SequenceReaderFile Class Reference

#include <SequenceReaderFasta.h>

Inheritance diagram for SequenceReaderFile:

[legend]Collaboration diagram for SequenceReaderFile:

[legend]List of all members.

Public Member Functions
	SequenceReaderFile (const char *fileName, char seqStartChar, char seqStopChar, SequenceEncoder *pEncoder, ostream &monitoringStream=cerr)
	SequenceReaderFile (istream &inputStream, char seqStartChar, char seqStopChar, SequenceEncoder *pEncoder, ostream &monitoringStream=cerr)
	SequenceReaderFile (const SequenceReaderFile &rhs)
virtual	~SequenceReaderFile ()
virtual SequenceReader *	clone (void)
virtual void	changeMode (SequenceReaderMode *pMode)
void	rewind (void)
virtual bool	findSequence (SequenceNumber seqNum)
virtual int	getNextSequence (WordSequence &nextSeq, int wordLength)
virtual int	getSequence (WordSequence &nextSeq, SequenceNumber sequenceNumber, int wordLength)
virtual void	getLastSequenceName (string &seqName) const
virtual int	getBitsPerSymbol (void) const
virtual SourceDataType	getSourceDataType (void) const
virtual bool	printName (ostream &os, SequenceNumber seqNum)
virtual bool	printSideInfo (ostream &os, SequenceNumber seqNum)
virtual bool	printSource (ostream &os, SequenceNumber seqNum)
virtual void	extractSource (char **pSource, SequenceNumber seqNum, SequenceOffset seqStart, SequenceOffset seqEnd)
virtual void	saveIndexImp (ostream &fileFile, ostream &indexFile, int &fileNumber)
virtual SequenceReaderState *	saveState (void) const
virtual void	restoreState (SequenceReaderState *pState)
Protected Types
enum	Constants { sideInfoBufferSize_ = 20000, inputBufferSize_ = 20000 }
Protected Member Functions
virtual SequenceNumber	computeNumSequencesInFile (void)
Protected Attributes
char	inputBuffer_ [inputBufferSize_]
string	sideInfoBuffer_
char	seqStartChar_
char	seqStopChar_
istream *	pInputFileStream_
string	fileName_
SequenceEncoder *	pEncoder_
vector< std::streampos >	seqPositions_
Private Member Functions
SequenceReaderFile &	operator= (const SequenceReaderFile &)

---

Detailed Description

Definition at line 67 of file SequenceReaderFasta.h.

---

Member Enumeration Documentation

enum SequenceReaderFile::Constants [protected]

Enumerator:

sideInfoBufferSize_
inputBufferSize_

Definition at line 253 of file SequenceReaderFasta.h.

{ sideInfoBufferSize_ = 20000, inputBufferSize_ = 20000 };

---

Constructor & Destructor Documentation

SequenceReaderFile::SequenceReaderFile	(	const char *	fileName,
		char	seqStartChar,
		char	seqStopChar,
		SequenceEncoder *	pEncoder,
		ostream &	monitoringStream = cerr
	)

Definition at line 74 of file SequenceReaderFasta.cpp.

Referenced by clone().

    : SequenceReader( monitoringStream ),
      seqStartChar_( seqStartChar ),
      seqStopChar_( seqStopChar ),
      //      lastSourceSeqNum_( 0 ),
      pInputFileStream_( new ifstream( fileName ) ),
      fileName_( fileName ),
      pEncoder_( pEncoder )
  {

    monitoringStream_ << "constructing SequenceReaderFile" << this << endl;
    if ( pInputFileStream_->fail() )
    {
      throw SSAHAException
      (   (string)"SequenceReaderFile - unable to open input file "
        + (string)fileName );

    } // ~if
    monitoringStream_ << "SequenceReaderFile::connected to file "
                      << fileName << endl;

  } // ~constructor

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SequenceReaderFile::SequenceReaderFile	(	istream &	inputStream,
		char	seqStartChar,
		char	seqStopChar,
		SequenceEncoder *	pEncoder,
		ostream &	monitoringStream = cerr
	)

Definition at line 102 of file SequenceReaderFasta.cpp.

