libpappsomspp
Library for mass spectrometry
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#include <mzidentmlwriter.h>
Public Member Functions | |
MzIdentMlWriter () | |
~MzIdentMlWriter () | |
void | writeDBSequence (const QString &id, const QString &db_ref_id, const pappso::Protein &protein, bool is_reverse) |
void | writeDBSequence (const QString &id, const QString &db_ref_id, const QString &accession, const QString &description, const QString &sequence, bool is_reverse) |
void | writeStartMzIdentMlDocument (const QString &id, const QString &version) |
void | writeCvList () |
void | writeCvParam (pappso::AaModificationP modification) |
void | writeCvParam (const pappso::OboPsiModTerm &term, const QString &value) |
void | writeCvParam (const QString &cv_ref, const QString &accession, const QString &name, const QString &value) |
void | writeCvParamUo (const QString &cv_ref, const QString &accession, const QString &name, const QString &value, const QString &unit_cv_ref, const QString &unit_accession, const QString &unit_name) |
void | writeCvParamUo (const QString &cv_ref, const QString &accession, const QString &name, const QString &value, pappso::PrecisionUnit precision_unit) |
void | writeUserParam (const QString &name, const QString &value) |
void | writeUserParam (const QString &name, double value) |
void | writeUserParam (pappso::DeepProtMatchType matchType) |
void | writeUserParam (pappso::DeepProtPeptideCandidateStatus status) |
Static Public Member Functions | |
static const QString | toXmlMass (double mass) |
static const QString | toXmlMassDelta (double mass) |
static const QString | toXmlDouble (double value) |
Definition at line 46 of file mzidentmlwriter.h.
pappso::MzIdentMlWriter::MzIdentMlWriter | ( | ) |
pappso::MzIdentMlWriter::~MzIdentMlWriter | ( | ) |
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Definition at line 353 of file mzidentmlwriter.cpp.
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Definition at line 335 of file mzidentmlwriter.cpp.
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static |
Definition at line 341 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeCvList | ( | ) |
Definition at line 75 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeCvParam | ( | const pappso::OboPsiModTerm & | term, |
const QString & | value ) |
Definition at line 201 of file mzidentmlwriter.cpp.
References pappso::OboPsiModTerm::m_accession, and pappso::OboPsiModTerm::m_name.
void pappso::MzIdentMlWriter::writeCvParam | ( | const QString & | cv_ref, |
const QString & | accession, | ||
const QString & | name, | ||
const QString & | value ) |
Definition at line 184 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeCvParam | ( | pappso::AaModificationP | pmod | ) |
cvParam accession="MS:1000894" cvRef="PSI-MS" name="retention time" value="5468.0193" unitAccession="UO:0000010" unitName="second" unitCvRef="UO"/>
Definition at line 226 of file mzidentmlwriter.cpp.
References pappso::AaModification::getAccession(), and pappso::AaModification::getName().
void pappso::MzIdentMlWriter::writeCvParamUo | ( | const QString & | cv_ref, |
const QString & | accession, | ||
const QString & | name, | ||
const QString & | value, | ||
const QString & | unit_cv_ref, | ||
const QString & | unit_accession, | ||
const QString & | unit_name ) |
Definition at line 256 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeCvParamUo | ( | const QString & | cv_ref, |
const QString & | accession, | ||
const QString & | name, | ||
const QString & | value, | ||
pappso::PrecisionUnit | precision_unit ) |
Definition at line 278 of file mzidentmlwriter.cpp.
References pappso::dalton, and pappso::ppm.
void pappso::MzIdentMlWriter::writeDBSequence | ( | const QString & | id, |
const QString & | db_ref_id, | ||
const pappso::Protein & | protein, | ||
bool | is_reverse ) |
Definition at line 123 of file mzidentmlwriter.cpp.
References pappso::Protein::getAccession(), pappso::Protein::getDescription(), and pappso::Protein::getSequence().
void pappso::MzIdentMlWriter::writeDBSequence | ( | const QString & | id, |
const QString & | db_ref_id, | ||
const QString & | accession, | ||
const QString & | description, | ||
const QString & | sequence, | ||
bool | is_reverse ) |
Definition at line 138 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeStartMzIdentMlDocument | ( | const QString & | id, |
const QString & | version ) |
Definition at line 42 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeUserParam | ( | const QString & | name, |
const QString & | value ) |
Definition at line 310 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeUserParam | ( | const QString & | name, |
double | value ) |
Definition at line 347 of file mzidentmlwriter.cpp.
void pappso::MzIdentMlWriter::writeUserParam | ( | pappso::DeepProtMatchType | matchType | ) |
Definition at line 321 of file mzidentmlwriter.cpp.
References pappso::DeepProtEnumStr::toString().
void pappso::MzIdentMlWriter::writeUserParam | ( | pappso::DeepProtPeptideCandidateStatus | status | ) |
Definition at line 328 of file mzidentmlwriter.cpp.
References pappso::DeepProtEnumStr::toString().