From 0ad05745610f76d9ff7a3ff2b10c9a0ee05dffa9 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 3 Oct 2018 19:23:02 +0200
Subject: [PATCH] fix adding modification at position -1 in pwiz reader
---
src/input/identificationpwizreader.cpp | 29 ++++++++++++++++++++++----
src/input/mascot/mascotdatparser.cpp | 14 +++++--------
2 files changed, 30 insertions(+), 13 deletions(-)
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 088b4db08..c3afa93b4 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -247,7 +247,8 @@ getQVariantDoubleParam(pwiz::data::ParamContainer *item, pwiz::cv::CVID param)
void
IdentificationPwizReader::read(
- IdentificationDataSource *p_identification_data_source, Project *p_project,
+ IdentificationDataSource *p_identification_data_source,
+ Project *p_project,
IdentificationGroup *p_identification_group)
{
qDebug() << "IdentificationPwizReader::read begin";
@@ -314,9 +315,29 @@ IdentificationPwizReader::read(
pappso::pappso_double mass_delta =
mod_ptr.get()->monoisotopicMassDelta;
- peptide.addAaModification(
- Utils::guessAaModificationPbyMonoisotopicMassDelta(mass_delta),
- location - 1);
+ if(location > 0)
+ {
+ location = location - 1;
+ }
+
+ try
+ {
+ peptide.addAaModification(
+ Utils::guessAaModificationPbyMonoisotopicMassDelta(
+ mass_delta),
+ location);
+ }
+ catch(pappso::PappsoException &error)
+ {
+ throw pappso::PappsoException(
+ QObject::tr("ERROR adding modification mass delta %1 to "
+ "peptide %2 at "
+ "position %3 :\n %4")
+ .arg(mass_delta)
+ .arg(peptide.toAbsoluteString())
+ .arg(location)
+ .arg(error.qwhat()));
+ }
// std::vector<CVParam> cvParams;
for(const pwiz::data::CVParam ¶m : mod_ptr.get()->cvParams)
{
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index 5f8140792..2751237a0 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -911,16 +911,12 @@ MascotDatParser::setVariableModifications(PeptideXtpSp &peptide_sp,
[variable_modifications_string.mid(i, 1).toUInt() - 1];
try
{
- if(i == 0)
+ if(i > 0)
{
- peptide_sp.get()->addAaModification(
- mascot_modification.modification, 0);
- }
- else
- {
- peptide_sp.get()->addAaModification(
- mascot_modification.modification, i - 1);
+ i = i - 1;
}
+ peptide_sp.get()->addAaModification(
+ mascot_modification.modification, i);
}
catch(pappso::PappsoException &error)
{
@@ -929,7 +925,7 @@ MascotDatParser::setVariableModifications(PeptideXtpSp &peptide_sp,
"position %3 :\n %4")
.arg(mascot_modification.modification->getAccession())
.arg(peptide_sp.get()->toAbsoluteString())
- .arg(i - 1)
+ .arg(i)
.arg(error.qwhat()));
}
}
--
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