SequenceReaderFilter Class Reference

#include <SequenceReaderFilter.h>

Inheritance diagram for SequenceReaderFilter:

[legend]Collaboration diagram for SequenceReaderFilter:

[legend]List of all members.

Public Member Functions
	SequenceReaderFilter (SequenceReader *pSeq, ifstream *pFilterSource, ostream &monitoringStream=cerr)
	SequenceReaderFilter (SequenceReader *pSeq, const char *filterFileName, ostream &monitoringStream=cerr)
	SequenceReaderFilter (const SequenceReaderFilter &rhs)
	~SequenceReaderFilter ()
virtual SequenceReader *	clone (void)
void	readFilterNames (ifstream *pFilterSource)
virtual void	changeMode (SequenceReaderMode *pMode)
virtual void	rewind (void)
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
int	getNumFiltered (void) const
virtual bool	printName (ostream &os, SequenceNumber seqNum)
virtual bool	printSideInfo (ostream &os, SequenceNumber seqNum)
virtual bool	printSource (ostream &os, SequenceNumber seqNum)
virtual bool	findSequence (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
SequenceReader *	pSeq_
StringHash *	pFilterNames_
vector< SequenceNumber >	filterNums_
int	numFiltered_
Private Member Functions
SequenceReaderFilter &	operator= (const SequenceReaderFilter &)

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Detailed Description

Definition at line 127 of file SequenceReaderFilter.h.

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Constructor & Destructor Documentation

SequenceReaderFilter::SequenceReaderFilter	(	SequenceReader *	pSeq,
		ifstream *	pFilterSource,
		ostream &	monitoringStream = cerr
	)

Definition at line 49 of file SequenceReaderFilter.cpp.

Referenced by clone().

                              :
  SequenceReader( monitoringStream ),
  pSeq_(pSeq),
  pFilterNames_( new StringHash ),
  numFiltered_(0)
{
  monitoringStream_ 
    << "constructing SequenceReaderFilter" << endl;
  readFilterNames( pFilterSource );
} // ~constructor

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SequenceReaderFilter::SequenceReaderFilter	(	SequenceReader *	pSeq,
		const char *	filterFileName,
		ostream &	monitoringStream = cerr
	)

Definition at line 63 of file SequenceReaderFilter.cpp.

                              :
  SequenceReader( monitoringStream ),
  pSeq_(pSeq),
  pFilterNames_( new StringHash ),
  numFiltered_(0)
{
  monitoringStream_ 
    << "constructing SequenceReaderFilter for file " 
    << filterFileName << endl;
  readFilterNames( new ifstream( filterFileName ) );
} // ~constructor

SequenceReaderFilter::SequenceReaderFilter

(

const SequenceReaderFilter &

rhs

)

Definition at line 111 of file SequenceReaderFilter.cpp.

References SequenceReader::monitoringStream_.

                                                                           :
SequenceReader( rhs.monitoringStream_ ),
pSeq_( rhs.pSeq_->clone() )
{
  monitoringStream_ << "copy constructing SequenceReaderFilter" << endl;
  // copy set across
  monitoringStream_ << "copy constructor not implemented!!" << endl;
  assert(1==0);
} // ~destructor

SequenceReaderFilter::~SequenceReaderFilter

(

)

Definition at line 123 of file SequenceReaderFilter.cpp.

References SequenceReader::monitoringStream_, pFilterNames_, and pSeq_.

{
  monitoringStream_ << "destructing SequenceReaderFilter" << endl;
  delete pSeq_;
  delete pFilterNames_;
} // ~destructor

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Member Function Documentation

virtual SequenceReader* SequenceReaderFilter::clone

(

void

)

[inline, virtual]

Implements SequenceReader.

Definition at line 168 of file SequenceReaderFilter.h.

References SequenceReaderFilter().

  { 
    return new SequenceReaderFilter( *this ); 
  }

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void SequenceReaderFilter::readFilterNames

(

ifstream *

pFilterSource

)

Definition at line 82 of file SequenceReaderFilter.cpp.

References filterNums_, StringHash::makeBins(), SequenceReader::monitoringStream_, and pFilterNames_.

