pappso::FastaFileIndexer Class Reference

#include <fastafileindexer.h>

Inheritance diagram for pappso::FastaFileIndexer:

Public Member Functions
	FastaFileIndexer (const QFileInfo &fastaFile)
	FastaFileIndexer (const FastaFileIndexer &other)
virtual	~FastaFileIndexer ()
void	getSequenceByIndex (FastaHandlerInterface &fasta_handler, std::size_t index) override
void	open () override
void	close () override
FastaFileIndexerSPtr	makeFastaFileIndexerSPtr () const
std::size_t	size () const

Private Member Functions
void	parseFastaFile ()

Private Attributes
QFile	m_fasta_file
std::vector< qint64 >	m_indexArray
QTextStream *	mpa_sequenceTxtIn = nullptr

Detailed Description

Definition at line 51 of file fastafileindexer.h.

Constructor & Destructor Documentation

FastaFileIndexer() [1/2]

pappso::FastaFileIndexer::FastaFileIndexer

(

const QFileInfo &

fastaFile

)

Definition at line 39 of file fastafileindexer.cpp.

  : m_fasta_file(fastaFile.absoluteFilePath())
{
 
  if(m_fasta_file.fileName().isEmpty())
    {
      throw PappsoException(QObject::tr("No FASTA file name specified"));
    }
  if(m_fasta_file.open(QIODevice::ReadOnly))
    {
      parseFastaFile();
      m_fasta_file.close();
    }
  else
    {
      throw PappsoException(QObject::tr("ERROR opening FASTA file %1 for read")
                              .arg(fastaFile.fileName()));
    }
}

References m_fasta_file.

Referenced by FastaFileIndexer().

FastaFileIndexer() [2/2]

pappso::FastaFileIndexer::FastaFileIndexer

(

const FastaFileIndexer &

other

)

Definition at line 59 of file fastafileindexer.cpp.

  : m_fasta_file(other.m_fasta_file.fileName())
{
 
  m_indexArray      = other.m_indexArray;
  mpa_sequenceTxtIn = nullptr;
}

References FastaFileIndexer(), m_fasta_file, m_indexArray, and mpa_sequenceTxtIn.

~FastaFileIndexer()

pappso::FastaFileIndexer::~FastaFileIndexer ( )

virtual

Definition at line 66 of file fastafileindexer.cpp.

{
  close();
}

References close().

Member Function Documentation

close()

void pappso::FastaFileIndexer::close ( )

overridevirtual

Implements pappso::FastaFileIndexerInterface.

Definition at line 138 of file fastafileindexer.cpp.

{
  if(mpa_sequenceTxtIn != nullptr)
    {
      delete mpa_sequenceTxtIn;
      mpa_sequenceTxtIn = nullptr;
      m_fasta_file.close();
    }
}

References m_fasta_file, and mpa_sequenceTxtIn.

Referenced by ~FastaFileIndexer().

getSequenceByIndex()

void pappso::FastaFileIndexer::getSequenceByIndex ( FastaHandlerInterface & fasta_handler, std::size_t index )

overridevirtual

Implements pappso::FastaFileIndexerInterface.

Definition at line 149 of file fastafileindexer.cpp.

{
  open();
 
  qDebug() << " goto=" << index << " pos=" << m_indexArray[index];
  bool seek_ok;
  if((index < m_indexArray.size()) &&
     (seek_ok = mpa_sequenceTxtIn->seek(m_indexArray[index])))
    {
 
      qDebug() << " realpos=" << mpa_sequenceTxtIn->pos();
      ;
      if(!seek_ok)
        {
 
          throw PappsoException(QObject::tr("ERROR FastaFileIndexer : seek to "
                                            "sequence %1, position %2 failed")
                                  .arg(index)
                                  .arg(m_indexArray[index]));
        }
      FastaReader reader(fasta_handler);
      reader.parseOnlyOne(*mpa_sequenceTxtIn);
    }
  else
    {
      throw ExceptionOutOfRange(
        QObject::tr("ERROR reading FASTA file %1 : sequence index %2 "
                    "unreachable, array size=%3")
          .arg(m_fasta_file.fileName())
          .arg(index)
          .arg(m_indexArray.size()));
    }
}