    : SequenceReader( monitoringStream ),
      seqStartChar_( seqStartChar ),
      seqStopChar_( seqStopChar ),
      //   lastSourceSeqNum_( 0 ),
      pInputFileStream_( &inputStream ),
      //      fileName_( fileName ),
      pEncoder_( pEncoder )
  {

    monitoringStream_ << "constructing SequenceReaderFile" << this << endl;
    if ( pInputFileStream_->fail() )
    {
      throw SSAHAException
      ( "SequenceReaderFile - unable to open input stream " );

    } // ~if
    monitoringStream_ << "SequenceReaderFile::connected to input file stream."
                      << endl;

  } // ~constructor

SequenceReaderFile::SequenceReaderFile

(

const SequenceReaderFile &

rhs

)

Definition at line 132 of file SequenceReaderFasta.cpp.

References fileName_, SequenceReader::monitoringStream_, and pInputFileStream_.

  : SequenceReader( rhs.monitoringStream_ ),
    seqStartChar_( rhs.seqStartChar_ ),
    seqStopChar_( rhs.seqStopChar_ ),
    pInputFileStream_( new ifstream( rhs.fileName_.c_str() ) ),
    fileName_( rhs.fileName_.c_str() ),
    seqPositions_( rhs.seqPositions_ ),
    //   lastSourceSeqNum_(0),
    pEncoder_( rhs.pEncoder_->clone() )
  {
    monitoringStream_ << "copy constructing SequenceReaderFile" << this 
                      << endl;
    if (pInputFileStream_->fail())
    {
       throw SSAHAException
             (   (string)"SequenceReaderFile - unable to open input file " 
               + (string)fileName_ );

    } // ~if

    monitoringStream_ << "SequenceReaderFile:SequenceReader: "
                      << "connected to file " << fileName_ << endl;

  } // ~copy constructor

SequenceReaderFile::~SequenceReaderFile

(

)

[virtual]

Definition at line 157 of file SequenceReaderFasta.cpp.

References SequenceReader::monitoringStream_, pEncoder_, and pInputFileStream_.

  {
    monitoringStream_ << "destructing SequenceReaderFile" << this << endl;
    delete pEncoder_;
    ifstream*  pf(dynamic_cast<ifstream*>(pInputFileStream_));
    if (pf!=NULL) 
    {
        pf->close();
        delete pInputFileStream_;
    }
  } // ~destructor

---

Member Function Documentation

virtual SequenceReader* SequenceReaderFile::clone

(

void

)

[inline, virtual]

Implements SequenceReader.

Reimplemented in SequenceReaderFastq.

Definition at line 107 of file SequenceReaderFasta.h.

References SequenceReaderFile().

Referenced by main().

  { return new SequenceReaderFile( *this ); }

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void SequenceReaderFile::changeMode

(

SequenceReaderMode *

pMode

)

[virtual]

Implements SequenceReader.

Definition at line 172 of file SequenceReaderFasta.cpp.

References SequenceEncoder::changeMode(), and pEncoder_.

Referenced by main().

  {
    pEncoder_->changeMode( pMode );
  }

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void SequenceReaderFile::rewind

(

void

)

[virtual]

Implements SequenceReader.

Definition at line 183 of file SequenceReaderFasta.cpp.

References SequenceReader::lastSequenceNumber_, and pInputFileStream_.

Referenced by main().

  {
    // rewind to start of file
    pInputFileStream_->clear();
    pInputFileStream_->seekg( 0 );
    lastSequenceNumber_ = 0;
  } // ~SequenceReaderFile::rewind( void )

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bool SequenceReaderFile::findSequence

(

SequenceNumber

seqNum

)

[virtual]

Implements SequenceReader.

Definition at line 197 of file SequenceReaderFasta.cpp.

References SequenceReader::allSequencesRead_, inputBuffer_, inputBufferSize_, SequenceReader::lastSequenceNumber_, SequenceReader::monitoringStream_, SequenceReader::numSequencesInFile_, pInputFileStream_, seqPositions_, and seqStartChar_.

Referenced by extractSource(), getSequence(), main(), printName(), printSideInfo(), and printSource().

