SequenceReaderMulti Class Reference

#include <SequenceReaderMulti.h>

Inheritance diagram for SequenceReaderMulti:

[legend]Collaboration diagram for SequenceReaderMulti:

[legend]List of all members.

Public Member Functions
	SequenceReaderMulti (ostream &monitoringStream=cerr)
	SequenceReaderMulti (const SequenceReaderMulti &rhs)
virtual	~SequenceReaderMulti ()
virtual SequenceReader *	clone (void)
void	addReader (SequenceReader &seq)
void	addReader (SequenceReader *pSeq)
virtual void	changeMode (SequenceReaderMode *pMode)
int	getNumReaders (void)
bool	findReader (SequenceNumber &seqNum)
virtual 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 Member Functions
virtual SequenceNumber	computeNumSequencesInFile (void)
Protected Attributes
vector< SeqReaderInfo >	allReaders_
vector< SeqReaderInfo >::iterator	thisReader_
SequenceNumber	currentSeqNum_
bool	isFirstSeq_
int	bitsPerSymbol_
SourceDataType	sourceDataType_
Private Member Functions
	SequenceReaderMulti (const SequenceReader &)
SequenceReaderMulti &	operator= (const SequenceReader &)

---

Detailed Description

Definition at line 98 of file SequenceReaderMulti.h.

---

Constructor & Destructor Documentation

SequenceReaderMulti::SequenceReaderMulti

(

ostream &

monitoringStream = cerr

)

Definition at line 42 of file SequenceReaderMulti.cpp.

References SequenceReader::monitoringStream_.

Referenced by clone().

  : SequenceReader( monitoringStream ), thisReader_( allReaders_.begin() ),
    isFirstSeq_(true)
{
  monitoringStream_ << "constructing SequenceReaderMulti" << endl;
}

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SequenceReaderMulti::SequenceReaderMulti

(

const SequenceReaderMulti &

rhs

)

Definition at line 56 of file SequenceReaderMulti.cpp.

References allReaders_, and SequenceReader::monitoringStream_.

  : SequenceReader( rhs.monitoringStream_ ),
    allReaders_( rhs.allReaders_ ),
    thisReader_( allReaders_.begin() ),
    isFirstSeq_( rhs.isFirstSeq_ ),
    bitsPerSymbol_( rhs.bitsPerSymbol_ ),
    sourceDataType_( rhs.sourceDataType_ )
{
  monitoringStream_ << "copy constructing SequenceReaderMulti\n";
  for ( vector<SeqReaderInfo>::const_iterator i(rhs.allReaders_.begin());
        i!=rhs.allReaders_.end(); i++)
  {
    allReaders_.push_back( SeqReaderInfo() );
    allReaders_.back().ptr_=i->ptr_->clone();
  } // ~for

} // ~constructor

SequenceReaderMulti::~SequenceReaderMulti

(

)

[virtual]

Definition at line 49 of file SequenceReaderMulti.cpp.

References allReaders_, and SequenceReader::monitoringStream_.

{
  monitoringStream_ << "destructing SequenceReaderMulti" << endl;
  for ( vector<SeqReaderInfo>::iterator i( allReaders_.begin() );
        i != allReaders_.end() ; i++ ) delete i->ptr_;
} // destructor

SequenceReaderMulti::SequenceReaderMulti

(

const SequenceReader &

)

[private]

---

Member Function Documentation

virtual SequenceReader* SequenceReaderMulti::clone

(

void

)

[inline, virtual]

Implements SequenceReader.

Definition at line 124 of file SequenceReaderMulti.h.

References SequenceReaderMulti().

  { return new SequenceReaderMulti( *this ); }

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void SequenceReaderMulti::addReader

(

SequenceReader &

seq

)

Definition at line 107 of file SequenceReaderMulti.cpp.

References allReaders_, bitsPerSymbol_, SequenceReader::clone(), SequenceReader::getBitsPerSymbol(), SequenceReader::getSourceDataType(), isFirstSeq_, sourceDataType_, and thisReader_.

Referenced by fillSequenceReaderMulti(), and main().

