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             filenames[s] = m->getFullPathName(filenames[s]);
 310                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 311
 312                         string accnos = "";
 313                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 314
 315                         int numReads = extractSffInfo(filenames[s], accnos);
 316
 317                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 318                 }
 319
 320                 if (sfftxtFilename != "") {  parseSffTxt(); }
 321
 322                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 323
 324                 //set fasta file as new current fastafile
 325                 string current = "";
 326                 itTypes = outputTypes.find("fasta");
 327                 if (itTypes != outputTypes.end()) {
 328                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 329                 }
 330
 331                 itTypes = outputTypes.find("qfile");
 332                 if (itTypes != outputTypes.end()) {
 333                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 334                 }
 335
 336                 itTypes = outputTypes.find("flow");
 337                 if (itTypes != outputTypes.end()) {
 338                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
 339                 }
 340
 341                 //report output filenames
 342                 m->mothurOutEndLine();
 343                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 344                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 345                 m->mothurOutEndLine();
 346
 347                 return 0;
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "SffInfoCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354 //**********************************************************************************************************************
 355 int SffInfoCommand::extractSffInfo(string input, string accnos){
 356         try {
 357
 358                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 359
 360                 if (accnos != "")       {  readAccnosFile(accnos);  }
 361                 else                            {       seqNames.clear();               }
 362
 363                 ofstream outSfftxt, outFasta, outQual, outFlow;
 364                 string outFastaFileName, outQualFileName;
 365         string rootName = outputDir + m->getRootName(m->getSimpleName(input));
 366         if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
 367
 368                 string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 369                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 370                 if (trim) {
 371                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 372                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 373                 }else{
 374                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 375                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 376                 }
 377
 378                 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); }
 379                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 380                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
 381                 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);  }
 382
 383                 ifstream in;
 384                 in.open(input.c_str(), ios::binary);
 385
 386                 CommonHeader header;
 387                 readCommonHeader(in, header);
 388
 389                 int count = 0;
 390                 mycount = 0;
 391
 392                 //check magic number and version
 393                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 394                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 395
 396                 //print common header
 397                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 398                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 399
 400                 //read through the sff file
 401                 while (!in.eof()) {
 402
 403                         bool print = true;
 404
 405                         //read header
 406                         Header readheader;
 407                         readHeader(in, readheader);
 408
 409                         //read data
 410                         seqRead read;
 411                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 412             bool okay = sanityCheck(readheader, read);
 413             if (!okay) { break; }
 414
 415                         //if you have provided an accosfile and this seq is not in it, then dont print
 416                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 417
 418                         //print
 419                         if (print) {
 420                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 421                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 422                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 423                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 424                         }
 425
 426                         count++;
 427                         mycount++;
 428
 429                         //report progress
 430                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 431
 432                         if (m->control_pressed) { count = 0; break;   }
 433
 434                         if (count >= header.numReads) { break; }
 435                 }
 436
 437                 //report progress
 438                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 439
 440                 in.close();
 441
 442                 if (sfftxt) {  outSfftxt.close();       }
 443                 if (fasta)      {  outFasta.close();    }
 444                 if (qual)       {  outQual.close();             }
 445                 if (flow)       {  outFlow.close();             }
 446
 447                 return count;
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 451                 exit(1);
 452         }
 453 }
 454 //**********************************************************************************************************************
 455 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 456         try {
 457
 458                 if (!in.eof()) {
 459
 460                         //read magic number
 461                         char buffer[4];
 462                         in.read(buffer, 4);
 463                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 464
 465                         //read version
 466                         char buffer9[4];
 467                         in.read(buffer9, 4);
 468                         header.version = "";
