Inheritance diagram for pappso::cbor::psm::SageReader::FastaSeq:

Public Member Functions
	FastaSeq (SageReader *self)
void	setSequence (const QString &description_in, const QString &sequence_in) override

Private Attributes
SageReader *	mp_self
QString	m_decoyTag

Detailed Description

Definition at line 86 of file sagereader.h.

Constructor & Destructor Documentation

◆ FastaSeq()

pappso::cbor::psm::SageReader::FastaSeq::FastaSeq ( SageReader * self )

Definition at line 73 of file sagereader.cpp.

{
  mp_self    = self;
  m_decoyTag = mp_self->getDecoyTag();
}

References pappso::cbor::psm::SageReader::SageReader(), m_decoyTag, and mp_self.

Member Function Documentation

◆ setSequence()

void pappso::cbor::psm::SageReader::FastaSeq::setSequence	(	const QString &	description_in,
		const QString &	sequence_in )

overridevirtual

Implements pappso::FastaHandlerInterface.

Definition at line 80 of file sagereader.cpp.

{
 
  QStringList description_split = description_in.split(" ", Qt::SkipEmptyParts);
  QString accession             = description_split.at(0);
  if(description_split.length() > 0)
    description_split.remove(0);
  try
    {
      const PsmProtein &psm_protein = mp_self->m_psmProteinMap.getByAccession(accession);
      psm_protein.protein_sp.get()->setSequence(sequence_in);
      psm_protein.protein_sp.get()->setDescription(description_split.join(" "));
    }
  catch(pappso::ExceptionNotFound &err)
    {
    }
  try
    {
      QString rev_accession         = accession.prepend(m_decoyTag);
      const PsmProtein &psm_protein = mp_self->m_psmProteinMap.getByAccession(rev_accession);
      psm_protein.protein_sp.get()->setSequence(sequence_in);
 
      // description_split[0] = rev_accession;
      psm_protein.protein_sp.get()->setDescription(description_split.join(" "));
      psm_protein.protein_sp.get()->reverse();
    }
  catch(pappso::ExceptionNotFound &err)
    {
    }
}

References m_decoyTag, mp_self, and pappso::cbor::psm::PsmProtein::protein_sp.

Member Data Documentation

◆ m_decoyTag

QString pappso::cbor::psm::SageReader::FastaSeq::m_decoyTag

private

Definition at line 94 of file sagereader.h.

Referenced by FastaSeq(), and setSequence().

◆ mp_self

SageReader* pappso::cbor::psm::SageReader::FastaSeq::mp_self