  {
    
    //    cout << "SRF::findSeq start" << pInputFileStream_->tellg() << endl; 
    pInputFileStream_->clear();
    if ( seqNum ==0 )
    { 
      monitoringStream_ 
        << "SRF::findSeq: Requested sequence number (0) is not valid (must start at 1)." 
        << endl;
      return false;
    } // ~if
    else if ( seqNum <= seqPositions_.size() )
    {
      pInputFileStream_->seekg(seqPositions_[ seqNum - 1 ],ios::beg);
    } // ~if
    else if ( allSequencesRead_ == false )
    { // need to find more sequences in the file

      if ( seqPositions_.size() != 0 )
      {
        pInputFileStream_->seekg
        (seqPositions_.back(), ios::beg);
        pInputFileStream_->getline
        ( inputBuffer_ , inputBufferSize_, '\n' );
      } // ~if
   
      while(1)
      {
        //        pInputFileStream_->getline
        //      ( inputBuffer_ , inputBufferSize_, '\n' );
              //     getline( *pInputFileStream_, inputBuffer_, '\n' );
        if (pInputFileStream_->peek() == EOF) 
        {
          numSequencesInFile_ = seqPositions_.size();
          //      cout << "SRF::findSeq: asr = true" << endl;
          allSequencesRead_ = true;
          monitoringStream_ 
          << "SRF::findSeq(EOF): Requested sequence number (" << seqNum 
          << ")\nis outside range of sequences in file (1 to " 
          << numSequencesInFile_ << ")." << endl;
          //          throw NumberOutOfRange();
          // cout << "SRF::findSeq end" << pInputFileStream_->tellg() << endl; 
          return false;
        } // ~if
        else if (pInputFileStream_->peek() == seqStartChar_) 
        {
          seqPositions_.push_back(pInputFileStream_->tellg());
          if( seqPositions_.size() == seqNum ) break;
        } // ~else if
        pInputFileStream_->getline
        ( inputBuffer_ , inputBufferSize_, '\n' );
      } // ~while
      //      while ( seqPositions_.size() != seqNum );

    lastSequenceNumber_ = seqNum - 1;
    
    } // ~else if
    else
    { 
      monitoringStream_ 
        << "SRF::findSeq(asr): Requested sequence number (" << seqNum 
        << ")\nis outside range of sequences in file (1 to " 
        << numSequencesInFile_ << ")." << endl;
      //      throw NumberOutOfRange();

      //      if (seqNum == numSequencesInFile_+1)
      //     {
      //        cout << "SRF::findSeq - flicking to end" << endl; 
      //        pInputFileStream_->seekg( 0, ios::end );
      //  }
      //  cout << "SRF::findSeq end" << pInputFileStream_->tellg() << endl; 
      return false;
    } // ~else

    lastSequenceNumber_ = seqNum - 1;
    //  cout << "SRF::findSeq end" << pInputFileStream_->tellg() << endl; 
    return true;
  } // ~SequenceReaderFile::findSequence( SequenceNumber seqNum )

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int SequenceReaderFile::getNextSequence	(	WordSequence &	nextSeq,
		int	wordLength
	)			[virtual]

Implements SequenceReader.

Reimplemented in SequenceReaderFastq.

Definition at line 284 of file SequenceReaderFasta.cpp.

References SequenceReader::allSequencesRead_, DEBUG_L2, SequenceEncoder::encode(), WordSequence::getNumBasesInLast(), inputBuffer_, inputBufferSize_, SequenceReader::lastSequenceNumber_, SequenceEncoder::linkSeq(), SequenceReader::monitoringStream_, SequenceReader::numSequencesInFile_, pEncoder_, pInputFileStream_, seqPositions_, seqStartChar_, seqStopChar_, SequenceEncoder::setWordLength(), sideInfoBuffer_, and SequenceEncoder::unlinkSeq().

Referenced by SequenceReaderFastq::getNextSequence(), getSequence(), and main().