 469                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 470
 471                         //read offset
 472                         char buffer2 [8];
 473                         in.read(buffer2, 8);
 474                         header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 475
 476                         //read index length
 477                         char buffer3 [4];
 478                         in.read(buffer3, 4);
 479                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 480
 481                         //read num reads
 482                         char buffer4 [4];
 483                         in.read(buffer4, 4);
 484                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 485
 486                         //read header length
 487                         char buffer5 [2];
 488                         in.read(buffer5, 2);
 489                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 490
 491                         //read key length
 492                         char buffer6 [2];
 493                         in.read(buffer6, 2);
 494                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 495
 496                         //read number of flow reads
 497                         char buffer7 [2];
 498                         in.read(buffer7, 2);
 499                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 500
 501                         //read format code
 502                         char buffer8 [1];
 503                         in.read(buffer8, 1);
 504                         header.flogramFormatCode = (int)(buffer8[0]);
 505
 506                         //read flow chars
 507                         char* tempBuffer = new char[header.numFlowsPerRead];
 508                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 509                         header.flowChars = tempBuffer;
 510                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 511                         delete[] tempBuffer;
 512
 513                         //read key
 514                         char* tempBuffer2 = new char[header.keyLength];
 515                         in.read(&(*tempBuffer2), header.keyLength);
 516                         header.keySequence = tempBuffer2;
 517                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 518                         delete[] tempBuffer2;
 519
 520                         /* Pad to 8 chars */
 521                         unsigned long long spotInFile = in.tellg();
 522                         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 523                         in.seekg(spot);
 524
 525                 }else{
 526                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 527                 }
 528
 529                 return 0;
 530         }
 531         catch(exception& e) {
 532                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 533                 exit(1);
 534         }
 535 }
 536 //**********************************************************************************************************************
 537 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 538         try {
 539
 540                 if (!in.eof()) {
 541
 542                         //read header length
 543                         char buffer [2];
 544                         in.read(buffer, 2);
 545                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 546
 547                         //read name length
 548                         char buffer2 [2];
 549                         in.read(buffer2, 2);
 550                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 551
 552                         //read num bases
 553                         char buffer3 [4];
 554                         in.read(buffer3, 4);
 555                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 556
 557                         //read clip qual left
 558                         char buffer4 [2];
 559                         in.read(buffer4, 2);
 560                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 561                         header.clipQualLeft = 5;
 562
 563                         //read clip qual right
 564                         char buffer5 [2];
 565                         in.read(buffer5, 2);
 566                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 567
 568                         //read clipAdapterLeft
 569                         char buffer6 [2];
 570                         in.read(buffer6, 2);
 571                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 572
 573                         //read clipAdapterRight
 574                         char buffer7 [2];
 575                         in.read(buffer7, 2);
 576                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 577
 578                         //read name
 579                         char* tempBuffer = new char[header.nameLength];
 580                         in.read(&(*tempBuffer), header.nameLength);
 581                         header.name = tempBuffer;
 582                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 583                         delete[] tempBuffer;
 584
 585                         //extract info from name
 586                         decodeName(header.timestamp, header.region, header.xy, header.name);
 587
 588                         /* Pad to 8 chars */
 589                         unsigned long long spotInFile = in.tellg();
 590                         unsigned long long spot = (spotInFile + 7)& ~7;
 591                         in.seekg(spot);
 592
 593                 }else{
 594                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 595                 }
 596
 597                 return 0;
 598         }
 599         catch(exception& e) {
 600                 m->errorOut(e, "SffInfoCommand", "readHeader");
 601                 exit(1);
 602         }
 603 }
 604 //**********************************************************************************************************************
 605 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 606         try {
 607
 608                 if (!in.eof()) {
 609
 610                         //read flowgram
 611                         read.flowgram.resize(numFlowReads);
 612                         for (int i = 0; i < numFlowReads; i++) {
 613                                 char buffer [2];
 614                                 in.read(buffer, 2);
 615                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 616                         }
 617
 618                         //read flowIndex
 619                         read.flowIndex.resize(numBases);
 620                         for (int i = 0; i < numBases; i++) {
 621                                 char temp[1];
 622                                 in.read(temp, 1);
