From 9b3b8529f42fb72e8b6bbc8c6862d57dd3480191 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sun, 17 Dec 2017 13:57:45 +0100
Subject: [PATCH] refactoring
---
src/core/identificationgroup.cpp | 14 ++++++++++++--
src/core/identificationgroup.h | 4 ++++
src/core/proteinmatch.cpp | 16 ----------------
src/core/proteinmatch.h | 4 ----
4 files changed, 16 insertions(+), 22 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index b833fcf53..71c2ab936 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -231,14 +231,24 @@ std::size_t IdentificationGroup::countSubGroup()const {
}
void IdentificationGroup::collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const {
- std::set<const PeptideEvidence *> already_counted;
+ std::set<const PeptideEvidence *> peptide_evidence_list;
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(already_counted, delta_list, unit, state);
+ //p_protein_match->collectMhDelta(already_counted, delta_list, unit, state);
+ p_protein_match->collectPeptideEvidences(peptide_evidence_list, state);
}
}
}
+ for (const PeptideEvidence * p_peptide_evidence: peptide_evidence_list) {
+ if (unit == pappso::PrecisionUnit::ppm) {
+ delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
+ }
+ else {
+ delta_list.push_back(p_peptide_evidence->getDeltaMass());
+ }
+ }
+
}
void IdentificationGroup::startGrouping (const GroupingType & grouping_type, WorkMonitorInterface * p_work_monitor) {
qDebug() << "IdentificationGroup::startGrouping begin ";
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index fcd3e485f..bfb0d532d 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -126,6 +126,10 @@ public:
bool contains (const MsRun * p_msrun) const;
+
+ /** @brief collect mass delta between theoretical mass and observed mass
+ * each peptide evidence is only counted once
+ */
void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
private :
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 3d43d3d7b..ced11738b 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -445,22 +445,6 @@ void ProteinMatch::setGroupInstance(GroupStore & group_store) {
}
-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) {
- const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
- if ((p_peptide_evidence->getValidationState() >= state)&&(already_counted.find(p_peptide_evidence) == already_counted.end())) {
- if (unit == pappso::PrecisionUnit::ppm) {
- delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
- }
- else {
- delta_list.push_back(p_peptide_evidence->getDeltaMass());
- }
-
- already_counted.insert(p_peptide_evidence);
- }
- }
-}
-
void ProteinMatch::collectPeptideEvidences(std::set<const PeptideEvidence *> & peptide_evidence_set, ValidationState state) const {
for (auto & peptide_match : _peptide_match_list) {
const PeptideEvidence * p_peptide_evidence = peptide_match.getPeptideEvidence();
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 22c31745c..37ccefb7e 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -114,10 +114,6 @@ public:
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
- /** @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 collect distinct peptide evidences
*/
--
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