  {
    DEBUG_L2( "SequenceReaderFile::getNextSequence" );
    //   cout << "SRF::getNext start" << pInputFileStream_->tellg() << endl; 
    //    char firstOfLine;
    // `Interesting' standard library quirk: even though we are exclusively
    // reading chars firstOfLine must be an int (cos EOF is an int not a char)
    int firstOfLine;
    pInputFileStream_->clear();
    firstOfLine = pInputFileStream_->peek();
    if ( firstOfLine == EOF )
    {
      monitoringStream_ << "End of file has been reached." << endl;
      if ( allSequencesRead_ == false )
      {
        monitoringStream_ << "Setting numSequencesInFile to " 
                          << lastSequenceNumber_ << "." << endl;
        numSequencesInFile_ = lastSequenceNumber_;
        //  cout << "SRF::getNextSeq: asr = true" << endl;
        //  cout << pInputFileStream_->tellg() << endl;
          assert(!pInputFileStream_->fail());
          
        allSequencesRead_ = true;
      } // ~if
      // cout << "SRF::getNext end" << pInputFileStream_->tellg() << endl; 
      return -1;
    } // ~if

    std::streampos startPos( pInputFileStream_->tellg() );     

    if ( (char)firstOfLine == seqStartChar_ )
    { // then everything until the next '\n' is side info 
      //      pInputFileStream_->getline( sideInfoBuffer_, sideInfoBufferSize_, '\n' );
      getline( *pInputFileStream_, sideInfoBuffer_, '\n' );
      DEBUG_L2( "Read " << pInputFileStream_->gcount()
                        << " bytes of side info to buffer" );
    } // ~if
    else
    {
      monitoringStream_ 
        << "Error: file not in expected format (expected \"" 
        << seqStartChar_ << "\", received \"" << (char) firstOfLine
        << "\" instead).\n";
      throw SSAHAException("Data in wrong format!");
      //      sideInfoBuffer_="No side info for sequence.";
    } // ~else

    //    int basesInSequence(0); // this accumulates to the total number of
    // bases in the sequence (may be spread across multiple lines)
    //    Word thisWord(0);

    pEncoder_->setWordLength(wordLength);
    pEncoder_->linkSeq(nextSeq);

    while (1==1)
    {

      int numChars; // this is the number of bases on a line of FASTA file
                    // info (i.e. from one '\n' to the next) 
      firstOfLine = pInputFileStream_->peek();

      if (((char)firstOfLine == seqStopChar_) || ( firstOfLine == EOF )) break;
      pInputFileStream_->getline( inputBuffer_, inputBufferSize_, '\n' );
      //          getline( *pInputFileStream_, inputBuffer_, '\n' );

      DEBUG_L2( "Read " << pInputFileStream_->gcount()
                        << " bytes of sequence data to buffer" );


          numChars = pInputFileStream_->gcount() - 1; 
          // the '-1' accounts for '\n' at end of read
          //          numChars = inputBuffer_.size();

      pEncoder_->encode( inputBuffer_, numChars );

    }; // ~while

    pEncoder_->unlinkSeq();

    //    shiftLastWord( nextSeq, basesInSequence, wordLength );

    // If the last word is not completely full (as will be the case if
    // wordLength does not divide numBases) then shift the word so the
    // valid bases occupy the most significant bits of the word.
    //    nextSeq.numBasesInLast = basesInSequence % wordLength;
    //    thisWord = ( numBasesInLast == 0 ) ? 0 
    //     : thisWord << 2 * ( wordLength - numBasesInLast - 1);
    //   nextSeq.push_back(thisWord);
    //    if ( nextSeq.numBasesInLast != 0 )  
    //    nextSeq.back() <<= 2 * ( wordLength - nextSeq.numBasesInLast - 1);

    //    DEBUG_L2(    "There were " << basesInSequence
    //        << " base pairs in this sequence." );
      
    //    DEBUG_L2(    "Last word (" << printWord( nextSeq.back(), wordLength )
    //        << ") contains " << nextSeq.numBasesInLast
    //        << " valid base pairs" );

    DEBUG_L2("Finished reading sequence " << lastSequenceNumber_ );

    lastSequenceNumber_++;

    if ( lastSequenceNumber_ > seqPositions_.size() )
    {
      seqPositions_.push_back( startPos );
    } // ~if
    //    cout << "SRF::getNext end" << pInputFileStream_->tellg() << endl; 

    return nextSeq.getNumBasesInLast(); 

  } // ~SequenceReaderFile::getNextSequence

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int SequenceReaderFile::getSequence	(	WordSequence &	nextSeq,
		SequenceNumber	sequenceNumber,
		int	wordLength
	)			[virtual]

Implements SequenceReader.

