From dd5989d8037d325ba394fd49f59a4ed2494b4c40 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 3 May 2018 15:33:50 +0200
Subject: [PATCH] first NSAF version
---
src/core/identificationgroup.cpp | 10 ++++++++++
src/core/identificationgroup.h | 6 ++++++
src/core/proteinmatch.cpp | 3 +++
src/core/proteinmatch.h | 12 ++++++++++--
src/gui/protein_list_view/proteinlistwindow.cpp | 11 +++++++++++
src/gui/protein_list_view/proteinlistwindow.h | 3 +++
src/gui/protein_list_view/proteintablemodel.cpp | 11 ++++++++++-
src/gui/protein_list_view/proteintablemodel.h | 1 +
8 files changed, 54 insertions(+), 3 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 82ab9dd3..666e75c8 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -48,6 +48,16 @@ const GroupStore & IdentificationGroup::getGroupStore() const {
return _group_store;
}
+pappso::pappso_double IdentificationGroup::computeProtoNsafSum(const MsRun * p_msrun_id ) const {
+ pappso::pappso_double nsaf_sum = 0;
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->getValidationState() >= ValidationState::grouped) {
+ nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id);
+ }
+ }
+ return nsaf_sum;
+}
+
unsigned int IdentificationGroup::countPeptideMass(ValidationState state) const {
std::vector<pappso::GrpPeptide *> count_peptide_mass;
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 110d7d9a..2e162785 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -54,6 +54,12 @@ public:
void addIdentificationDataSourceP(IdentificationDataSource * p_identification_source);
const PtmGroupingExperiment * getPtmGroupingExperiment() const;
+
+ /** @brief compute proto NSAF sum within msrun
+ * Warning: this is not NSAF, just a part
+ * @param p_msrun_id pointer on the msrun to get NSAF. if not defined, NSAF is computed overall msruns
+ * */
+ pappso::pappso_double computeProtoNsafSum(const MsRun * p_msrun_id = nullptr) const;
/** @brief count groups
* */
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 093d6585..cf3ba339 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -325,6 +325,9 @@ pappso::pappso_double ProteinMatch::getLogEvalue(const MsRun * sp_msrun_id) cons
return (evalue_prot);
}
+pappso::pappso_double ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id) const {
+ return (getProtoNsaf(p_msrun_id)/proto_nsaf_sum);
+}
pappso::pappso_double ProteinMatch::getProtoNsaf(const MsRun * sp_msrun_id) const {
try {
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index a9e41967..4b1bcebb 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -64,10 +64,18 @@ public:
**/
const QString getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate = nullptr) const;
- /** @brief compute proto NSAF within sample
+ /** @brief compute proto NSAF within msrun
* Warning: this is not NSAF, just a part
+ * @param p_msrun_id pointer on the msrun to get NSAF. if not defined, NSAF is computed overall msruns
* */
- pappso::pappso_double getProtoNsaf(const MsRun * sp_msrun_id = nullptr) const;
+ pappso::pappso_double getProtoNsaf(const MsRun * p_msrun_id = nullptr) const;
+
+ /** @brief compute NSAF within msrun
+ * Warning: this is not NSAF, just a part
+ * @param proto_nsaf_sum the sum of proto nsaf of all proteins within the msrun
+ * @param p_msrun_id pointer on the msrun to get NSAF. if not defined, NSAF is computed overall msruns
+ * */
+ pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id = nullptr) const;
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index e71b9ecd..d7c02cf4 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -272,6 +272,9 @@ void ProteinListWindow::doIdentificationGroupGrouped(IdentificationGroup * p_ide
if (_p_identification_group == p_identification_group) {
//_protein_table_model_p->setIdentificationGroup(p_identification_group);
//_p_proxy_model->setSourceModel(_protein_table_model_p);
+ //if(getProteinListColumnDisplay) {
+ sumProtoNsaf();
+ //}
emit proteinDataChanged();
}
@@ -347,3 +350,11 @@ void ProteinListWindow::resizeColumnsToContents() {
ProjectWindow * ProteinListWindow::getProjectWindow() {
return _project_window;
}
+
+
+ pappso::pappso_double ProteinListWindow::getProtoNsafSum() const {
+ return _sum_proto_nsaf;
+ }
+ void ProteinListWindow::sumProtoNsaf() {
+ _sum_proto_nsaf = _p_identification_group->computeProtoNsafSum();
+ }
diff --git a/src/gui/protein_list_view/proteinlistwindow.h b/src/gui/protein_list_view/proteinlistwindow.h
index e5d1d9d7..98a3e632 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -98,6 +98,8 @@ protected :
void askProteinDetailView(ProteinMatch * p_protein_match);
void askPeptideListView(ProteinMatch * p_protein_match);
ProjectWindow * getProjectWindow();
+ pappso::pappso_double getProtoNsafSum() const;
+ void sumProtoNsaf();
@@ -110,6 +112,7 @@ private:
QMenu * _p_context_menu = nullptr;
bool _display_evalue = true;
bool _display_accession = true;
+ pappso::pappso_double _sum_proto_nsaf;
};
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index a6e3cd24..ee1dbfc6 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -65,7 +65,7 @@ int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
//qDebug() << "ProteinTableModel::columnCount begin ";
if (_p_identification_group != nullptr) {
- return 14;
+ return 15;
}
return 0;
}
@@ -127,6 +127,10 @@ const QString ProteinTableModel::getTitle(std::int8_t column) {
case (std::int8_t) ProteinListColumn::molecular_weight:
return "MW";
break;
+
+ case (std::int8_t) ProteinListColumn::nsaf:
+ return "NSAF";
+ break;
}
return "";
@@ -180,6 +184,8 @@ const QString ProteinTableModel::getDescription(std::int8_t column) {
case (std::int8_t) ProteinListColumn::molecular_weight:
return "protein molecular weight in Dalton";
+ case (std::int8_t) ProteinListColumn::nsaf:
+ return "NSAF";
}
return "";
}
@@ -331,6 +337,9 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
if (col == (std::int8_t) ProteinListColumn::molecular_weight ) {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getProteinXtpSp().get()->getMass());
}
+ if (col == (std::int8_t) ProteinListColumn::nsaf ) {
+ return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getNsaf(_p_protein_list_window->getProtoNsafSum()));
+ }
return QVariant();
}
return QVariant();
diff --git a/src/gui/protein_list_view/proteintablemodel.h b/src/gui/protein_list_view/proteintablemodel.h
index a3f10326..04f37015 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -47,6 +47,7 @@ enum class ProteinListColumn: std::int8_t {
molecular_weight=11, ///< protein molecular weight in Dalton
pai=12, ///< PAI
empai=13, ///< emPAI
+ nsaf=14, ///< NSAF
};
class ProteinListWindow;
--
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