From 29591281c1cb5c2ccda5d709acf888d292f8e8cf Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 21 Mar 2019 16:03:02 +0100
Subject: [PATCH] mutation support
---
src/input/xtandemsaxhandler.cpp | 70 ++++++++++++++++++++++-----------
src/utils/peptidestore.cpp | 17 +++++---
2 files changed, 59 insertions(+), 28 deletions(-)
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 57b17071..dfb409b7 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -40,7 +40,8 @@
XtandemSaxHandler::XtandemSaxHandler(
- Project *p_project, IdentificationGroup *p_identification_group,
+ Project *p_project,
+ IdentificationGroup *p_identification_group,
IdentificationDataSource *p_identification_data_source)
: _p_project(p_project)
{
@@ -57,7 +58,8 @@ XtandemSaxHandler::~XtandemSaxHandler()
bool
XtandemSaxHandler::startElement(const QString &namespaceURI,
- const QString &localName, const QString &qName,
+ const QString &localName,
+ const QString &qName,
const QXmlAttributes &attributes)
{
// qDebug() << namespaceURI << " " << localName << " " << qName ;
@@ -96,8 +98,9 @@ XtandemSaxHandler::startElement(const QString &namespaceURI,
}
catch(pappso::PappsoException &exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag "
- "%1, PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -116,7 +119,8 @@ XtandemSaxHandler::startElement(const QString &namespaceURI,
bool
XtandemSaxHandler::endElement(const QString &namespaceURI,
- const QString &localName, const QString &qName)
+ const QString &localName,
+ const QString &qName)
{
bool is_ok = true;
@@ -138,8 +142,9 @@ XtandemSaxHandler::endElement(const QString &namespaceURI,
}
catch(pappso::PappsoException &exception_pappso)
{
- _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, "
- "PAPPSO exception:\n%2")
+ _errorStr = QObject::tr(
+ "ERROR in XtandemSaxHandler::endElement tag %1, "
+ "PAPPSO exception:\n%2")
.arg(qName)
.arg(exception_pappso.qwhat());
return false;
@@ -219,9 +224,10 @@ XtandemSaxHandler::startElement_file(QXmlAttributes attributes)
// attrs.getValue("URL")));
if(_p_protein_match == nullptr)
{
- throw pappso::PappsoException("ERROR in "
- "XtandemSaxHandler::startElement_file "
- ": _p_protein_match == nullptr");
+ throw pappso::PappsoException(
+ "ERROR in "
+ "XtandemSaxHandler::startElement_file "
+ ": _p_protein_match == nullptr");
}
_p_protein_match->getProteinXtpSp().get()->setFastaFileP(
_p_project->getFastaFileStore()
@@ -251,9 +257,10 @@ XtandemSaxHandler::startElement_domain(QXmlAttributes attributes)
//""));
if(_p_protein_match == nullptr)
{
- throw pappso::PappsoException("ERROR in "
- "XtandemSaxHandler::startElement_"
- "domain : _p_protein_match == nullptr");
+ throw pappso::PappsoException(
+ "ERROR in "
+ "XtandemSaxHandler::startElement_"
+ "domain : _p_protein_match == nullptr");
}
_p_protein_match->getProteinXtpSp().get()->setSequence(_current_text);
@@ -387,11 +394,25 @@ bool
XtandemSaxHandler::startElement_aa(QXmlAttributes attributes)
{
//<aa type="M" at="624" modified="15.99491" />
+
bool is_ok = true;
// qDebug() << "startElement_aa ";
- pappso::AaModificationP modif =
- Utils::guessAaModificationPbyMonoisotopicMassDelta(
- attributes.value("modified").simplified().toDouble());
+ pappso::AaModificationP modif = nullptr;
+ if(attributes.value("pm").isEmpty())
+ {
+
+ modif = Utils::guessAaModificationPbyMonoisotopicMassDelta(
+ attributes.value("modified").simplified().toDouble());
+ }
+ else
+ {
+ //<aa type="P" at="59" modified="31.98983" pm="E" />
+ //<aa type="C" at="64" modified="-15.97716" pm="S" />
+ // point mutation
+ QChar mut_from(attributes.value("type")[0]);
+ QChar mut_to(attributes.value("pm")[0]);
+ modif = pappso::AaModification::getInstanceMutation(mut_from, mut_to);
+ }
unsigned int position_in_prot =
attributes.value("at").simplified().toUInt() - 1;
_current_peptide_sp.get()->addAaModification(
@@ -415,9 +436,10 @@ XtandemSaxHandler::endElement_domain()
.getInstance(_p_peptide_evidence));
if(_p_protein_match == nullptr)
{
- throw pappso::PappsoException("ERROR in "
- "XtandemSaxHandler::endElement_domain : "
- "_p_protein_match == nullptr");
+ throw pappso::PappsoException(
+ "ERROR in "
+ "XtandemSaxHandler::endElement_domain : "
+ "_p_protein_match == nullptr");
}
_p_protein_match->addPeptideMatch(_current_peptide_match);
@@ -713,8 +735,9 @@ XtandemSaxHandler::endElement_note()
bool
XtandemSaxHandler::error(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
@@ -726,8 +749,9 @@ XtandemSaxHandler::error(const QXmlParseException &exception)
bool
XtandemSaxHandler::fatalError(const QXmlParseException &exception)
{
- _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
- "%3")
+ _errorStr = QObject::tr(
+ "Parse error at line %1, column %2 :\n"
+ "%3")
.arg(exception.lineNumber())
.arg(exception.columnNumber())
.arg(exception.message());
diff --git a/src/utils/peptidestore.cpp b/src/utils/peptidestore.cpp
index 6001f002..c99aa05d 100644
--- a/src/utils/peptidestore.cpp
+++ b/src/utils/peptidestore.cpp
@@ -113,11 +113,18 @@ PeptideStore::checkPsimodCompliance() const
}
else
{
- throw pappso::PappsoException(
- QObject::tr("Modification %1 is not a PSIMOD accession. Please "
- "go into the edit=>modifications menu to replace "
- "modifications masses by PSIMOD accessions")
- .arg(modification->getAccession()));
+ if(modification->getAccession().startsWith("MUTATION:"))
+ {
+ }
+ else
+ {
+ throw pappso::PappsoException(
+ QObject::tr(
+ "Modification %1 is not a PSIMOD accession. Please "
+ "go into the edit=>modifications menu to replace "
+ "modifications masses by PSIMOD accessions")
+ .arg(modification->getAccession()));
+ }
}
}
}
--
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