pappso::FastaReader Class Reference

#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 49 of file fastareader.h.

Constructor & Destructor Documentation

FastaReader()

pappso::FastaReader::FastaReader

(

FastaHandlerInterface &

handler

)

Definition at line 45 of file fastareader.cpp.

    {
      parse(&fastaFile);

References parse().

~FastaReader()

pappso::FastaReader::~FastaReader

(

)

Definition at line 49 of file fastareader.cpp.

    {

Member Function Documentation

parse() [1/2]

void pappso::FastaReader::parse

(

QFile &

fastaFile

)

Definition at line 55 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())
    {

Referenced by FastaReader().

parse() [2/2]

void pappso::FastaReader::parse

(

QIODevice *

p_inputstream

)

Definition at line 74 of file fastareader.cpp.

            {
              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__;
}
 
 
void
FastaReader::parseOnlyOne(QTextStream &p_in)
{
 
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
 
  QString accession = "";
  QString sequence  = "";
  // Search accession conta
  // QTextStream in(p_in);
  QString line = p_in.readLine();
  while(!p_in.atEnd())

References m_handler, and pappso::FastaHandlerInterface::setSequence().

parseOnlyOne()

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

protected

Definition at line 115 of file fastareader.cpp.

            {
              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__;
}
 
} // namespace pappso

References m_handler, and pappso::FastaHandlerInterface::setSequence().

Member Data Documentation

FastaFileIndexer

friend pappso::FastaReader::FastaFileIndexer

private

Definition at line 51 of file fastareader.h.

m_handler

FastaHandlerInterface& pappso::FastaReader::m_handler

private

Definition at line 64 of file fastareader.h.

Referenced by parse(), and parseOnlyOne().

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

• pappsomspp/fasta/fastareader.h
• pappsomspp/fasta/fastareader.cpp