From b7c9c59ea34193b7306a2f469de59ca1c2fe9d62 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 20:43:46 +0200
Subject: [PATCH] FDR computation OK
---
src/core/identificationgroup.cpp | 55 ++++++++------------------------
src/core/peptidematch.cpp | 10 +++---
src/core/proteinmatch.cpp | 12 +++----
src/utils/types.h | 11 ++++---
4 files changed, 30 insertions(+), 58 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index df013590e..602d9cf02 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -54,34 +54,20 @@ unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state)
return i;
}
unsigned int IdentificationGroup::countDecoyProtein(ValidationState state) const {
- unsigned int i=0;
- for (auto & p_protein_match : _protein_match_list) {
- if (!p_protein_match->getProteinXtpSp().get()->isDecoy()) continue;
- if (state == ValidationState::grouped) {
- if (p_protein_match->isGrouped()) {
- i++;
- }
- }
- else if(state == ValidationState::valid) {
- if (p_protein_match->isValid()) {
- i++;
- }
-
+ return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
+ if ((p_protein_match->getProteinXtpSp().get()->isDecoy()) && (p_protein_match->getValidationState() >= state)) {
+ return true;
}
- else if (state == ValidationState::validAndChecked) {
- if (p_protein_match->isValidAndChecked()) {
- i++;
- }
-
+ else {
+ return false;
}
- }
- return i;
+ });
}
unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
unsigned int i=0;
for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->getValidationState() == state) {
+ if (p_protein_match->getValidationState() >= state) {
i+=p_protein_match->countPeptideMatch(state);
}
}
@@ -89,29 +75,14 @@ unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const
}
unsigned int IdentificationGroup::countProtein(ValidationState state) const {
- unsigned int i=0;
- if (state == ValidationState::grouped) {
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->isGrouped()) {
- i++;
- }
- }
- }
- else if(state == ValidationState::valid) {
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->isValid()) {
- i++;
- }
+ return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
+ if (p_protein_match->getValidationState() >= state) {
+ return true;
}
- }
- else if (state == ValidationState::validAndChecked) {
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->isValidAndChecked()) {
- i++;
- }
+ else {
+ return false;
}
- }
- return i;
+ });
}
void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 81706face..d38bad251 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -70,13 +70,13 @@ void PeptideMatch::setChecked(bool arg1) {
}
ValidationState PeptideMatch::getValidationState() const {
- if (isValid()) {
- return ValidationState::valid;
+ if (isGrouped()) {
+ return ValidationState::grouped;
} else if (isValidAndChecked()) {
return ValidationState::validAndChecked;
- } else if (isGrouped()) {
- return ValidationState::grouped;
- }
+ } else if (isValid()) {
+ return ValidationState::valid;
+ }
return ValidationState::notValid;
}
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 792634523..799f6ceca 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -44,13 +44,13 @@ ProteinMatch::~ProteinMatch()
}
}
ValidationState ProteinMatch::getValidationState() const {
- if (isValid()) {
- return ValidationState::valid;
+ if (isGrouped()) {
+ return ValidationState::grouped;
} else if (isValidAndChecked()) {
return ValidationState::validAndChecked;
- } else if (isGrouped()) {
- return ValidationState::grouped;
- }
+ } else if (isValid()) {
+ return ValidationState::valid;
+ }
return ValidationState::notValid;
}
bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
@@ -178,7 +178,7 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch * p_peptide_match) {
- if (p_peptide_match->getValidationState() == state) {
+ if (p_peptide_match->getValidationState() >= state) {
return true;
}
else {
diff --git a/src/utils/types.h b/src/utils/types.h
index c87465c67..19244ecd2 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -25,6 +25,7 @@
#ifndef _TYPES_H_
#define _TYPES_H_ 1
+#include <cstdint>
/*********** enumerations *********************************/
/** \def GroupingType list of available grouping algoritms
@@ -50,11 +51,11 @@ enum class MzFormat {
*
*/
-enum class ValidationState {
- notValid,///< notValid : automatic filter validation failed
- valid, ///< valid : automatic filter validation passed
- validAndChecked, ///< validAndChecked : automatic filter validation passed + manual checking
- grouped, ///< grouped : automatic filter validation passed + manual checking + grouped
+enum class ValidationState: std::int8_t {
+ notValid = 0,///< notValid : automatic filter validation failed
+ valid =1, ///< valid : automatic filter validation passed
+ validAndChecked=2, ///< validAndChecked : automatic filter validation passed + manual checking
+ grouped=3 ///< grouped : automatic filter validation passed + manual checking + grouped
};
--
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