From b25cf7c7c2bb8f9dc090598d9053491874f006e5 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 3 May 2018 15:59:21 +0200
Subject: [PATCH] no NSAF on overall msruns
---
src/core/identificationgroup.h | 4 ++--
src/core/proteinmatch.h | 8 ++++----
src/gui/protein_list_view/proteinlistwindow.cpp | 11 -----------
src/gui/protein_list_view/proteinlistwindow.h | 3 ---
src/gui/protein_list_view/proteintablemodel.cpp | 13 ++-----------
src/gui/protein_list_view/proteintablemodel.h | 1 -
6 files changed, 8 insertions(+), 32 deletions(-)
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 2e162785..eac9dd5f 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -57,9 +57,9 @@ public:
/** @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
+ * @param p_msrun_id pointer on the msrun to get NSAF.
* */
- pappso::pappso_double computeProtoNsafSum(const MsRun * p_msrun_id = nullptr) const;
+ pappso::pappso_double computeProtoNsafSum(const MsRun * p_msrun_id) const;
/** @brief count groups
* */
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 4b1bcebb..bb86106c 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -66,16 +66,16 @@ public:
/** @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
+ * @param p_msrun_id pointer on the msrun to get NSAF.
* */
- pappso::pappso_double getProtoNsaf(const MsRun * p_msrun_id = nullptr) const;
+ pappso::pappso_double getProtoNsaf(const MsRun * p_msrun_id) 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
+ * @param p_msrun_id pointer on the msrun to get NSAF
* */
- pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id = nullptr) const;
+ pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum, const MsRun * p_msrun_id) 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 d7c02cf4..e71b9ecd 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -272,9 +272,6 @@ 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();
}
@@ -350,11 +347,3 @@ 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 98a3e632..e5d1d9d7 100644
--- a/src/gui/protein_list_view/proteinlistwindow.h
+++ b/src/gui/protein_list_view/proteinlistwindow.h
@@ -98,8 +98,6 @@ protected :
void askProteinDetailView(ProteinMatch * p_protein_match);
void askPeptideListView(ProteinMatch * p_protein_match);
ProjectWindow * getProjectWindow();
- pappso::pappso_double getProtoNsafSum() const;
- void sumProtoNsaf();
@@ -112,7 +110,6 @@ 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 ee1dbfc6..efd5d1f6 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 15;
+ return 14;
}
return 0;
}
@@ -127,10 +127,7 @@ 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 "";
@@ -183,9 +180,6 @@ 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 "";
}
@@ -337,9 +331,6 @@ 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 04f37015..a3f10326 100644
--- a/src/gui/protein_list_view/proteintablemodel.h
+++ b/src/gui/protein_list_view/proteintablemodel.h
@@ -47,7 +47,6 @@ 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;
--
GitLab