pappso::cbor::psm::SageReader::FastaSeq Class Reference

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::getDecoyTag().

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.

{
  QString accession = description_in.split(" ", Qt::SkipEmptyParts).at(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_in);
    }
  catch(pappso::ExceptionNotFound &err)
    {
    }
  try
    {
      accession                     = accession.prepend(m_decoyTag);
      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_in);
      psm_protein.protein_sp.get()->reverse();
    }
  catch(pappso::ExceptionNotFound &err)
    {
    }
}

References 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.

mp_self

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

private

Definition at line 93 of file sagereader.h.

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

• pappsomspp/core/processing/cbor/psm/sage/sagereader.h
• pappsomspp/core/processing/cbor/psm/sage/sagereader.cpp