From 51144af49ba87b59c4f49a569dd2379e9019bbae Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sun, 17 Dec 2017 09:07:33 +0100
Subject: [PATCH] new function to get mass delta in ppm
---
src/core/peptideevidence.cpp | 11 ++++++++++-
src/core/peptideevidence.h | 5 +++++
src/core/proteinmatch.cpp | 11 +++++------
3 files changed, 20 insertions(+), 7 deletions(-)
diff --git a/src/core/peptideevidence.cpp b/src/core/peptideevidence.cpp
index 2ca7d6b3e..748513258 100644
--- a/src/core/peptideevidence.cpp
+++ b/src/core/peptideevidence.cpp
@@ -52,7 +52,7 @@ PeptideEvidence::PeptideEvidence(const PeptideEvidence & other): PeptideEvidence
_params = other._params;
_checked = other._checked;
_proxy_valid = other._proxy_valid;
-
+
}
PeptideEvidenceSp PeptideEvidence::makePeptideEvidenceSp() const {
@@ -117,6 +117,15 @@ void PeptideEvidence::setExperimentalMass(pappso::pappso_double exp_mass) {
pappso::mz PeptideEvidence::getDeltaMass() const {
return (_peptide_sp.get()->getMz(1) - (_exp_mass+pappso::MHPLUS));
}
+pappso::mz PeptideEvidence::getPpmDeltaMass() const {
+ //return (_peptide_sp.get()->getMz(1) - (_exp_mass+pappso::MHPLUS));
+ pappso::pappso_double diff = getDeltaMass();
+ while (diff < -0.5) {
+ diff = diff + pappso::DIFFC12C13;
+ }
+ diff = (diff / getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
+ return diff;
+}
void PeptideEvidence::setCharge(unsigned int charge) {
_charge =charge;
}
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index 89f1771b6..ff8cfc925 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -113,6 +113,11 @@ public :
* theoretical mhplus mass - mhplus experimental mass
*/
pappso::mz getDeltaMass() const;
+
+ /** @brief get delta in ppm between theoretical mhplus mass and mhplus experimental mass
+ * theoretical mhplus mass - mhplus experimental mass
+ */
+ pappso::mz getPpmDeltaMass() const;
ValidationState getValidationState() const;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 7fb0b3e6a..3d43d3d7b 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -449,14 +449,13 @@ void ProteinMatch::collectMhDelta(std::set< const PeptideEvidence *> & already_c
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())) {
- pappso::pappso_double diff = p_peptide_evidence->getDeltaMass();
if (unit == pappso::PrecisionUnit::ppm) {
- while (diff < -0.5) {
- diff = diff + pappso::DIFFC12C13;
- }
- diff = (diff / p_peptide_evidence->getPeptideXtpSp().get()->getMz(1)) * pappso::ONEMILLION;
+ delta_list.push_back(p_peptide_evidence->getPpmDeltaMass());
+ }
+ else {
+ delta_list.push_back(p_peptide_evidence->getDeltaMass());
}
- delta_list.push_back(diff);
+
already_counted.insert(p_peptide_evidence);
}
}
--
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