From 26d3343c191f67087414a8392ce018acd237ffc7 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 23 Mar 2017 22:28:01 +0100
Subject: [PATCH] protein store and peptide store inside the project,
contaminant groups removed
---
src/CMakeLists.txt | 4 ++--
src/core/project.cpp | 10 +++++++++-
src/core/project.h | 9 ++++++++-
src/core/proteinmatch.cpp | 8 +++++++-
src/core/proteinxtp.cpp | 4 ++--
src/core/proteinxtp.h | 4 ++--
src/grouping/groupingexperiment.h | 1 +
src/grouping/groupingpeptidemass.cpp | 4 ++++
src/grouping/groupingpeptidemass.h | 2 ++
src/input/xpipsaxhandler.cpp | 8 ++++++--
src/input/xpipsaxhandler.h | 2 --
src/utils/proteinstore.cpp | 10 +++++++---
src/utils/proteinstore.h | 1 +
13 files changed, 51 insertions(+), 16 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9ddba1dee..d0ea825a9 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/project.cpp b/src/core/project.cpp
index f4a69901d..b5b3940dc 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -39,6 +39,14 @@ Project::~Project()
}
}
+PeptideStore & Project::getPeptideStore() {
+ return _peptide_store;
+}
+
+ProteinStore & Project::getProteinStore() {
+ return _protein_store;
+}
+
void Project::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
_automatic_filter_parameters = automatic_filter_parameters;
for (auto & p_id_group : _identification_goup_list) {
@@ -91,7 +99,7 @@ IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
void Project::startGrouping() {
- for (auto & p_id_group : _identification_goup_list) {
+ for (auto & p_id_group : _identification_goup_list) {
p_id_group->startGrouping(_grouping_type);
}
diff --git a/src/core/project.h b/src/core/project.h
index 5992dbf88..2e98fc3cf 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -26,7 +26,9 @@
#include<memory>
#include "identificationgroup.h"
#include "automaticfilterparameters.h"
-#include "utils/types.h"
+#include "../utils/types.h"
+#include "../utils/peptidestore.h"
+#include "../utils/proteinstore.h"
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -41,6 +43,8 @@ public:
~Project();
ProjectSp makeProjectSp() const;
+ ProteinStore & getProteinStore();
+ PeptideStore & getPeptideStore();
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
IdentificationGroup* getCurrentIdentificationGroupP() const;
@@ -58,6 +62,9 @@ private :
AutomaticFilterParameters _automatic_filter_parameters;
GroupingType _grouping_type = GroupingType::PeptideMass;
+
+ ProteinStore _protein_store;
+ PeptideStore _peptide_store;
};
#endif // PROJECT_H
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index b03473c2a..e750622d0 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -116,13 +116,19 @@ void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment)
_sp_grp_protein = nullptr;
if (isValidAndChecked()) {
_sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
-
+
for (auto & p_peptide_match : _peptide_match_list) {
p_peptide_match->setGrpPeptideSp(nullptr);
if (p_peptide_match->isValidAndChecked()) {
p_peptide_match->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match));
}
}
+
+
+ if (_protein_sp.get()->isContaminant()) {
+ p_grp_experiment->addPostGroupingGrpProteinSpRemoval(_sp_grp_protein);
+ }
+
}
}
diff --git a/src/core/proteinxtp.cpp b/src/core/proteinxtp.cpp
index 32cb090ad..ed3226324 100644
--- a/src/core/proteinxtp.cpp
+++ b/src/core/proteinxtp.cpp
@@ -55,9 +55,9 @@ ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
void ProteinXtp::setIsDecoy(bool conta){
_is_decoy = conta;
}
- bool ProteinXtp::getIsContaminant() const{
+ bool ProteinXtp::isContaminant() const{
return _is_contaminant;
}
- bool ProteinXtp::getIsDecoy() const{
+ bool ProteinXtp::isDecoy() const{
return _is_decoy;
}
diff --git a/src/core/proteinxtp.h b/src/core/proteinxtp.h
index 935dc282c..764266d3e 100644
--- a/src/core/proteinxtp.h
+++ b/src/core/proteinxtp.h
@@ -46,8 +46,8 @@ public:
void setIsContaminant(bool conta);
void setIsDecoy(bool conta);
- bool getIsContaminant() const;
- bool getIsDecoy() const;
+ bool isContaminant() const;
+ bool isDecoy() const;
private:
SequenceDatabase * _p_sequence_database;
diff --git a/src/grouping/groupingexperiment.h b/src/grouping/groupingexperiment.h
index e05d9e0f1..af56449df 100644
--- a/src/grouping/groupingexperiment.h
+++ b/src/grouping/groupingexperiment.h
@@ -41,6 +41,7 @@ public:
virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) = 0;
virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) = 0;
+ virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) = 0;
virtual void startGrouping()= 0;
};
