From acea4912f301251793f0bd208721f780997c5477 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 3 May 2018 12:04:11 +0200
Subject: [PATCH] WIP: compute NSAF
---
src/core/proteinmatch.cpp | 11 +++++++++++
src/core/proteinmatch.h | 5 +++++
2 files changed, 16 insertions(+)
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 2ffadd6fd..093d6585d 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -326,6 +326,17 @@ pappso::pappso_double ProteinMatch::getLogEvalue(const MsRun * sp_msrun_id) cons
}
+pappso::pappso_double ProteinMatch::getProtoNsaf(const MsRun * sp_msrun_id) const {
+ try {
+ pappso::pappso_double proto_nsaf = (pappso::pappso_double) countSampleScan(ValidationState::validAndChecked ,sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->size();
+ return proto_nsaf;
+
+ }
+ catch (pappso::PappsoException error) {
+ throw pappso::PappsoException(QObject::tr("Error computing proto NSAF for protein %1 :\n%2").arg(this->getProteinXtpSp().get()->getAccession()).arg(error.qwhat()));
+ }
+}
+
pappso::pappso_double ProteinMatch::getPAI(const MsRun * sp_msrun_id) const {
try {
pappso::pappso_double PAI = (pappso::pappso_double) countPeptideMassCharge(ValidationState::validAndChecked ,sp_msrun_id) / (pappso::pappso_double) _protein_sp.get()->countTrypticPeptidesForPAI();
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 2104a7120..a9e419670 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -64,6 +64,11 @@ public:
**/
const QString getHtmlSequence(PeptideEvidence * peptide_evidence_to_locate = nullptr) const;
+ /** @brief compute proto NSAF within sample
+ * Warning: this is not NSAF, just a part
+ * */
+ pappso::pappso_double getProtoNsaf(const MsRun * sp_msrun_id = nullptr) const;
+
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
* */
--
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