SequenceReaderStringBase Class Reference

#include <SequenceReaderString.h>

Inheritance diagram for SequenceReaderStringBase:

[legend]Collaboration diagram for SequenceReaderStringBase:

[legend]List of all members.

Public Member Functions
	SequenceReaderStringBase (const string &sequenceString, SequenceEncoder *pEncoder, ostream &monitoringStream=cerr)
	SequenceReaderStringBase (const SequenceReaderStringBase &rhs)
virtual	~SequenceReaderStringBase ()
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)
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)
SequenceNumber	computeNumSequencesInFile (void)
Private Member Functions
SequenceReaderStringBase &	operator= (const SequenceReaderStringBase &)
Private Attributes
const string	sequenceString_
SequenceEncoder *	pEncoder_

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Detailed Description

Definition at line 51 of file SequenceReaderString.h.

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Constructor & Destructor Documentation

SequenceReaderStringBase::SequenceReaderStringBase	(	const string &	sequenceString,
		SequenceEncoder *	pEncoder,
		ostream &	monitoringStream = cerr
	)			[inline]

Definition at line 64 of file SequenceReaderString.h.

References SequenceReader::monitoringStream_.

Referenced by clone().

                                     :
  sequenceString_( sequenceString ), 
  pEncoder_( pEncoder ),
  SequenceReader( monitoringStream )
{
  monitoringStream_ << "constructing SequenceReaderStringBase" << endl;
} // constructor

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SequenceReaderStringBase::SequenceReaderStringBase

(

const SequenceReaderStringBase &

rhs

)

[inline]

Definition at line 80 of file SequenceReaderString.h.

References SequenceReader::monitoringStream_.

                                                                :
sequenceString_( rhs.sequenceString_ ), 
pEncoder_( rhs.pEncoder_->clone() ),
SequenceReader( rhs.monitoringStream_ )
{
  monitoringStream_ << "copy constructing SequenceReaderStringBase" << endl;
} // copy constructor

virtual SequenceReaderStringBase::~SequenceReaderStringBase

(

)

[inline, virtual]

Definition at line 94 of file SequenceReaderString.h.

References SequenceReader::monitoringStream_, and pEncoder_.

{
  monitoringStream_ << "destructing SequenceReaderStringBase" << endl;
  delete pEncoder_;
} // destructor

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Member Function Documentation

virtual SequenceReader* SequenceReaderStringBase::clone

(

void

)

[inline, virtual]

Implements SequenceReader.

Definition at line 103 of file SequenceReaderString.h.

References SequenceReaderStringBase().

  { return new SequenceReaderStringBase( *this ); }

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virtual void SequenceReaderStringBase::changeMode

(

SequenceReaderMode *

pMode

)

[inline, virtual]

Implements SequenceReader.

Definition at line 114 of file SequenceReaderString.h.

References SequenceEncoder::changeMode(), and pEncoder_.

Referenced by main().

{
  pEncoder_->changeMode( pMode );
  //  pEncoder_->changeMode( pMode );
}

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void SequenceReaderStringBase::rewind

(

void

)

[inline, virtual]

Implements SequenceReader.

Definition at line 132 of file SequenceReaderString.h.

References SequenceReader::lastSequenceNumber_.

Referenced by main().

  { lastSequenceNumber_ = 0; } // ~rewind

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virtual bool SequenceReaderStringBase::findSequence

(

SequenceNumber

seqNum

)

[inline, virtual]

Implements SequenceReader.

Definition at line 141 of file SequenceReaderString.h.

{
  return (seqNum == 1);
} 

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

Implements SequenceReader.

Definition at line 51 of file SequenceReaderString.cpp.

References WordSequence::getNumBasesInLast().

Referenced by getSequence(), and main().

{

      if (lastSequenceNumber_ != 0) 
      {
        monitoringStream_ 
          << "String already read - call rewind before trying to reread" 
          << endl;
        return -1;
      } // ~if

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

      pEncoder_->encode
      ( sequenceString_ );

      pEncoder_->unlinkSeq();
    // 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.


    lastSequenceNumber_ = 1;

    return nextSeq.getNumBasesInLast();

} // ~getNextSequence

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

Implements SequenceReader.

Definition at line 163 of file SequenceReaderString.h.

References getNextSequence().

{
  // only one sequence in a string, so just ignore sequenceNumber
  return getNextSequence( nextSeq, wordLength );
} // ~getSequence

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void SequenceReaderStringBase::getLastSequenceName

(

string &

seqName

)

const [inline, virtual]

Implements SequenceReader.

Definition at line 173 of file SequenceReaderString.h.

{
  seqName = "UnnamedSequence";
} // ~SequenceReaderStringBase::getLastSequenceName

virtual int SequenceReaderStringBase::getBitsPerSymbol

(

void

)

const [inline, virtual]

Implements SequenceReader.

Definition at line 182 of file SequenceReaderString.h.

References SequenceEncoder::getBitsPerSymbol(), and pEncoder_.

Referenced by main().

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

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virtual SourceDataType SequenceReaderStringBase::getSourceDataType

(

void

)

const [inline, virtual]

Implements SequenceReader.

Definition at line 191 of file SequenceReaderString.h.

References SequenceEncoder::getSourceDataType(), and pEncoder_.

{
  return pEncoder_->getSourceDataType();
}

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

Implements SequenceReader.

Definition at line 204 of file SequenceReaderString.h.

{
  os << "UnnamedSequence" << endl;
  return true;
} // ~SequenceReaderStringBase::printName

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

Implements SequenceReader.

Definition at line 216 of file SequenceReaderString.h.

{
  return true;
} // ~SequenceReaderStringBase::printName

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

Implements SequenceReader.

Definition at line 227 of file SequenceReaderString.h.

References sequenceString_.

{
  os << sequenceString_;
  return true;
} // ~SequenceReaderStringBase::printName

SequenceNumber SequenceReaderStringBase::computeNumSequencesInFile

(

void

)

[inline, virtual]

Implements SequenceReader.

Definition at line 238 of file SequenceReaderString.h.

{ return 1; } 

SequenceReaderStringBase& SequenceReaderStringBase::operator=

(

const SequenceReaderStringBase &

)

[private]

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Member Data Documentation

const string SequenceReaderStringBase::sequenceString_ [private]

Definition at line 255 of file SequenceReaderString.h.

Referenced by printSource().

SequenceEncoder* SequenceReaderStringBase::pEncoder_ [private]

Definition at line 257 of file SequenceReaderString.h.

Referenced by changeMode(), getBitsPerSymbol(), getSourceDataType(), and ~SequenceReaderStringBase().

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

• SequenceReader/SequenceReaderString.h
• SequenceReader/SequenceReaderString.cpp

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