diff --git a/src/grouping/groupingpeptidemass.cpp b/src/grouping/groupingpeptidemass.cpp
index 7dc382e8c..8368af9d7 100644
--- a/src/grouping/groupingpeptidemass.cpp
+++ b/src/grouping/groupingpeptidemass.cpp
@@ -50,3 +50,7 @@ pappso::GrpPeptideSp & GroupingPeptideMass::setGrpPeptide(pappso::GrpProteinSp p
void GroupingPeptideMass::startGrouping() {
_p_grp_experiment->startGrouping();
}
+
+void GroupingPeptideMass::addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) {
+ _p_grp_experiment->addPostGroupingGrpProteinSpRemoval(sp_protein);
+}
diff --git a/src/grouping/groupingpeptidemass.h b/src/grouping/groupingpeptidemass.h
index 2d585026c..2391bba35 100644
--- a/src/grouping/groupingpeptidemass.h
+++ b/src/grouping/groupingpeptidemass.h
@@ -34,6 +34,8 @@ public:
virtual pappso::GrpProteinSp & getGrpProteinSp(ProteinMatch* p_protein_match) override;
virtual pappso::GrpPeptideSp & setGrpPeptide(pappso::GrpProteinSp proteinSp, PeptideMatch* p_peptide_match) override;
+ virtual void addPostGroupingGrpProteinSpRemoval(pappso::GrpProteinSp sp_protein) override;
+
virtual void startGrouping() override;
protected :
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 719ebbd8e..921d4262a 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -24,6 +24,8 @@
#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/exception/exceptionnotfound.h>
#include <cmath>
+#include "../utils/peptidestore.h"
+#include "../utils/proteinstore.h"
XpipSaxHandler::XpipSaxHandler(Project * p_project):_p_project(p_project)
{
@@ -277,7 +279,7 @@ bool XpipSaxHandler::endElement_peptide() {
qDebug() << "endElement_peptide ";
pappso::PeptideSp peptide_const = pappso::Peptide(*(_current_peptide_sp.get())).makePeptideSp();
- peptide_const = _peptide_store.getInstance(peptide_const);
+ peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
_p_peptide_match->setPeptideSp(peptide_const);
return true;
}
@@ -292,7 +294,9 @@ bool XpipSaxHandler::endElement_sequence() {
return true;
}
bool XpipSaxHandler::endElement_protein() {
- _p_protein_match->setProteinXtpSp(_current_protein.makeProteinXtpSp());
+ ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
+
+ _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
return true;
}
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index 804a40c61..063d13d04 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -30,7 +30,6 @@
#include <pappsomspp/amino_acid/aamodification.h>
#include "../core/project.h"
#include "../core/proteinmatch.h"
-#include "../utils/peptidestore.h"
class XpipSaxHandler: public QXmlDefaultHandler
{
@@ -87,7 +86,6 @@ private:
pappso::NoConstPeptideSp _current_peptide_sp;
IdentificationGroup * _current_identification_group_p;
- PeptideStore _peptide_store;
QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
QMap<QString, pappso::MsRunIdSp> _map_msrunid;
};
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index d4d11d8ac..acb0a8763 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -28,13 +28,14 @@
******************************************************************************/
#include "proteinstore.h"
+#include <QDebug>
ProteinStore::ProteinStore()
{
-_regexp_contaminant.setPattern("([KR])([^P])");
+ _regexp_contaminant.setPattern("^conta\\|");
-_regexp_decoy.setPattern(".*\\|reversed$");
+ _regexp_decoy.setPattern(".*\\|reversed$");
}
ProteinStore::~ProteinStore()
@@ -45,7 +46,7 @@ ProteinStore::~ProteinStore()
ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
std::pair<std::map< QString, ProteinXtpSp>::iterator,bool> ret = _map_accession_protein_list.insert(std::pair<QString, ProteinXtpSp>(peptide_in.get()->getAccession(),peptide_in));
-
+
if (ret.second) {
setProteinInformations(ret.first->second);
}
@@ -54,11 +55,14 @@ ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
}
void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
+ qDebug() << "ProteinStore::setProteinInformations begin";
QString accession = peptide_in.get()->getAccession();
if (_regexp_contaminant.indexIn(accession, 0)>-1) {
+ qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
peptide_in.get()->setIsContaminant(true);
}
if (_regexp_decoy.indexIn(accession, 0)>-1) {
peptide_in.get()->setIsDecoy(true);
}
+ qDebug() << "ProteinStore::setProteinInformations end";
}
diff --git a/src/utils/proteinstore.h b/src/utils/proteinstore.h
index fb09cdf6d..14d7f1945 100644
--- a/src/utils/proteinstore.h
+++ b/src/utils/proteinstore.h
@@ -39,6 +39,7 @@
class ProteinStore
{
+public:
ProteinStore();
~ProteinStore();
--
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