From 11b044ef970faed3d4279f332b7ea8752498895b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 27 Jan 2018 14:19:46 +0100
Subject: [PATCH] look for peptide evidence in Msrun
---
src/core/identificationgroup.cpp | 8 ++++----
src/core/identificationgroup.h | 6 ++++--
src/core/project.cpp | 4 ++--
src/core/project.h | 6 ++++--
src/gui/xic_view/xic_box/xicbox.cpp | 6 ++++--
src/utils/peptideevidencestore.cpp | 8 ++++----
src/utils/peptideevidencestore.h | 8 ++++++--
7 files changed, 28 insertions(+), 18 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 267c9e895..9825c9f18 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -321,11 +321,11 @@ pappso::pappso_double IdentificationGroup::getProteinFdr(ValidationState state)
}
-void IdentificationGroup::getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const {
- if (!contains(p_peptide_evidence->getMsRunP())) return;
+void IdentificationGroup::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
+ if (!contains(p_msrun)) return;
for (const IdentificationDataSource * p_identification_source:_id_source_list) {
- if (p_peptide_evidence->getMsRunP() == p_identification_source->getMsRunSp().get()) {
- p_identification_source->getPeptideEvidenceStore().getSameXicPeptideEvidenceList(p_peptide_evidence, peptide_evidence_list);
+ if (p_msrun == p_identification_source->getMsRunSp().get()) {
+ p_identification_source->getPeptideEvidenceStore().getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index ea4ade657..110d7d9af 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -135,10 +135,12 @@ public:
/** @brief look for a peptide in the same XIC
- * @param p_peptide_evidence the peptide to look for
* @param peptide_evidence_list the peptide evidence list to build
+ * @param p_msrun MSrun to look for
+ * @param p_peptide peptide to look for
+ * @param charge charge to look for
*/
- void getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const;
+ void getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const;
private :
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 1bd84997c..9beaae9a6 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -201,8 +201,8 @@ bool Project::hasPtmExperiment() const {
return false;
}
-void Project::getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const {
+void Project::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
for (const IdentificationGroup * p_ident_group: _identification_goup_list) {
- p_ident_group->getSameXicPeptideEvidenceList(p_peptide_evidence, peptide_evidence_list);
+ p_ident_group->getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
diff --git a/src/core/project.h b/src/core/project.h
index b21d48385..3710b3d3e 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -88,10 +88,12 @@ public:
bool hasPtmExperiment() const;
/** @brief look for a peptide in the same XIC
- * @param p_peptide_evidence the peptide to look for
* @param peptide_evidence_list the peptide evidence list to build
+ * @param p_msrun MSrun to look for
+ * @param p_peptide peptide to look for
+ * @param charge charge to look for
*/
- void getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const;
+ void getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const;
private :
LabelingMethodSp _labeling_method_sp;
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 6abf1eaae..8f7dd617c 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -167,14 +167,14 @@ void XicBox::setPeptideEvidence(const PeptideEvidence * p_peptide_evidence) {
//get same xic peptide evidence (msrun, peptide, charge)
//p_projet
_peptide_evidence_list.clear();
- _p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence, _peptide_evidence_list);
+ _p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(_peptide_evidence_list, _msrun_sp.get(),_p_peptide_evidence->getPeptideXtpSp().get(),_p_peptide_evidence->getCharge());
emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(), _p_peptide_evidence->getCharge(), _p_xic_window->getXicExtractPrecision(), 0.8);
}
void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp) {
- _p_peptide_evidence = p_peptide_evidence;
+ _p_peptide_evidence = p_peptide_evidence;
_msrun_sp = msrun_sp;
ui->peptide_label->setText(_p_peptide_evidence->getPeptideXtpSp().get()->toString());
@@ -185,6 +185,8 @@ void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidenc
//get same xic peptide evidence (msrun, peptide, charge)
//p_projet
_peptide_evidence_list.clear();
+
+ _p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(_peptide_evidence_list, _msrun_sp.get(),_p_peptide_evidence->getPeptideXtpSp().get(),_p_peptide_evidence->getCharge());
//_p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence, _peptide_evidence_list);
emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(), _p_peptide_evidence->getCharge(), _p_xic_window->getXicExtractPrecision(), 0.8);
diff --git a/src/utils/peptideevidencestore.cpp b/src/utils/peptideevidencestore.cpp
index 28b2928f6..c6ab7295f 100644
--- a/src/utils/peptideevidencestore.cpp
+++ b/src/utils/peptideevidencestore.cpp
@@ -95,11 +95,11 @@ const std::vector<std::shared_ptr<PeptideEvidence>> & PeptideEvidenceStore::getP
}
-void PeptideEvidenceStore::getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const {
+void PeptideEvidenceStore::getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const {
for (const PeptideEvidenceSp & peptide_evidence_sp:_peptide_evidence_list) {
- if (p_peptide_evidence->getMsRunP() != peptide_evidence_sp.get()->getMsRunP()) continue;
- if (p_peptide_evidence->getPeptideXtpSp().get() != peptide_evidence_sp.get()->getPeptideXtpSp().get()) continue;
- if (p_peptide_evidence->getCharge() != peptide_evidence_sp.get()->getCharge()) continue;
+ if (p_msrun != peptide_evidence_sp.get()->getMsRunP()) continue;
+ else if (p_peptide != peptide_evidence_sp.get()->getPeptideXtpSp().get()) continue;
+ else if (charge != peptide_evidence_sp.get()->getCharge()) continue;
peptide_evidence_list.push_back(peptide_evidence_sp.get());
}
}
diff --git a/src/utils/peptideevidencestore.h b/src/utils/peptideevidencestore.h
index c1d4ff894..1ae1889c3 100644
--- a/src/utils/peptideevidencestore.h
+++ b/src/utils/peptideevidencestore.h
@@ -35,6 +35,8 @@
#include <vector>
#include <map>
#include "../core/automaticfilterparameters.h"
+#include "../core/peptidextp.h"
+#include "../core/msrun.h"
class PeptideEvidence;
@@ -56,10 +58,12 @@ public:
/** @brief look for a peptide in the same XIC
- * @param p_peptide_evidence the peptide to look for
* @param peptide_evidence_list the peptide evidence list to build
+ * @param p_msrun MSrun to look for
+ * @param p_peptide peptide to look for
+ * @param charge charge to look for
*/
- void getSameXicPeptideEvidenceList(const PeptideEvidence * p_peptide_evidence, std::vector<const PeptideEvidence *> & peptide_evidence_list) const;
+ void getSameXicPeptideEvidenceList(std::vector<const PeptideEvidence *> & peptide_evidence_list, const MsRun * p_msrun, const PeptideXtp * p_peptide, unsigned int charge) const;
private:
std::vector<std::shared_ptr<PeptideEvidence>> _peptide_evidence_list;
--
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