SequenceReaderFastq Class Reference

#include <SequenceReaderFastq.h>

Inheritance diagram for SequenceReaderFastq:

[legend]Collaboration diagram for SequenceReaderFastq:

[legend]List of all members.

Public Member Functions
	SequenceReaderFastq (const char *fileName, SequenceEncoder *pEncoder, ostream &monitoringStream=cerr)
	SequenceReaderFastq (const char *fileName, ostream &monitoringStream=cerr)
	SequenceReaderFastq (const SequenceReaderFastq &rhs)
	~SequenceReaderFastq ()
virtual SequenceReader *	clone (void)
virtual int	getNextSequence (WordSequence &nextSeq, int wordLength)
Private Member Functions
SequenceReaderFastq &	operator= (const SequenceReaderFastq &)

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Detailed Description

Definition at line 50 of file SequenceReaderFastq.h.

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Constructor & Destructor Documentation

SequenceReaderFastq::SequenceReaderFastq	(	const char *	fileName,
		SequenceEncoder *	pEncoder,
		ostream &	monitoringStream = cerr
	)

Definition at line 47 of file SequenceReaderFastq.cpp.

Referenced by clone().

                               : 
SequenceReaderFile
( fileName, '@', '+', pEncoder->clone(), monitoringStream )
{
  monitoringStream_ << "constructing SequenceReaderFastq" << endl;
} // ~constructor

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SequenceReaderFastq::SequenceReaderFastq	(	const char *	fileName,
		ostream &	monitoringStream = cerr
	)

Definition at line 57 of file SequenceReaderFastq.cpp.

                                                    : 
SequenceReaderFile
( fileName, '@', '+', new SequenceEncoderDNA(12), monitoringStream )
{
  monitoringStream_ << "constructing SequenceReaderFastq" << endl;
} // ~constructor

SequenceReaderFastq::SequenceReaderFastq

(

const SequenceReaderFastq &

rhs

)

Definition at line 64 of file SequenceReaderFastq.cpp.

References SequenceReader::monitoringStream_.

                                                                       :
SequenceReaderFile((SequenceReaderFile)rhs)
{
  monitoringStream_ << "copy constructing SequenceReaderFastq" << endl;
}

SequenceReaderFastq::~SequenceReaderFastq

(

)

Definition at line 73 of file SequenceReaderFastq.cpp.

References SequenceReader::monitoringStream_.

{
  monitoringStream_ << "destructing SequenceReaderFastq" << endl;
} // ~destructor

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Member Function Documentation

virtual SequenceReader* SequenceReaderFastq::clone

(

void

)

[inline, virtual]

Reimplemented from SequenceReaderFile.

Definition at line 85 of file SequenceReaderFastq.h.

References SequenceReaderFastq().

  { 
    return new SequenceReaderFastq( *this ); 
  }

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

Reimplemented from SequenceReaderFile.

Definition at line 94 of file SequenceReaderFastq.cpp.

References DEBUG_L2, SequenceReaderFile::getNextSequence(), SequenceReaderFile::inputBuffer_, SequenceReaderFile::inputBufferSize_, SequenceReaderFile::pInputFileStream_, and SequenceReaderFile::seqStartChar_.

Referenced by main().

  {
    DEBUG_L2( "SequenceReaderFastq::getNextSequence" );
    if (SequenceReaderFile::getNextSequence( nextSeq, wordLength ) == -1 )
    {
      return -1;
    } // ~if

    // Now spool past the quality info 
    
    //    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;
    while (1==1)
    {
      firstOfLine = pInputFileStream_->peek();
      if (    ( firstOfLine == EOF ) 
           || ( (char)firstOfLine == seqStartChar_)) 
      {      
        return nextSeq.getNumBasesInLast();
      } // ~if 
      pInputFileStream_->getline( inputBuffer_, inputBufferSize_, '\n' );

    } // ~while
    return nextSeq.getNumBasesInLast(); 

  } // ~SequenceReaderFastq::getNextSequence

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SequenceReaderFastq& SequenceReaderFastq::operator=

(

const SequenceReaderFastq &

)

[private]

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

• SequenceReader/SequenceReaderFastq.h
• SequenceReader/SequenceReaderFastq.cpp

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