{
  if ( pFilterSource->fail() )
  {
    throw SSAHAException
      ( "SequenceReaderFile - unable to open filter file ");

  } // ~if

  //  string thisName;

  //  while (*pFilterSource>>thisName) pFilterNames_->insert(thisName);
  pFilterNames_->push_back( (string) "" );
  while (*pFilterSource>>pFilterNames_->back()) pFilterNames_->push_back( (string) "" );
  pFilterNames_->pop_back();
  pFilterNames_->makeBins();

  monitoringStream_ << "Read in " << pFilterNames_->size() 
                    << " names to filter out" << endl;
  filterNums_.push_back(0);
  pFilterSource->close();
  delete pFilterSource;
}

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virtual void SequenceReaderFilter::changeMode

(

SequenceReaderMode *

pMode

)

[inline, virtual]

Implements SequenceReader.

Definition at line 191 of file SequenceReaderFilter.h.

References SequenceReader::changeMode(), and pSeq_.

  {
    pSeq_->changeMode( pMode );
  }

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void SequenceReaderFilter::rewind

(

void

)

[virtual]

Implements SequenceReader.

Definition at line 243 of file SequenceReaderFilter.cpp.

References SequenceReader::lastSequenceNumber_, pSeq_, and SequenceReader::rewind().

Referenced by main().

{
  pSeq_->rewind();
  lastSequenceNumber_ = 0;
} // ~rewind 

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

Implements SequenceReader.

Definition at line 210 of file SequenceReaderFilter.cpp.

References filterNums_, findSequence(), SequenceReader::getSequence(), SequenceReader::lastSequenceNumber_, and pSeq_.

Referenced by main().

{
  if (!findSequence(lastSequenceNumber_+1)) 
  {
    assert(filterNums_.size()==lastSequenceNumber_+1);
    return -1;
  } // ~if
  else 
  {
    ++lastSequenceNumber_;
    return pSeq_->getSequence( nextSeq, filterNums_[lastSequenceNumber_], 
                                 wordLength );
  } // ~else
} // ~SequenceReaderFilter::getNextSequence

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

Implements SequenceReader.

Definition at line 232 of file SequenceReaderFilter.cpp.

References filterNums_, findSequence(), SequenceReader::getSequence(), SequenceReader::lastSequenceNumber_, and pSeq_.

Referenced by main().

{
  if (!findSequence(sequenceNumber)) return -1;
  assert(filterNums_.size()>=sequenceNumber+1);
  lastSequenceNumber_=sequenceNumber;
  return pSeq_->getSequence
    ( nextSeq, filterNums_[sequenceNumber], wordLength );
  
} // ~SequenceReaderFilter::getSequence

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void SequenceReaderFilter::getLastSequenceName

(

string &

seqName

)

const [virtual]

Implements SequenceReader.

Definition at line 253 of file SequenceReaderFilter.cpp.

References SequenceReader::getLastSequenceName(), and pSeq_.

Referenced by main().

{
  return pSeq_->getLastSequenceName(seqName);
} // ~SequenceReaderFilter::getLastSequenceName( string& seqName ) const

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virtual int SequenceReaderFilter::getBitsPerSymbol

(

void

)

const [inline, virtual]

Implements SequenceReader.

Definition at line 233 of file SequenceReaderFilter.h.

References SequenceReader::getBitsPerSymbol(), and pSeq_.

Referenced by main().

  {
    return pSeq_->getBitsPerSymbol();
  }

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virtual SourceDataType SequenceReaderFilter::getSourceDataType

(

void

)

const [inline, virtual]

Implements SequenceReader.

Definition at line 242 of file SequenceReaderFilter.h.

References SequenceReader::getSourceDataType(), and pSeq_.

Referenced by main().

  {
    return pSeq_->getSourceDataType();
  }

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int SequenceReaderFilter::getNumFiltered

(

void

)

const [inline]

Definition at line 252 of file SequenceReaderFilter.h.

References numFiltered_.

Referenced by main().

  {
    return numFiltered_;
  }

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

Implements SequenceReader.

Definition at line 262 of file SequenceReaderFilter.cpp.

References filterNums_, findSequence(), SequenceReader::printName(), and pSeq_.

{
  if (!findSequence(seqNum)) return false;
  assert(filterNums_.size()>=seqNum+1);
  pSeq_->printName(os, filterNums_[seqNum]);
  return true;
} // ~SequenceReaderFilter::printName( ostream& os, SequenceNumber seqNum)  

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

Implements SequenceReader.

Definition at line 275 of file SequenceReaderFilter.cpp.

References filterNums_, findSequence(), SequenceReader::printName(), and pSeq_.