  {
    if (isFirstSeq_)
    {
      isFirstSeq_ = false;
      bitsPerSymbol_ = seq.getBitsPerSymbol();
      sourceDataType_ = seq.getSourceDataType();
    } // ~if
    else
    {
      assert(bitsPerSymbol_ == seq.getBitsPerSymbol());
      assert(sourceDataType_ == seq.getSourceDataType());
    } // ~else
    //    assert(1==0);
    //    allReaders_.push_back( SeqReaderInfo( seq.clone() ));
    allReaders_.push_back( SeqReaderInfo() );
    allReaders_.back().ptr_=seq.clone();
    thisReader_
      = static_cast<vector<SeqReaderInfo>::iterator>(&allReaders_.back());
  } // ~addReader( SequenceReader& seq )

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void SequenceReaderMulti::addReader

(

SequenceReader *

pSeq

)

Definition at line 133 of file SequenceReaderMulti.cpp.

References allReaders_, bitsPerSymbol_, SequenceReader::getBitsPerSymbol(), SequenceReader::getSourceDataType(), isFirstSeq_, sourceDataType_, and thisReader_.

  {
    if (isFirstSeq_)
    {
      isFirstSeq_ = false;
      bitsPerSymbol_ = pSeq->getBitsPerSymbol();
      sourceDataType_ = pSeq->getSourceDataType();
    } // ~if
    else
    {
      assert(bitsPerSymbol_ == pSeq->getBitsPerSymbol());
      assert(sourceDataType_ == pSeq->getSourceDataType());
    } // ~else

    allReaders_.push_back( SeqReaderInfo() );
    allReaders_.back().ptr_=pSeq;
    thisReader_
      = static_cast<vector<SeqReaderInfo>::iterator>(&allReaders_.back());
  } // ~addReader( SequenceReader* pSeq )

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void SequenceReaderMulti::changeMode

(

SequenceReaderMode *

pMode

)

[virtual]

Implements SequenceReader.

Definition at line 255 of file SequenceReaderMulti.cpp.

References allReaders_.

  {
    for ( vector<SeqReaderInfo>::iterator i = allReaders_.begin(); 
          i != allReaders_.end(); i++ ) 
          {
            (i->ptr_)->changeMode(pMode);
          }
  } // ~SequenceReaderMulti::changeMode( SequenceReaderMode* pMode )

int SequenceReaderMulti::getNumReaders

(

void

)

[inline]

Definition at line 152 of file SequenceReaderMulti.h.

References allReaders_.

Referenced by findSequenceReader().

  { 
    return allReaders_.size();
  }

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bool SequenceReaderMulti::findReader

(

SequenceNumber &

seqNum

)

Definition at line 223 of file SequenceReaderMulti.cpp.

References allReaders_, DEBUG_L3, SequenceReader::getNumSequencesInFile(), and thisReader_.

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

  {
    DEBUG_L3( "SequenceReaderMulti::findReader" );

    // NB calling getNumSequencesInFile also makes sure numSeqs_ has
    // been set up

    if ( seqNum > getNumSequencesInFile() )
    {
      return false;
      //      monitoringStream_ 
      //   << "findReader: Requested sequence number (" << seqNum 
      //   << ")\n is outside range of sequences in file (1 to " 
      //  << getNumSequencesInFile() << ")." << endl;
      //   throw SSAHAException("Invalid sequence number.");
    } // ~if

    for ( vector<SeqReaderInfo>::iterator i = allReaders_.begin(); 
          i != allReaders_.end(); i++ )
    {
      if ( seqNum <= i->size_ ) { thisReader_ = i; break; } // %%%%%
      seqNum -= i->size_;
    } // ~for i

    return true;
    
    // cout << allReaders_.begin().size_ << " " << seqNum << " " << i << endl;
  } // ~void SequenceReaderMulti::findReader( int& seqNum )

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void SequenceReaderMulti::rewind

(

void

)

[virtual]

Implements SequenceReader.

Definition at line 84 of file SequenceReaderMulti.cpp.

References allReaders_, SequenceReader::lastSequenceNumber_, and thisReader_.

Referenced by getSequence(), and main().

{

    for ( vector<SeqReaderInfo>::iterator i 
          = allReaders_.begin(); 
          i != allReaders_.end();
          i++ )
    {
      (i->ptr_)->rewind();       
    } // ~for i
    thisReader_ = allReaders_.begin();
    lastSequenceNumber_ = 0;
} // ~SequenceReaderMulti::rewind( void )

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bool SequenceReaderMulti::findSequence

(

SequenceNumber

seqNum

)

[virtual]

Implements SequenceReader.

Definition at line 159 of file SequenceReaderMulti.cpp.

References allReaders_, currentSeqNum_, SequenceReader::lastSequenceNumber_, and thisReader_.