References m_fasta_file, m_indexArray, mpa_sequenceTxtIn, open(), and pappso::FastaReader::parseOnlyOne().

makeFastaFileIndexerSPtr()

FastaFileIndexerSPtr pappso::FastaFileIndexer::makeFastaFileIndexerSPtr

(

)

const

Definition at line 186 of file fastafileindexer.cpp.

{
 
  return std::make_shared<FastaFileIndexer>(*this);
}

open()

void pappso::FastaFileIndexer::open ( )

overridevirtual

Implements pappso::FastaFileIndexerInterface.

Definition at line 122 of file fastafileindexer.cpp.

{
  if(mpa_sequenceTxtIn != nullptr)
    return;
  if(m_fasta_file.open(QIODevice::ReadOnly))
    {
      mpa_sequenceTxtIn = new QTextStream(&m_fasta_file);
    }
  else
    {
      throw PappsoException(QObject::tr("ERROR opening FASTA file %1 for read")
                              .arg(m_fasta_file.fileName()));
    }
}

References m_fasta_file, and mpa_sequenceTxtIn.

Referenced by getSequenceByIndex().

parseFastaFile()

void pappso::FastaFileIndexer::parseFastaFile ( )

private

Definition at line 73 of file fastafileindexer.cpp.

{
 
  qDebug();
  QDataStream bin_in(&m_fasta_file);
  qint64 position = 0;
 
  // QChar first_char;
  // txt_in >> first_char;
  qint8 char_in;
  bin_in >> char_in;
  while(!bin_in.atEnd() && (char_in < (qint8)21))
    { // eat Windows \r\n
      position++;
      bin_in >> char_in;
    }
  while(!bin_in.atEnd())
    {
      // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
      //         << " first_char=" << first_char;
      if(char_in == (qint8)'>')
        {
 
          // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
          //        << " index=" << m_indexArray.size()
          //         << " position=" << position;
          m_indexArray.push_back(position);
        }
      // eat line
      position++;
      bin_in >> char_in;
      while(!bin_in.atEnd() && (char_in > (qint8)20))
        {
          position++;
          bin_in >> char_in;
        }
      position++;
      bin_in >> char_in;
 
      if(!bin_in.atEnd() && (char_in < (qint8)21))
        { // eat Windows \r\n
          position++;
          bin_in >> char_in;
        }
    }
  qDebug();
}

References m_fasta_file, and m_indexArray.

size()

std::size_t pappso::FastaFileIndexer::size

(

)

const

Definition at line 194 of file fastafileindexer.cpp.

{
  return m_indexArray.size();
}

References m_indexArray.

Member Data Documentation

m_fasta_file

QFile pappso::FastaFileIndexer::m_fasta_file

private

Definition at line 73 of file fastafileindexer.h.

Referenced by FastaFileIndexer(), FastaFileIndexer(), close(), getSequenceByIndex(), open(), and parseFastaFile().

m_indexArray

std::vector<qint64> pappso::FastaFileIndexer::m_indexArray

private

Definition at line 74 of file fastafileindexer.h.

Referenced by FastaFileIndexer(), getSequenceByIndex(), parseFastaFile(), and size().

mpa_sequenceTxtIn

QTextStream* pappso::FastaFileIndexer::mpa_sequenceTxtIn = nullptr

private

Definition at line 75 of file fastafileindexer.h.

Referenced by FastaFileIndexer(), close(), getSequenceByIndex(), and open().

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

• pappsomspp/core/fasta/fastafileindexer.h
• pappsomspp/core/fasta/fastafileindexer.cpp