 623                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 624                         }
 625
 626                         //read bases
 627                         char* tempBuffer = new char[numBases];
 628                         in.read(&(*tempBuffer), numBases);
 629                         read.bases = tempBuffer;
 630                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 631                         delete[] tempBuffer;
 632
 633                         //read qual scores
 634                         read.qualScores.resize(numBases);
 635                         for (int i = 0; i < numBases; i++) {
 636                                 char temp[1];
 637                                 in.read(temp, 1);
 638                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 639                         }
 640
 641                         /* Pad to 8 chars */
 642                         unsigned long long spotInFile = in.tellg();
 643                         unsigned long long spot = (spotInFile + 7)& ~7;
 644                         in.seekg(spot);
 645
 646                 }else{
 647                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 648                 }
 649
 650                 return 0;
 651         }
 652         catch(exception& e) {
 653                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 654                 exit(1);
 655         }
 656 }
 657 //**********************************************************************************************************************
 658 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 659         try {
 660
 661                 if (name.length() >= 6) {
 662                         string time = name.substr(0, 6);
 663                         unsigned int timeNum = m->fromBase36(time);
 664
 665                         int q1 = timeNum / 60;
 666                         int sec = timeNum - 60 * q1;
 667                         int q2 = q1 / 60;
 668                         int minute = q1 - 60 * q2;
 669                         int q3 = q2 / 24;
 670                         int hr = q2 - 24 * q3;
 671                         int q4 = q3 / 32;
 672                         int day = q3 - 32 * q4;
 673                         int q5 = q4 / 13;
 674                         int mon = q4 - 13 * q5;
 675                         int year = 2000 + q5;
 676
 677                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
 678                 }
 679
 680                 if (name.length() >= 9) {
 681                         region = name.substr(7, 2);
 682
 683                         string xyNum = name.substr(9);
 684                         unsigned int myXy = m->fromBase36(xyNum);
 685                         int x = myXy >> 12;
 686                         int y = myXy & 4095;
 687
 688                         xy = toString(x) + "_" + toString(y);
 689                 }
 690
 691                 return 0;
 692         }
 693         catch(exception& e) {
 694                 m->errorOut(e, "SffInfoCommand", "decodeName");
 695                 exit(1);
 696         }
 697 }
 698 //**********************************************************************************************************************
 699 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 700         try {
 701
 702                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 703                 out << "Version: " << header.version << endl;
 704                 out << "Index Offset: " << header.indexOffset << endl;
 705                 out << "Index Length: " << header.indexLength << endl;
 706                 out << "Number of Reads: " << header.numReads << endl;
 707                 out << "Header Length: " << header.headerLength << endl;
 708                 out << "Key Length: " << header.keyLength << endl;
 709                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 710                 out << "Format Code: " << header.flogramFormatCode << endl;
 711                 out << "Flow Chars: " << header.flowChars << endl;
 712                 out << "Key Sequence: " << header.keySequence << endl << endl;
 713
 714                 return 0;
 715         }
 716         catch(exception& e) {
 717                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 718                 exit(1);
 719         }
 720 }
 721 //**********************************************************************************************************************
 722 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 723         try {
 724
 725                 out << ">" << header.name << endl;
 726                 out << "Run Prefix: " << header.timestamp << endl;
 727                 out << "Region #:  " << header.region << endl;
 728                 out << "XY Location: " << header.xy << endl << endl;
 729
 730                 out << "Run Name:  " << endl;
 731                 out << "Analysis Name:  " << endl;
 732                 out << "Full Path: " << endl << endl;
 733
 734                 out << "Read Header Len: " << header.headerLength << endl;
 735                 out << "Name Length: " << header.nameLength << endl;
 736                 out << "# of Bases: " << header.numBases << endl;
 737                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 738                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 739                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 740                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 741
 742                 return 0;
 743         }
 744         catch(exception& e) {
 745                 m->errorOut(e, "SffInfoCommand", "printHeader");
 746                 exit(1);
 747         }
 748 }
 749 //**********************************************************************************************************************
 750 bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
 751         try {
 752         bool okay = true;
 753         string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
 754
 755         if (header.clipQualLeft > read.bases.length()) {
 756             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
 757         }
 758         if (header.clipQualRight > read.bases.length()) {
 759             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
 760         }
 761         if (header.clipQualLeft > read.qualScores.size()) {
 762             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
 763         }
 764         if (header.clipQualRight > read.qualScores.size()) {
 765             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
 766         }
 767
 768         if (okay == false) {
 769             m->mothurOut(message); m->mothurOutEndLine();
 770         }
 771
 772                 return okay;
 773         }
 774         catch(exception& e) {