Referenced by extractSource(), and main().

{

  //  SequenceNumber currentSeqNum(seqNum);
  currentSeqNum_ = seqNum;
  for ( thisReader_ = allReaders_.begin(); 
        thisReader_ != allReaders_.end(); thisReader_++ )
  {
    if (thisReader_->allSeqsRead_)
    {
      if ( currentSeqNum_ <= thisReader_->size_ )
      {
        //      assert( thisReader_->ptr_->findSequence( currentSeqNum_ ) == true );
        lastSequenceNumber_ = --seqNum; // last read = 1 behind current
        return true;    
      } // ~if
    } // ~if
    else
    {
      if ( thisReader_->ptr_->findSequence( currentSeqNum_ ) == true )
      {
        lastSequenceNumber_ = --seqNum; // last read = 1 behind current
        return true;
      }
      else
        thisReader_->size_ = thisReader_->ptr_->getNumSequencesInFile();
      //      thisReader_->ptr_->rewind();
    } // ~else
    
    
    currentSeqNum_ -= thisReader_->ptr_->getNumSequencesInFile();


  } // ~for

  return false;

    //    if (thisReader_->ptr_->findSequence( currentSeqNum )) 
    //    {
      //      if (!thisReader_->allSeqsRead_)
      //   {
      //      thisReader_->allSeqsRead_=true;
      //      thisReader_->size_ = thisReader_->ptr_->getNumSequencesInFile();
      //    } // ~if
    //      return true;
    //   }
    //    if (!thisReader_->allSeqsRead_)
    //    {
    //     thisReader_->allSeqsRead_=true;
    //    thisReader_->size_ = thisReader_->ptr_->getNumSequencesInFile();
    //    } // ~if
    //  } // ~for
  //  return false;

} // ~SequenceReaderMulti::findSequence( SequenceNumber seqNum )

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

Implements SequenceReader.

Definition at line 275 of file SequenceReaderMulti.cpp.

References allReaders_, DEBUG_L2, SequenceReader::getNumSequencesInFile(), SequenceReader::lastSequenceNumber_, SequenceReader::monitoringStream_, and thisReader_.

Referenced by main().

  {
    DEBUG_L2( "SequenceReaderMulti::getNextSequence" );

    int numInLast;

    while 
      (    ( thisReader_ 
             != allReaders_.end() )
        && ( (   numInLast
               = thisReader_->ptr_->getNextSequence( nextSeq, wordLength ) )
              == -1 )    )
    {
      if ( thisReader_->allSeqsRead_ == false )
      {
        thisReader_->size_ = (thisReader_->ptr_)->getNumSequencesInFile();
        thisReader_->allSeqsRead_ = true;
      } // ~if
      thisReader_++;
      //      if (thisReader_!=allReaders_.end()) thisReader_->ptr_->rewind();
    } // ~while

    if (thisReader_ == allReaders_.end()) 
    {
      monitoringStream_ 
      << "SequenceReaderMulti::getNextSequence - last seq has been read.\n";
      return -1;
    } // ~if

    if ( numInLast != -1 ) lastSequenceNumber_++;

    return numInLast; 

  } // ~SequenceReaderMulti::getNextSequence

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

Implements SequenceReader.

Definition at line 317 of file SequenceReaderMulti.cpp.

References DEBUG_L2, findReader(), SequenceReader::lastSequenceNumber_, rewind(), and thisReader_.

  {
    DEBUG_L2( "SequenceReaderMulti::getSequence" );

    //    findReader( sequenceNumber ); 
    if (!findReader( sequenceNumber )) return -1;

    lastSequenceNumber_ = sequenceNumber;
            (thisReader_->ptr_)->rewind();

    return (thisReader_->ptr_)->getSequence
                                  ( nextSeq, sequenceNumber, wordLength );

  } // ~SequenceReaderMulti::getSequence

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void SequenceReaderMulti::getLastSequenceName

(

string &

seqName

)

const [virtual]

Implements SequenceReader.

Definition at line 336 of file SequenceReaderMulti.cpp.

References thisReader_.

Referenced by main().

  {
    (thisReader_->ptr_)->getLastSequenceName( seqName );
  } // ~SequenceReaderMulti::getLastSequenceName( string& seqName ) const 

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int SequenceReaderMulti::getBitsPerSymbol

(

void

)

const [virtual]

Implements SequenceReader.

Definition at line 371 of file SequenceReaderMulti.cpp.