{
  if (!findSequence(seqNum)) return false;
  assert(filterNums_.size()>=seqNum+1);
  pSeq_->printName(os, filterNums_[seqNum]);
  return true;
} // ~bool SequenceReaderFilter::printSideInfo

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

Implements SequenceReader.

Definition at line 288 of file SequenceReaderFilter.cpp.

References filterNums_, findSequence(), SequenceReader::printName(), and pSeq_.

{
  if (!findSequence(seqNum)) return false;
  assert(filterNums_.size()>=seqNum+1);
  pSeq_->printName(os, filterNums_[seqNum]);
  return true;
} // ~SequenceReaderFilter::printSource

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bool SequenceReaderFilter::findSequence

(

SequenceNumber

seqNum

)

[virtual]

Implements SequenceReader.

Definition at line 130 of file SequenceReaderFilter.cpp.

References SequenceReader::allSequencesRead_, filterNums_, StringHash::isPresent(), SequenceReader::monitoringStream_, numFiltered_, SequenceReader::numSequencesInFile_, pFilterNames_, SequenceReader::printName(), and pSeq_.

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

{
  if ( seqNum <= filterNums_.size()-1 ) return true; // no neeed!
  if (allSequencesRead_)
  {
    monitoringStream_ 
      << "Requested sequence number (" << seqNum 
      << ")\nis outside range of sequences in file (1 to " 
      << numSequencesInFile_ << ")." << endl;
    return false;
  } // ~if

  SequenceNumber lastInSource(filterNums_.back());
  // = (filterNums_.empty() ? 0 : filterNums_.back()); no need, never empty
  std::ostrstream buffer;
  string name;

  while (filterNums_.size()!=seqNum+1)
  {

    ++lastInSource;

    if ( pSeq_->printName( buffer, lastInSource ) == false )
    {
      if(allSequencesRead_==false)
      {
        allSequencesRead_=true;
        if (pFilterNames_!=NULL) 
        {
          monitoringStream_ 
          << "deleting filter name data, no longer needed" << endl;
          delete pFilterNames_;
          pFilterNames_=NULL;  
        } // ~if
        numSequencesInFile_ = filterNums_.size()-1;
        monitoringStream_ 
          << "Requested sequence number (" << seqNum
          << ")\nis outside range of sequences in file (1 to " 
          << numSequencesInFile_ << ")." << endl;

      } // ~if
      return false;
    } // ~catch

    name=buffer.str();
    string::size_type nameEnd=name.find_first_of('\t');
    // NB stop at tab not spc
    if (nameEnd!=string::npos) name.erase(nameEnd,name.size());

    //    if ( pFilterNames_->find(name)==pFilterNames_->end() )
    if ( !pFilterNames_->isPresent(name) )
    {
      filterNums_.push_back(lastInSource);
      //  monitoringStream_ << filterNums_.size()-1 << " " << lastInSource << endl;
    } // ~if
    else
    {
      //      monitoringStream_ << filterNums_.size()-1 << " " << lastInSource 
      //                << " Filtered: " << name << " " 
      //                << *(pFilterNames_->find(name)) << endl;
      numFiltered_++;
    } // ~else


    buffer.freeze(false); // release memory to write further stuff to buffer  
    buffer.seekp(0,ios::beg); // ensure next write is to start of buffer
  
  } // ~while

  return true;

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

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

Reimplemented from SourceReader.

Definition at line 316 of file SequenceReaderFilter.cpp.

References SourceReader::extractSource(), filterNums_, and pSeq_.

{
  //  cout << seqNum << " " << filterNums_[seqNum] << " " << seqStart << " " << seqEnd << endl; 
  pSeq_->extractSource( pSource, filterNums_[seqNum], seqStart, seqEnd );
} // ~void SequenceReaderFilter::extractSource

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

Reimplemented from SourceReader.

Definition at line 330 of file SequenceReaderFilter.cpp.

References filterNums_, SequenceReader::getNumSequencesInFile(), pSeq_, and SourceReader::saveIndexImp().

