From 4391a47c305d105bdeef9e47352caf8b68f2c86d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 6 Apr 2017 22:42:47 +0200
Subject: [PATCH] get protein match instance
---
src/CMakeLists.txt | 4 ++--
src/core/identificationgroup.cpp | 24 ++++++------------------
src/core/identificationgroup.h | 3 +--
src/core/peptidematch.cpp | 2 +-
src/core/peptidematch.h | 2 +-
src/input/xtandemsaxhandler.cpp | 14 ++++----------
6 files changed, 15 insertions(+), 34 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 42d4fb8f..9d83c283 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index dcbf38ed..a56976d9 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -50,19 +50,17 @@ void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters
}
}
-ProteinMatch * IdentificationGroup::getProteinMatch(const QString accession) {
+ProteinMatch * IdentificationGroup::getProteinMatchInstance(const QString accession) {
if (accession.isEmpty()) {
throw pappso::PappsoException(QObject::tr("Error protein match not found : accession is empty"));
}
auto it_cache = _cache_accession_protein_match.find(accession);
if (it_cache == _cache_accession_protein_match.end()) {
//accession not found in cache
- for (ProteinMatch * p_protein_match : _protein_match_list) {
- if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
- _cache_accession_protein_match.insert(std::pair<QString, ProteinMatch *>(accession, p_protein_match));
- return p_protein_match;
- }
- }
+ ProteinMatch * p_protein_match = new ProteinMatch();
+ _cache_accession_protein_match.insert(std::pair<QString, ProteinMatch *>(accession, p_protein_match));
+ _protein_match_list.push_back(p_protein_match);
+ return p_protein_match;
}
else {
return it_cache->second;
@@ -70,17 +68,7 @@ ProteinMatch * IdentificationGroup::getProteinMatch(const QString accession) {
return nullptr;
}
void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
- QString accession = protein_match->getProteinXtpSp().get()->getAccession();
- if (accession.isEmpty()) {
- throw pappso::PappsoException(QObject::tr("Error adding protein match : accession is empty"));
- }
- auto it_cache = _cache_already_added_protein_match.find(protein_match);
- if (it_cache == _cache_already_added_protein_match.end()) {
- //accession not found in cache
- _cache_already_added_protein_match.insert(protein_match);
- _protein_match_list.push_back(protein_match);
- }
-
+ _protein_match_list.push_back(protein_match);
}
bool IdentificationGroup::contains (const MsRun * p_msrun) const {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 279b7a8b..27986627 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -44,7 +44,7 @@ public:
IdentificationGroup(Project * project);
~IdentificationGroup();
- ProteinMatch * getProteinMatch(const QString accession);
+ ProteinMatch * getProteinMatchInstance(const QString accession);
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
void addMsRunSp(MsRunSp ms_run_sp);
@@ -95,7 +95,6 @@ private :
std::vector<MsRunSp> _ms_run_list;
std::map<QString, ProteinMatch *> _cache_accession_protein_match;
- std::set<ProteinMatch *> _cache_already_added_protein_match;
};
#endif // IDENTIFICATIONGROUP_H
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index faba2b9a..c95a4d48 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -52,7 +52,7 @@ void PeptideMatch::setStart(unsigned int start) {
_start =start;
}
pappso::mz PeptideMatch::getDeltaMass() const {
- return (_exp_mass - _peptide_sp.get()->getMass());
+ return ((_exp_mass+pappso::MHPLUS) - _peptide_sp.get()->getMz(1));
}
unsigned int PeptideMatch::getStart() const {
return _start;
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 49c58b63..bd150ed5 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -72,7 +72,7 @@ public :
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
- /** @brief get delta between theoretical mass and experimental mass
+ /** @brief get delta between theoretical mhplus mass and mhplus experimental mass
*/
pappso::mz getDeltaMass() const;
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index 0f63fe24..001cb943 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -132,7 +132,7 @@ bool XtandemSaxHandler::startElement_group(QXmlAttributes attrs) {
_scan = attrs.value("id").toUInt();
_mhplus_obser = attrs.value("mh").toDouble();
_charge = attrs.value("z").toUInt();
- //_retention_time = attrs.value("rt");
+ _retention_time = attrs.value("rt").replace("PT","").replace("S","").toDouble();
}
return is_ok;
}
@@ -156,22 +156,16 @@ bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) {
//qDebug() << "startElement_protein begin";
QString accession = attributes.value("label").simplified().split(" ", QString::SkipEmptyParts).at(0);
//qDebug() << "startElement_protein accession" << accession;
- _p_protein_match = _p_identification_group->getProteinMatch(accession);
+ _p_protein_match = _p_identification_group->getProteinMatchInstance(accession);
//qDebug() << "startElement_protein p_protein_match 1 " << _p_protein_match;
_current_protein.setAccession(accession);
- if (_p_protein_match == nullptr) {
- _p_protein_match = new ProteinMatch();
- //qDebug() << "startElement_protein p_protein_match 2 " << _p_protein_match;
- _p_protein_match->setChecked(false);
-
- }
+ _p_protein_match->setChecked(false);
//qDebug() << "startElement_protein p_protein_match 3 " << _p_protein_match;
ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
_p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
_p_protein_match->setChecked(true);
- _p_identification_group->addProteinMatch(_p_protein_match);
//qDebug() << "startElement_protein end" ;
return is_ok;
}
@@ -247,7 +241,7 @@ bool XtandemSaxHandler::startElement_aa(QXmlAttributes attributes) {
}
bool XtandemSaxHandler::endElement_domain() {
- bool is_ok = true;
+ bool is_ok = true;
_current_peptide_sp = _p_project->getPeptideStore().getInstance(_current_peptide_sp);
_p_peptide_match->setPeptideXtpSp(_current_peptide_sp);
--
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