 775                 m->errorOut(e, "SffInfoCommand", "sanityCheck");
 776                 exit(1);
 777         }
 778 }
 779 //**********************************************************************************************************************
 780 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 781         try {
 782                 out << "Flowgram: ";
 783                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 784
 785                 out << endl <<  "Flow Indexes: ";
 786                 int sum = 0;
 787                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 788
 789                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 790                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 791                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 792                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 793                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 794
 795                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 796                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 797
 798
 799                 out << endl << endl;
 800
 801                 return 0;
 802         }
 803         catch(exception& e) {
 804                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 805                 exit(1);
 806         }
 807 }
 808 //**********************************************************************************************************************
 809 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 810         try {
 811                 string seq = read.bases;
 812
 813         if (trim) {
 814                         if(header.clipQualRight < header.clipQualLeft){
 815                                 seq = "NNNN";
 816                         }
 817                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 818                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 819                         }
 820                         else {
 821                                 seq = seq.substr(header.clipQualLeft-1);
 822                         }
 823                 }else{
 824                         //if you wanted the sfftxt then you already converted the bases to the right case
 825                         if (!sfftxt) {
 826                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 827                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 828                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 829                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 830                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 831                         }
 832                 }
 833
 834                 out << ">" << header.name  << " xy=" << header.xy << endl;
 835                 out << seq << endl;
 836
 837                 return 0;
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 841                 exit(1);
 842         }
 843 }
 844
 845 //**********************************************************************************************************************
 846 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 847         try {
 848
 849                 if (trim) {
 850                         if(header.clipQualRight < header.clipQualLeft){
 851                                 out << ">" << header.name << " xy=" << header.xy << endl;
 852                                 out << "0\t0\t0\t0";
 853                         }
 854                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 855                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 856                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 857                         }
 858                         else{
 859                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 860                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 861                         }
 862                 }else{
 863                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
 864                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 865                 }
 866
 867                 out << endl;
 868
 869                 return 0;
 870         }
 871         catch(exception& e) {
 872                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 873                 exit(1);
 874         }
 875 }
 876
 877 //**********************************************************************************************************************
 878 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 879         try {
 880                 if(header.clipQualRight > header.clipQualLeft){
 881
 882                         int rightIndex = 0;
 883                         for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
 884
 885                         out << header.name << ' ' << rightIndex;
 886                         for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
 887                         out << endl;
 888                 }
 889
 890
 891                 return 0;
 892         }
 893         catch(exception& e) {
 894                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 895                 exit(1);
 896         }
 897 }
 898 //**********************************************************************************************************************
 899 int SffInfoCommand::readAccnosFile(string filename) {
 900         try {
 901                 //remove old names
 902                 seqNames.clear();
 903
 904                 ifstream in;
 905                 m->openInputFile(filename, in);
 906                 string name;
 907
 908                 while(!in.eof()){
 909                         in >> name; m->gobble(in);
 910
 911                         seqNames.insert(name);
 912
 913                         if (m->control_pressed) { seqNames.clear(); break; }
 914                 }
 915                 in.close();
 916
 917                 return 0;
 918         }
 919         catch(exception& e) {
 920                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 921                 exit(1);
 922         }
 923 }
 924 //**********************************************************************************************************************
 925 int SffInfoCommand::parseSffTxt() {
 926         try {
 927
 928                 ifstream inSFF;
 929                 m->openInputFile(sfftxtFilename, inSFF);
 930
 931                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
 932
 933                 //output file names
 934                 ofstream outFasta, outQual, outFlow;
 935                 string outFastaFileName, outQualFileName;
 936                 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
 937                 if (fileRoot.length() > 0) {
 938                         //rip off last .
