From 97e01aecb469c206efe5aba6aa5da3657ad77a0e Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sat, 6 May 2017 21:44:48 +0200
Subject: [PATCH] log10 evalue on protein
---
src/core/proteinmatch.cpp | 8 ++++++--
src/core/proteinmatch.h | 4 ++++
src/gui/protein_view/proteinwindow.cpp | 2 +-
3 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 233d8b06..ec243cca 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -266,6 +266,10 @@ unsigned int ProteinMatch::countPeptideMassCharge(ValidationState state, const M
}
pappso::pappso_double ProteinMatch::getEvalue(const MsRun * sp_msrun_id) const {
+ return (std::pow ((double) 10.0,getLogEvalue(sp_msrun_id)));
+}
+
+pappso::pappso_double ProteinMatch::getLogEvalue(const MsRun * sp_msrun_id) const {
std::map<QString, pappso::pappso_double> map_sequence_evalue;
for (auto & p_peptide_match : _peptide_match_list) {
if (p_peptide_match->isValidAndChecked()) {
@@ -296,8 +300,8 @@ pappso::pappso_double ProteinMatch::getEvalue(const MsRun * sp_msrun_id) const {
pappso::pappso_double evalue_prot = 1;
for (auto && peptide_pair: map_sequence_evalue) {
- //evalue_prot += std::log10(peptide_pair.second);
- evalue_prot *= peptide_pair.second;
+ evalue_prot += std::log10(peptide_pair.second);
+ //evalue_prot *= peptide_pair.second;
}
//return (std::pow ((double) 10.0,evalue_prot));
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index f239bf50..687ff075 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -44,6 +44,10 @@ public:
~ProteinMatch();
const ProteinXtpSp & getProteinXtpSp() const;
+
+ /** @brief compute protein log10(Evalue) within samples
+ * */
+ pappso::pappso_double getLogEvalue(const MsRun * sp_msrun_id = nullptr) const;
/** @brief compute protein Evalue within samples
* */
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 2788a4ab..faafebfb 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -80,7 +80,7 @@ void ProteinWindow::updateDisplay() {
ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
ui->coverage_label->setText(QString("%1 %").arg(_p_protein_match->getCoverage()*100));
ui->mw_label->setText(QString("%1 kDa").arg(_p_protein_match->getProteinXtpSp().get()->getMass()/1000));
- ui->evalue_label->setText(QString("%1 (log10: %2)").arg(_p_protein_match->getEvalue()).arg(std::log10(_p_protein_match->getEvalue())));
+ ui->evalue_label->setText(QString("%1 (log10: %2)").arg(_p_protein_match->getEvalue()).arg(_p_protein_match->getLogEvalue()));
}
catch (pappso::PappsoException exception_pappso) {
QMessageBox::warning(this,
--
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