //text = m->getline(file);
1088                                 file >> text;
1089                                 break;
1090                         }
1091                 }
1092                 m->gobble(file);
1093
1094                 return text;
1095         }
1096         catch(exception& e) {
1097                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1098                 exit(1);
1099         }
1100 }
1101
1102 //**********************************************************************************************************************
1103
1104 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1105         try {
1106                 vector<unsigned short> floatVector(length);
1107
1108                 while (!file.eof())     {
1109                         char c = file.get();
1110                         if (c == ':'){
1111                                 float temp;
1112                                 for(int i=0;i<length;i++){
1113                                         file >> temp;
1114                                         floatVector[i] = temp * 100;
1115                                 }
1116                                 break;
1117                         }
1118                 }
1119                 m->gobble(file);
1120                 return floatVector;
1121         }
1122         catch(exception& e) {
1123                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1124                 exit(1);
1125         }
1126 }
1127
1128 //**********************************************************************************************************************
1129
1130 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1131         try {
1132                 vector<unsigned int> intVector(length);
1133
1134                 while (!file.eof())     {
1135                         char c = file.get();
1136                         if (c == ':'){
1137                                 for(int i=0;i<length;i++){
1138                                         file >> intVector[i];
1139                                 }
1140                                 break;
1141                         }
1142                 }
1143                 m->gobble(file);
1144                 return intVector;
1145         }
1146         catch(exception& e) {
1147                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1148                 exit(1);
1149         }
1150 }
1151
1152 //**********************************************************************************************************************
1153
1154
1155
1156