References bitsPerSymbol_, and isFirstSeq_.

Referenced by main().

{
  if (isFirstSeq_) assert(1==0);
  return bitsPerSymbol_;
  // fails if thisReader is at end 
  //  return ((thisReader_->ptr_)->getBitsPerSymbol());
} // ~SequenceReaderMulti::getBitsPerSymbol ( void ) const

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SourceDataType SequenceReaderMulti::getSourceDataType

(

void

)

const [virtual]

Implements SequenceReader.

Definition at line 383 of file SequenceReaderMulti.cpp.

References isFirstSeq_, and sourceDataType_.

{
  if (isFirstSeq_) assert(1==0);
  return sourceDataType_;
  // fails if thisReader is at end 
  //  return ((thisReader_->ptr_)->getSourceDataType());
} // ~SequenceReaderMulti::getSourceDataType ( void ) const

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

Implements SequenceReader.

Definition at line 395 of file SequenceReaderMulti.cpp.

References findReader(), SequenceReader::lastSequenceNumber_, and thisReader_.

{

  lastSequenceNumber_ = seqNum;
  //  findReader( seqNum ); 
  if (!findReader(seqNum)) return false;
  (thisReader_->ptr_)->printName( os, seqNum );
  return true;
} // ~SequenceReaderMulti::printName

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

Implements SequenceReader.

Definition at line 409 of file SequenceReaderMulti.cpp.

References findReader(), SequenceReader::lastSequenceNumber_, and thisReader_.

{

  lastSequenceNumber_ = seqNum;
  //  findReader( seqNum ); 
  if (!findReader(seqNum)) return false;
  (thisReader_->ptr_)->printSideInfo( os, seqNum );
  return true;
} // ~SequenceReaderMulti::printName

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

Implements SequenceReader.

Definition at line 424 of file SequenceReaderMulti.cpp.

References findReader(), SequenceReader::lastSequenceNumber_, and thisReader_.

{
  lastSequenceNumber_ = seqNum;
  //findReader( seqNum ); 
  if (!findReader(seqNum)) return false;
  (thisReader_->ptr_)->printSource( os, seqNum );
  return true;
} // ~SequenceReaderMulti::printName

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

Reimplemented from SourceReader.

Definition at line 437 of file SequenceReaderMulti.cpp.

References currentSeqNum_, findSequence(), SequenceReader::getNumSequencesInFile(), SequenceReader::monitoringStream_, restoreState(), saveState(), and thisReader_.

Referenced by main().

{
  //  cout << "SRM::extractSource " << seqNum << endl;
  //  SequenceNumber savedSeqNum(lastSequenceNumber_);
  //  vector<SeqReaderInfo>::iterator savedReader(thisReader_);
  //  SequenceNumber savedSeqNumPtr(thisReader_->ptr_->getLastSequenceNumber());
  //  monitoringStream_ << "srm::Extract1 " << seqNum << " " << thisReader_ << endl;

  SequenceReaderState* pState(saveState());

  if (!findSequence(seqNum))
  { 
    monitoringStream_ << "extSource: Requested sequence number (" << seqNum
                      << ") exceeds number of sequences in collection ("
                      << getNumSequencesInFile() << ")." << endl;
    throw SSAHAException
      ("Invalid sequence number in SequenceReaderMulti::extractSource");
  } // ~if   
  //  monitoringStream_ << "srm::Extract2 " << seqNum << " " << thisReader_ << endl;
  (thisReader_->ptr_)->extractSource
    ( pSource, currentSeqNum_, seqStart, seqEnd );

  //  lastSequenceNumber_ = savedSeqNum;

  //  thisReader_->ptr_->rewind();
  //  findSequence( savedSeqNum+1 );

  restoreState(pState);
  //  lastSequenceNumber_=savedSeqNum;
  //  thisReader_=savedReader;
  //  thisReader_->ptr_->findSequence(savedSeqNumPtr+1);

} // ~SequenceReaderMulti::extractSource

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

Reimplemented from SourceReader.

Definition at line 476 of file SequenceReaderMulti.cpp.

References allReaders_, and computeNumSequencesInFile().

{
  computeNumSequencesInFile();
  for ( vector<SeqReaderInfo>::iterator i 
          = allReaders_.begin(); 
          i != allReaders_.end();
          i++ )
  {
    (i->ptr_)->saveIndexImp( fileFile, indexFile, fileNumber );
    fileNumber++;
  } // ~for i

} // ~SequenceReaderMulti::saveIndexImp

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virtual SequenceReaderState* SequenceReaderMulti::saveState

(

void

)

const [inline, virtual]

Reimplemented from SequenceReader.

