From 8efbec8a3037c354558e3343238c5bac3fb5061c Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 21 Jun 2017 18:43:46 +0200
Subject: [PATCH] reading mzIdentML
---
src/input/identificationpwizreader.cpp | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 484df0d3f..ba02347f6 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -162,6 +162,30 @@ void IdentificationPwizReader::read(
for (pwiz::identdata::PeptidePtr seq_ptr :_pwiz_ident_data_file->sequenceCollection.peptides) {
pwiz::identdata::Peptide * peptide_pwiz = seq_ptr.get();
PeptideXtp peptide(QString::fromStdString( peptide_pwiz->peptideSequence));
+
+
+ //<Modification monoisotopicMassDelta="42.01056468" location="1">
+ // <cvParam accession="MOD:00394" cvRef="PSI-MOD" name="acetylated residue"/>
+ //</Modification>
+ for (pwiz::identdata::ModificationPtr mod_ptr :peptide_pwiz->modification) {
+ unsigned int location = mod_ptr.get()->location;
+ //std::vector<CVParam> cvParams;
+ for (const pwiz::data::CVParam & param: mod_ptr.get()->cvParams) {
+ qDebug() << "IdentificationPwizReader::read param " << QString::fromStdString(param.name());
+ /*
+ if (pwiz::cv::cvTermInfo(param.cvid).prefix() == "PSI-MOD") {
+ }
+ else {
+ throw pappso::PappsoException(QObject::tr("Error reading file (%1) using proteowizard library : cvParam %2 not handled").arg(_identfile.absoluteFilePath()).arg(QString::fromStdString( pwiz::cv::cvTermInfo(param.cvid).id)));
+ }
+ */
+ }
+
+ for (const pwiz::data::UserParam & param: mod_ptr.get()->userParams) {
+ qDebug() << "IdentificationPwizReader::read UserParams " << QString::fromStdString(param.name);
+ }
+ }
+
PeptideXtpSp peptide_sp(peptide.makePeptideXtpSp());
peptide_sp = peptide_store.getInstance(peptide_sp);
map_id2peptide.insert(std::pair<QString, PeptideXtpSp>(QString::fromStdString( peptide_pwiz->id), peptide_sp));
--
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