From 444110bc04ff28aae47843526fd4ab39b2ee57b1 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 30 Oct 2018 21:52:42 +0100
Subject: [PATCH] write FDR in ODS file as percentage, compute peptide FDR on
all proteins
---
src/core/identificationgroup.cpp | 19 +++++++++----------
src/output/ods/groupingsheet.cpp | 4 ++--
2 files changed, 11 insertions(+), 12 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 3b9029ed4..b1e394a11 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -93,11 +93,10 @@ IdentificationGroup::countPeptideMassSample(ValidationState state) const
std::vector<std::size_t> count_peptide_mass_sample;
for(auto &p_protein_match : _protein_match_list)
{
- if(p_protein_match->getValidationState() >= state)
- {
- p_protein_match->countPeptideMassSample(count_peptide_mass_sample,
- state);
- }
+ // if(p_protein_match->getValidationState() >= state)
+ // {
+ p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+ // }
}
std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
auto last = std::unique(count_peptide_mass_sample.begin(),
@@ -113,11 +112,11 @@ IdentificationGroup::countDecoyPeptideMassSample(ValidationState state) const
{
if(p_protein_match->getProteinXtpSp().get()->isDecoy())
{
- if(p_protein_match->getValidationState() >= state)
- {
- p_protein_match->countPeptideMassSample(count_peptide_mass_sample,
- state);
- }
+ // if(p_protein_match->getValidationState() >= state)
+ // {
+ p_protein_match->countPeptideMassSample(count_peptide_mass_sample,
+ state);
+ //}
}
}
std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
diff --git a/src/output/ods/groupingsheet.cpp b/src/output/ods/groupingsheet.cpp
index 4b7d3095a..156bcacd6 100644
--- a/src/output/ods/groupingsheet.cpp
+++ b/src/output/ods/groupingsheet.cpp
@@ -73,8 +73,8 @@ GroupingSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
//_p_writer->writeCell(p_ident->countSequence(ValidationState::grouped));
_p_writer->writeCell(
p_ident->countPeptideMassSample(ValidationState::grouped));
- _p_writer->writeCell(p_ident->getProteinFdr(ValidationState::valid));
- _p_writer->writeCell(p_ident->getPeptideMassFdr(ValidationState::valid));
+ _p_writer->writeCellPercentage(p_ident->getProteinFdr(ValidationState::valid));
+ _p_writer->writeCellPercentage(p_ident->getPeptideMassFdr(ValidationState::valid));
}
--
GitLab