Definition at line 257 of file SequenceReaderMulti.h.

References allReaders_, SequenceReader::lastSequenceNumber_, and thisReader_.

Referenced by extractSource().

  {
    return new SequenceReaderMultiState
      ( lastSequenceNumber_, 
        thisReader_, 
        (thisReader_==allReaders_.end()) 
        ? NULL 
        : thisReader_->ptr_->saveState() );
  }

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virtual void SequenceReaderMulti::restoreState

(

SequenceReaderState *

pState

)

[inline, virtual]

Reimplemented from SequenceReader.

Definition at line 272 of file SequenceReaderMulti.h.

References allReaders_, SequenceReaderState::lastSequenceNumber_, SequenceReader::lastSequenceNumber_, SequenceReaderMultiState::pState_, SequenceReaderMultiState::thisReader_, and thisReader_.

Referenced by extractSource().

  {
    SequenceReaderMultiState* p
      (dynamic_cast<SequenceReaderMultiState*>(pState));
    assert(p!=NULL);
    lastSequenceNumber_ = p->lastSequenceNumber_;
    thisReader_->ptr_->rewind();
    thisReader_=p->thisReader_; 
    if (thisReader_!=allReaders_.end())
      thisReader_->ptr_->restoreState( p->pState_ ); 
    delete pState;
  }

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SequenceNumber SequenceReaderMulti::computeNumSequencesInFile

(

void

)

[protected, virtual]

Implements SequenceReader.

Definition at line 347 of file SequenceReaderMulti.cpp.

References allReaders_, SequenceReader::getNumSequencesInFile(), SequenceReader::lastSequenceNumber_, and thisReader_.

Referenced by saveIndexImp().

  {
    SequenceNumber numSeqs = 0;
    for ( vector<SeqReaderInfo>::iterator i 
          = allReaders_.begin(); 
          i != allReaders_.end();
          i++ )
    {
      if ( i->allSeqsRead_ == false )
      {
        i->size_ =  (i->ptr_)->getNumSequencesInFile();
        i->allSeqsRead_ = true;
      } // ~if
      numSeqs += i->size_;       
    } // ~for i
    thisReader_ = allReaders_.end();
    lastSequenceNumber_ = numSeqs;
    return numSeqs; 
  } // ~SequenceReaderMulti::computeNumSequencesInFile( void )

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SequenceReaderMulti& SequenceReaderMulti::operator=

(

const SequenceReader &

)

[private]

Reimplemented from SequenceReader.

---

Member Data Documentation

vector<SeqReaderInfo> SequenceReaderMulti::allReaders_ [protected]

Definition at line 309 of file SequenceReaderMulti.h.

Referenced by addReader(), changeMode(), computeNumSequencesInFile(), findReader(), findSequence(), getNextSequence(), getNumReaders(), restoreState(), rewind(), saveIndexImp(), saveState(), SequenceReaderMulti(), and ~SequenceReaderMulti().

vector<SeqReaderInfo>::iterator SequenceReaderMulti::thisReader_ [protected]

Definition at line 311 of file SequenceReaderMulti.h.

Referenced by addReader(), computeNumSequencesInFile(), extractSource(), findReader(), findSequence(), getLastSequenceName(), getNextSequence(), getSequence(), printName(), printSideInfo(), printSource(), restoreState(), rewind(), and saveState().

SequenceNumber SequenceReaderMulti::currentSeqNum_ [protected]

Definition at line 312 of file SequenceReaderMulti.h.

Referenced by extractSource(), and findSequence().

bool SequenceReaderMulti::isFirstSeq_ [protected]

Definition at line 314 of file SequenceReaderMulti.h.

Referenced by addReader(), getBitsPerSymbol(), and getSourceDataType().

int SequenceReaderMulti::bitsPerSymbol_ [protected]

Definition at line 315 of file SequenceReaderMulti.h.

Referenced by addReader(), and getBitsPerSymbol().

SourceDataType SequenceReaderMulti::sourceDataType_ [protected]

Definition at line 316 of file SequenceReaderMulti.h.

Referenced by addReader(), and getSourceDataType().

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

• SequenceReader/SequenceReaderMulti.h
• SequenceReader/SequenceReaderMulti.cpp

---