Definition at line 402 of file SequenceReaderFasta.cpp.

References DEBUG_L2, findSequence(), and getNextSequence().

Referenced by main().

  {
    DEBUG_L2( "SequenceReaderFile::getSequence" );

    if (!findSequence( sequenceNumber )) return -1;
    else return getNextSequence( nextSeq, wordLength );

  } // ~SequenceReaderFile::getSequence 

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void SequenceReaderFile::getLastSequenceName

(

string &

seqName

)

const [virtual]

Implements SequenceReader.

Definition at line 415 of file SequenceReaderFasta.cpp.

References DEBUG_L2, and sideInfoBuffer_.

Referenced by main().

  {
    DEBUG_L2( "SequenceReaderFile::getLastSequenceName" );
    string::size_type nameEnd = sideInfoBuffer_.find_first_of(' ');
    if ( nameEnd == string::npos ) nameEnd = sideInfoBuffer_.size();
    seqName = sideInfoBuffer_.substr( 1, nameEnd-1 );
    DEBUG_L2( "Last sequence name: " << seqName );
  } // ~SequenceReaderFile::getLastSequenceName

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int SequenceReaderFile::getBitsPerSymbol

(

void

)

const [virtual]

Implements SequenceReader.

Definition at line 543 of file SequenceReaderFasta.cpp.

References SequenceEncoder::getBitsPerSymbol(), and pEncoder_.

Referenced by main().

{
  return pEncoder_->getBitsPerSymbol();
} // ~SequenceReaderFile::getBitsPerSymbol ( void ) const

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SourceDataType SequenceReaderFile::getSourceDataType

(

void

)

const [virtual]

Implements SequenceReader.

Definition at line 552 of file SequenceReaderFasta.cpp.

References SequenceEncoder::getSourceDataType(), and pEncoder_.

{
  return pEncoder_->getSourceDataType();
}

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bool SequenceReaderFile::printName	(	ostream &	os,
		SequenceNumber	seqNum
	)			[virtual]

Implements SequenceReader.

Definition at line 429 of file SequenceReaderFasta.cpp.

References DEBUG_L3, findSequence(), and pInputFileStream_.

  {
    DEBUG_L3( "SequenceReaderFile::printName" );

    if (!findSequence( seqNum )) return false;


    string firstLine;

    getline(*pInputFileStream_,firstLine,'\n');

    string::size_type nameEnd = firstLine.find_first_of(' ');
    if ( nameEnd == string::npos ) nameEnd = firstLine.size();

    os << firstLine.substr( 1, nameEnd ); 

    findSequence( seqNum );

    return true;
  } // ~SequenceReaderFile::printName

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bool SequenceReaderFile::printSideInfo	(	ostream &	os,
		SequenceNumber	seqNum
	)			[virtual]

Implements SequenceReader.

Definition at line 457 of file SequenceReaderFasta.cpp.

References DEBUG_L2, findSequence(), and pInputFileStream_.

  {
    DEBUG_L2( "SequenceReaderFile::printSideInfo" );
 
    if (!findSequence( seqNum )) return false;

    string firstLine;

    getline(*pInputFileStream_,firstLine,'\n');

    string::size_type nameEnd = firstLine.find_first_of(' ');

    if ( nameEnd == string::npos ) os << "No side info for this sequence.";
    else os << firstLine.substr(firstLine.find_first_of(' ') ); 

    findSequence( seqNum );

    return true;
  } // ~SequenceReaderFile::printSideInfo

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bool SequenceReaderFile::printSource	(	ostream &	os,
		SequenceNumber	seqNum
	)			[virtual]

Implements SequenceReader.

Definition at line 483 of file SequenceReaderFasta.cpp.

References DEBUG_L2, findSequence(), inputBuffer_, inputBufferSize_, pInputFileStream_, and seqStartChar_.

