diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 2e1627856c49e97be7b8f31aae9ffa053b4a40ae..eac9dd5fa7e572b8bea424846dbe18b0755e76f7 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 4b1bcebbf4d770eeac710a3ab106388e98c7a308..bb86106c84a6219c59ffb7db545adc19ebd7d821 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 d7c02cf41537ed3d044e57472b50aaed261a1cd6..e71b9ecd24e37a61304bde62ab347616f397672b 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 98a3e63250cfe3eac27deb880ada6847203b54a4..e5d1d9d7163ebf27993b51e103bf703bf67bb721 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 ee1dbfc6194358dc73caedc745029496d07f8277..efd5d1f62a417553f2f1f6e6e3505a5a3ef272af 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 04f37015cb0587433c1899ae7d5fb51239101b05..a3f103260b31cb002f89ab043ae3e69519d17543 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;