#include <fastareader.h>

Public Member Functions
	FastaReader (FastaHandlerInterface &handler)

	~FastaReader ()

void	parse (QFile &fastaFile)

void	parse (QIODevice *p_inputstream)

Protected Member Functions
void	parseOnlyOne (QTextStream &p_in)

Private Attributes
friend	FastaFileIndexer

FastaHandlerInterface &	m_handler

Detailed Description

Definition at line 33 of file fastareader.h.

Constructor & Destructor Documentation

◆ FastaReader()

pappso::FastaReader::FastaReader ( FastaHandlerInterface & handler )

Definition at line 29 of file fastareader.cpp.

                                                       : m_handler(handler)
{
}

References m_handler.

◆ ~FastaReader()

pappso::FastaReader::~FastaReader ( )

Definition at line 33 of file fastareader.cpp.

34{

35}

Member Function Documentation

◆ parse() [1/2]

void pappso::FastaReader::parse ( QFile & fastaFile )

Definition at line 39 of file fastareader.cpp.

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

References parse().

Referenced by parse(), and pappso::cbor::psm::SageReader::readTsvFile().

◆ parse() [2/2]

void pappso::FastaReader::parse ( QIODevice * p_inputstream )

Definition at line 58 of file fastareader.cpp.

{
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
  QTextStream p_in(p_inputstream);
 
 
  QString accession = "";
  QString sequence  = "";
  // Search accession conta
  // QTextStream in(p_in);
  QString line = p_in.readLine();
  while(!p_in.atEnd())
    {
      if(line.startsWith(">"))
        {
          if(!accession.isEmpty())
            {
              m_handler.setSequence(accession, sequence);
            }
          sequence  = "";
          accession = line.remove(0, 1);
        }
      else
        {
          sequence.append(line);
          // m_handler.setSequence(line);
        }
      line = p_in.readLine();
    }
  if(!accession.isEmpty())
    {
      sequence.append(line);
      m_handler.setSequence(accession, sequence);
    }
  // p_in->close();
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}

References line, and m_handler.

◆ parseOnlyOne()

void pappso::FastaReader::parseOnlyOne ( QTextStream & p_in )

protected

Definition at line 99 of file fastareader.cpp.

{
 
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
 
  QString accession = "";
  QString sequence  = "";
  // Search accession conta
  // QTextStream in(p_in);
  QString line = p_in.readLine();
  while(!p_in.atEnd())
    {
      if(line.startsWith(">"))
        {
          if(!accession.isEmpty())
            {
              m_handler.setSequence(accession, sequence);
              return;
            }
          sequence  = "";
          accession = line.remove(0, 1);
        }
      else
        {
          sequence.append(line);
          // m_handler.setSequence(line);
        }
      line = p_in.readLine();
    }
  if(!accession.isEmpty())
    {
      sequence.append(line);
      m_handler.setSequence(accession, sequence);
    }
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}

References line, and m_handler.

Referenced by pappso::FastaFileIndexer::getSequenceByIndex().

Member Data Documentation

◆ FastaFileIndexer

friend pappso::FastaReader::FastaFileIndexer

private

Definition at line 35 of file fastareader.h.

◆ m_handler

FastaHandlerInterface& pappso::FastaReader::m_handler

private

Definition at line 48 of file fastareader.h.

Referenced by FastaReader(), parse(), and parseOnlyOne().

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

pappsomspp/core/fasta/fastareader.h
pappsomspp/core/fasta/fastareader.cpp

Public Member Functions

Protected Member Functions

Private Attributes