 939                         fileRoot = fileRoot.substr(0, fileRoot.length()-1);
 940                         fileRoot = m->getRootName(fileRoot);
 941                 }
 942
 943                 string outFlowFileName = outputDir + fileRoot + "flow";
 944                 if (trim) {
 945                         outFastaFileName = outputDir + fileRoot + "fasta";
 946                         outQualFileName = outputDir + fileRoot + "qual";
 947                 }else{
 948                         outFastaFileName = outputDir + fileRoot + "raw.fasta";
 949                         outQualFileName = outputDir + fileRoot + "raw.qual";
 950                 }
 951
 952                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 953                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 954                 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);  }
 955
 956                 //read common header
 957                 string commonHeader = m->getline(inSFF);
 958                 string magicNumber = m->getline(inSFF);
 959                 string version = m->getline(inSFF);
 960                 string indexOffset = m->getline(inSFF);
 961                 string indexLength = m->getline(inSFF);
 962                 int numReads = parseHeaderLineToInt(inSFF);
 963                 string headerLength = m->getline(inSFF);
 964                 string keyLength = m->getline(inSFF);
 965                 int numFlows = parseHeaderLineToInt(inSFF);
 966                 string flowgramCode = m->getline(inSFF);
 967                 string flowChars = m->getline(inSFF);
 968                 string keySequence = m->getline(inSFF);
 969                 m->gobble(inSFF);
 970
 971                 string seqName;
 972
 973                 if (flow)       {       outFlow << numFlows << endl;    }
 974
 975                 for(int i=0;i<numReads;i++){
 976
 977                         //sanity check
 978                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
 979
 980                         Header header;
 981
 982                         //parse read header
 983                         inSFF >> seqName;
 984                         seqName = seqName.substr(1);
 985                         m->gobble(inSFF);
 986                         header.name = seqName;
 987
 988                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
 989                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
 990                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
 991                         m->gobble(inSFF);
 992
 993                         string runName = parseHeaderLineToString(inSFF);
 994                         string analysisName = parseHeaderLineToString(inSFF);
 995                         string fullPath = parseHeaderLineToString(inSFF);
 996                         m->gobble(inSFF);
 997
 998                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
 999                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
1000                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
1001                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
1002                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
1003                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
1004                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
1005                         m->gobble(inSFF);
1006
1007                         seqRead read;
1008
1009                         //parse read
1010                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
1011                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
1012
1013                         //adjust for print
1014                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
1015                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
1016                         read.flowIndex = flowIndicesAdjusted;
1017
1018                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
1019                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
1020                         m->gobble(inSFF);
1021
1022                         //if you have provided an accosfile and this seq is not in it, then dont print
1023                         bool print = true;
1024                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
1025
1026                         //print
1027                         if (print) {
1028                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
1029                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
1030                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
1031                         }
1032
1033                         //report progress
1034                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
1035
1036                         if (m->control_pressed) {  break;  }
1037                 }
1038
1039                 //report progress
1040                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1041
1042                 inSFF.close();
1043
1044                 if (fasta)      {  outFasta.close();    }
1045                 if (qual)       {  outQual.close();             }
1046                 if (flow)       {  outFlow.close();             }
1047
1048                 return 0;
1049         }
1050         catch(exception& e) {
1051                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1052                 exit(1);
1053         }
1054 }
1055 //**********************************************************************************************************************
1056
1057 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1058         try {
1059                 int number;
1060
1061                 while (!file.eof())     {
1062
1063                         char c = file.get();
1064                         if (c == ':'){
1065                                 file >> number;
1066                                 break;
1067                         }
1068
1069                 }
1070                 m->gobble(file);
1071                 return number;
1072         }
1073         catch(exception& e) {
1074                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1075                 exit(1);
1076         }
1077
1078 }
1079
1080 //**********************************************************************************************************************
1081
1082 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1083         try {
1084                 string text;
1085
1086                 while (!file.eof())     {
1087                         char c = file.get();
1088
1089                         if (c == ':'){
1090                                 //m->gobble(file);
1091                                 //text = m->getline(file);
1092                                 file >> text;
1093                                 break;
1094                         }
1095                 }
1096                 m->gobble(file);
1097
1098                 return text;
1099         }
1100         catch(exception& e) {
1101                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1102                 exit(1);
1103         }
1104 }
1105
1106 //**********************************************************************************************************************
1107
1108 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1109         try {
1110                 vector<unsigned short> floatVector(length);
1111
1112                 while (!file.eof())     {
1113                         char c = file.get();
1114                         if (c == ':'){
1115                                 float temp;
1116                                 for(int i=0;i<length;i++){
1117                                         file >> temp;
1118                                         floatVector[i] = temp * 100;
1119                                 }
1120                                 break;
1121                         }
1122                 }
1123                 m->gobble(file);
1124                 return floatVector;
1125         }
1126         catch(exception& e) {
1127                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1128                 exit(1);
1129         }
1130 }
1131
1132 //**********************************************************************************************************************
1133
1134 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1135         try {
1136                 vector<unsigned int> intVector(length);
1137
1138                 while (!file.eof())     {
1139                         char c = file.get();
1140                         if (c == ':'){
1141                                 for(int i=0;i<length;i++){
1142                                         file >> intVector[i];
1143                                 }
1144                                 break;
1145                         }
1146                 }
1147                 m->gobble(file);
1148                 return intVector;
1149         }
1150         catch(exception& e) {
1151                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1152                 exit(1);
1153         }
1154 }
1155
1156 //**********************************************************************************************************************
1157
1158
1159
1160