  {
    DEBUG_L2( "SequenceReaderFile::getSequenceSource" );

    if (!findSequence( seqNum )) return false;

    int firstOfLine((int)'x');
    while( ( (char)firstOfLine != seqStartChar_ ) && ( firstOfLine != EOF ) )
    {
      pInputFileStream_->getline( inputBuffer_, inputBufferSize_, '\n' );
      os << inputBuffer_ << endl;
      firstOfLine = pInputFileStream_->peek();
    } // ~while

    findSequence( seqNum );

    return true;
  } // ~SequenceReaderFile::printSource

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void SequenceReaderFile::extractSource	(	char **	pSource,
		SequenceNumber	seqNum,
		SequenceOffset	seqStart,
		SequenceOffset	seqEnd
	)			[virtual]

Reimplemented from SourceReader.

Definition at line 562 of file SequenceReaderFasta.cpp.

References SourceReader::extractToCache(), findSequence(), SourceReader::lastSourceSeq_, SourceReader::lastSourceSeqNum_, pInputFileStream_, restoreState(), and saveState().

Referenced by main().

{

  if (seqNum!= lastSourceSeqNum_)
  {

    SequenceReaderState* pState(saveState());

    if (!findSequence( seqNum )) 
    {

      throw SSAHAException
        ("Could not find start of seq in SequenceReaderFile::extractSource");
    } // ~if

    //    cout << "moved to " << pInputFileStream_->tellg() << endl;

    // Check that this is a sensible place for sequence start
    //    int firstOfLine(pInputFileStream_->peek());
    //  if (((char)firstOfLine)!=seqStartChar_)
    //   {
    //   throw SSAHAException
    //  ("Did not find expected start char in SequenceReaderFile::extractSource");
    //  } // ~if    


    extractToCache( pInputFileStream_ );
    lastSourceSeqNum_=seqNum;

    // return to original position in file
    restoreState(pState);

  } // ~if

  // check for japes and tomfoolery

  if ( seqStart>seqEnd)
  {
      throw SSAHAException
        ("Requested seq start exceeds requested seq end in SequenceReaderFile::extractSource");
  } // ~if
  else if (seqEnd>lastSourceSeq_.size() )
  {
      throw SSAHAException
        ("Requested last byte exceeds end of seq in SequenceReaderFile::extractSource");
  } // ~else if

  *pSource = &lastSourceSeq_[seqStart-1];
  // copy relevant bit of sequence across (TBD this is a waste, just return ptr)
  //  vector<char>::size_type currentSize(source.size());
  //  source.resize(currentSize+seqEnd-seqStart+1);
  //  memcpy( (char*)&source[currentSize], (char*)&lastSourceSeq_[seqStart-1], seqEnd-seqStart+1);
  //  cout << "SRF::extract end" << pInputFileStream_->tellg() << endl; 

} // ~SequenceReaderFile::extractSource

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void SequenceReaderFile::saveIndexImp	(	ostream &	fileFile,
		ostream &	indexFile,
		int &	fileNumber
	)			[virtual]

Reimplemented from SourceReader.

Definition at line 624 of file SequenceReaderFasta.cpp.

References computeNumSequencesInFile(), fileName_, and seqPositions_.

{
  computeNumSequencesInFile(); // ensure have scanned to end of file
  fileFile << fileName_ << endl;
  SeqIndexInfo* pIndex = new SeqIndexInfo[seqPositions_.size()];
  for (int i(0) ; i < seqPositions_.size() ; i++)
  {
    pIndex[i].fileNum=fileNumber;
    pIndex[i].seqPos=seqPositions_[i];
  } // ~for

  indexFile.write( (const char*)pIndex, 
                   seqPositions_.size()*sizeof(SeqIndexInfo) );
  delete [] pIndex;
} // ~SequenceReaderFile::saveIndex

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virtual SequenceReaderState* SequenceReaderFile::saveState

(

void

)

const [inline, virtual]

Reimplemented from SequenceReader.

Definition at line 210 of file SequenceReaderFasta.h.

References SequenceReader::lastSequenceNumber_, and pInputFileStream_.

Referenced by extractSource().

  {
    return new SequenceReaderFileState
      ( lastSequenceNumber_, pInputFileStream_->tellg() );
  }

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virtual void SequenceReaderFile::restoreState

(

SequenceReaderState *

pState

)

[inline, virtual]

Reimplemented from SequenceReader.

Definition at line 221 of file SequenceReaderFasta.h.

