From a9ecf09d0ff051b6d665eaf31985e3096634a13d Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 16 Dec 2017 22:58:25 +0100
Subject: [PATCH] change in mass delta compute : a peptide evidence is only
counted once
---
src/core/identificationgroup.cpp | 4 ++--
src/core/proteinmatch.cpp | 10 ++++++----
src/core/proteinmatch.h | 6 +++++-
3 files changed, 13 insertions(+), 7 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index be027124b..ccc3f1ad0 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -209,11 +209,11 @@ std::size_t IdentificationGroup::countSubGroup()const {
}
void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
- std::set<PeptideEvidence *> already_counted;
+ std::set<const PeptideEvidence *> already_counted;
for (auto & p_protein_match : _protein_match_list) {
if (p_protein_match->getValidationState() >= state) {
if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) {
- p_protein_match->collectMhDelta(delta_list, unit, state);
+ p_protein_match->collectMhDelta(already_counted, delta_list, unit, state);
}
}
}
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 392ef2885..8d978579f 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -445,17 +445,19 @@ void ProteinMatch::setGroupInstance(GroupStore & group_store) {
}
-void ProteinMatch::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
+void ProteinMatch::collectMhDelta(std::set< const PeptideEvidence *> & already_counted, std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
for (auto & peptide_match : _peptide_match_list) {
- if (peptide_match.getPeptideEvidence()->getValidationState() >= state) {
- pappso::pappso_double diff = peptide_match.getPeptideEvidence()->getDeltaMass();
+ const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
+ if ((p_peptide_evidence->getValidationState() >= state)&&(already_counted.find(p_peptide_evidence) == already_counted.end())) {
+ pappso::pappso_double diff = p_peptide_evidence->getDeltaMass();
if (unit == pappso::PrecisionUnit::ppm) {
while (diff < -0.5) {
diff = diff + pappso::DIFFC12C13;
}
- diff = (diff / peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
+ diff = (diff / p_peptide_evidence->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
}
delta_list.push_back(diff);
+ already_counted.insert(p_peptide_evidence);
}
}
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index e397ea51a..aaee5c199 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -23,6 +23,7 @@
#include <QColor>
#include <vector>
+#include <set>
#include <pappsomspp/types.h>
#include "proteinxtp.h"
#include "peptidematch.h"
@@ -113,7 +114,10 @@ public:
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
- void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
+ /** @brief collect mass delta between theoretical mass and observed mass
+ * each peptide evidence is only counted once
+ */
+ void collectMhDelta(std::set<const PeptideEvidence *> & already_counted, std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
/** @brief count distinct sequence taking into account equivalence between Leucine and Isoleucine
* @param state validation state of peptides to count
--
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