{
  std::strstream indexTemp;
  pSeq_->saveIndexImp( fileFile, indexTemp, fileNumber );
  const SeqIndexInfo* pIndex= (const SeqIndexInfo*)indexTemp.str();

  // writing individually is slow as a slow thing on Valium ...
  //  int numSeqs(getNumSequencesInFile());
  //  for (int i(1); i<=numSeqs; i++)
  //  {
  //    //        cout << "Index: " << i << " " << filterNums_[i]-1 << " "  
  //    //     << pIndex[filterNums_[i]-1].fileNum
    //   << " " << pIndex[filterNums_[i]-1].seqPos << endl;
  //   indexFile.write
  //    ( (const char*)&pIndex[ filterNums_[i]-1 ], sizeof(SeqIndexInfo) );
  //  } // ~for

  int numSeqs(getNumSequencesInFile());
  vector<SeqIndexInfo> newIndex;
  newIndex.reserve(numSeqs);

  for (int i(1); i<=numSeqs; i++)
  {
    //        cout << "Index: " << i << " " << filterNums_[i]-1 << " "  
    //     << pIndex[filterNums_[i]-1].fileNum
    //   << " " << pIndex[filterNums_[i]-1].seqPos << endl;
    newIndex.push_back(pIndex[ filterNums_[i]-1 ]);
  } // ~for

  indexFile.write
    ( (const char*)&newIndex[ 0 ], numSeqs*sizeof(SeqIndexInfo) );



} // ~void SequenceReaderFilter::saveIndexImp

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virtual SequenceReaderState* SequenceReaderFilter::saveState

(

void

)

const [inline, virtual]

Reimplemented from SequenceReader.

Definition at line 299 of file SequenceReaderFilter.h.

References SequenceReader::lastSequenceNumber_, and pSeq_.

  {
    return new SequenceReaderFilterState( lastSequenceNumber_, pSeq_ );
  }

virtual void SequenceReaderFilter::restoreState

(

SequenceReaderState *

pState

)

[inline, virtual]

Reimplemented from SequenceReader.

Definition at line 309 of file SequenceReaderFilter.h.

References SequenceReaderState::lastSequenceNumber_, SequenceReader::lastSequenceNumber_, pSeq_, SequenceReaderFilterState::pState_, and SequenceReader::restoreState().

  {
    SequenceReaderFilterState* p
      (dynamic_cast<SequenceReaderFilterState*>(pState));
    assert(p!=NULL);
    lastSequenceNumber_ = p->lastSequenceNumber_;
    pSeq_->restoreState( p->pState_ );
    delete pState;
  }

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SequenceNumber SequenceReaderFilter::computeNumSequencesInFile

(

void

)

[protected, virtual]

Implements SequenceReader.

Definition at line 296 of file SequenceReaderFilter.cpp.

References findSequence(), SequenceReader::getNumSequencesInFile(), SequenceReader::numSequencesInFile_, and pSeq_.

{
  try
  {
    // this will always work out num seqs in pSeq_ 
    findSequence( 1+pSeq_->getNumSequencesInFile() );
  } // ~try
  catch( const NumberOutOfRange& err )
    {} // ~catch

  return numSequencesInFile_;

} // ~SequenceReaderFilter::computeNumSequencesInFile( void )

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SequenceReaderFilter& SequenceReaderFilter::operator=

(

const SequenceReaderFilter &

)

[private]

---

Member Data Documentation

SequenceReader* SequenceReaderFilter::pSeq_ [protected]

Definition at line 339 of file SequenceReaderFilter.h.

Referenced by changeMode(), computeNumSequencesInFile(), extractSource(), findSequence(), getBitsPerSymbol(), getLastSequenceName(), getNextSequence(), getSequence(), getSourceDataType(), printName(), printSideInfo(), printSource(), restoreState(), rewind(), saveIndexImp(), saveState(), and ~SequenceReaderFilter().

StringHash* SequenceReaderFilter::pFilterNames_ [protected]

Definition at line 342 of file SequenceReaderFilter.h.

Referenced by findSequence(), readFilterNames(), and ~SequenceReaderFilter().

vector<SequenceNumber> SequenceReaderFilter::filterNums_ [protected]

Definition at line 346 of file SequenceReaderFilter.h.

Referenced by extractSource(), findSequence(), getNextSequence(), getSequence(), printName(), printSideInfo(), printSource(), readFilterNames(), and saveIndexImp().

int SequenceReaderFilter::numFiltered_ [protected]

Definition at line 347 of file SequenceReaderFilter.h.

Referenced by findSequence(), and getNumFiltered().

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

• SequenceReader/SequenceReaderFilter.h
• SequenceReader/SequenceReaderFilter.cpp

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