References SequenceReaderFileState::filePos_, SequenceReaderState::lastSequenceNumber_, SequenceReader::lastSequenceNumber_, and pInputFileStream_.

Referenced by extractSource().

  {
    SequenceReaderFileState* p
      (dynamic_cast<SequenceReaderFileState*>(pState));
    assert(p!=NULL);
    lastSequenceNumber_ = p->lastSequenceNumber_;
    pInputFileStream_->seekg( p->filePos_, ios::beg );
    delete pState;
  }

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SequenceNumber SequenceReaderFile::computeNumSequencesInFile

(

void

)

[protected, virtual]

Implements SequenceReader.

Definition at line 508 of file SequenceReaderFasta.cpp.

References DEBUG_L2, inputBuffer_, inputBufferSize_, SequenceReader::lastSequenceNumber_, pInputFileStream_, seqPositions_, and seqStartChar_.

Referenced by saveIndexImp().

  {
    DEBUG_L2( "SequenceReaderFile::computeNumSequencesInFile" );

    SequenceNumber numSeqs = 0;

    // rewind to start of file
    pInputFileStream_->clear();
    pInputFileStream_->seekg( 0 );
    seqPositions_.clear();

    while ( pInputFileStream_->peek() != EOF )
    {
      if (pInputFileStream_->peek() == seqStartChar_) 
      {
        numSeqs++;
        seqPositions_.push_back(pInputFileStream_->tellg());
      } // ~if
              pInputFileStream_->getline
               ( inputBuffer_ , inputBufferSize_, '\n' );
              //     getline( *pInputFileStream_, inputBuffer_, '\n' );
    } // ~while

    lastSequenceNumber_ = numSeqs;

    DEBUG_L2( "Found " << numSeqs << " sequences in the file." );

    return numSeqs;

  } // ~SequenceReaderFile::computeNumSequencesInFile( void ) const

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SequenceReaderFile& SequenceReaderFile::operator=

(

const SequenceReaderFile &

)

[private]

---

Member Data Documentation

char SequenceReaderFile::inputBuffer_[inputBufferSize_] [protected]

Definition at line 254 of file SequenceReaderFasta.h.

Referenced by computeNumSequencesInFile(), findSequence(), SequenceReaderFastq::getNextSequence(), getNextSequence(), and printSource().

string SequenceReaderFile::sideInfoBuffer_ [protected]

Definition at line 257 of file SequenceReaderFasta.h.

Referenced by getLastSequenceName(), and getNextSequence().

char SequenceReaderFile::seqStartChar_ [protected]

Definition at line 258 of file SequenceReaderFasta.h.

Referenced by computeNumSequencesInFile(), findSequence(), SequenceReaderFastq::getNextSequence(), getNextSequence(), and printSource().

char SequenceReaderFile::seqStopChar_ [protected]

Definition at line 259 of file SequenceReaderFasta.h.

Referenced by getNextSequence().

istream* SequenceReaderFile::pInputFileStream_ [protected]

Definition at line 261 of file SequenceReaderFasta.h.

Referenced by computeNumSequencesInFile(), extractSource(), findSequence(), SequenceReaderFastq::getNextSequence(), getNextSequence(), printName(), printSideInfo(), printSource(), restoreState(), rewind(), saveState(), SequenceReaderFile(), and ~SequenceReaderFile().

string SequenceReaderFile::fileName_ [protected]

Definition at line 264 of file SequenceReaderFasta.h.

Referenced by saveIndexImp(), and SequenceReaderFile().

SequenceEncoder* SequenceReaderFile::pEncoder_ [protected]

Definition at line 265 of file SequenceReaderFasta.h.

Referenced by changeMode(), getBitsPerSymbol(), getNextSequence(), getSourceDataType(), and ~SequenceReaderFile().

vector<std::streampos> SequenceReaderFile::seqPositions_ [protected]

Definition at line 267 of file SequenceReaderFasta.h.

Referenced by computeNumSequencesInFile(), findSequence(), getNextSequence(), and saveIndexImp().

---

The documentation for this class was generated from the following files:

• SequenceReader/SequenceReaderFasta.h
• SequenceReader/SequenceReaderFasta.cpp

---