From 7ff56874254bcba663bc231fbca9513eb433ef9d Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sat, 7 Nov 2020 19:33:19 +0100
Subject: [PATCH] new function to collect mass delta for any kind of sequence
hit (target or decoy)
---
src/core/identificationgroup.cpp | 30 ++++++++++++++++++++++++++++++
src/core/identificationgroup.h | 23 +++++++++++++++++++++--
2 files changed, 51 insertions(+), 2 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 6f21a31e..2be63cef 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -385,6 +385,36 @@ IdentificationGroup::collectMhDelta(
}
}
}
+
+
+void
+IdentificationGroup::collectTargetDecoyMhDelta(
+ std::vector<pappso::pappso_double> &delta_list,
+ pappso::PrecisionUnit unit,
+ ValidationState state) const
+{
+ std::set<const PeptideEvidence *> peptide_evidence_list;
+ for(auto &p_protein_match : _protein_match_list)
+ {
+ if(p_protein_match->getValidationState() == 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(
ContaminantRemovalMode contaminantRemovalMode,
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 35bd50db..8a285a5b 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -157,14 +157,33 @@ class IdentificationGroup
bool containSample(const QString &sample) const;
- /** @brief collect mass delta between theoretical mass and observed mass
- * each peptide evidence is only counted once
+ /** @brief collect mass delta between theoretical mass and observed mass for
+ * target sequences
+ *
+ * each peptide evidence is only counted once it counts only
+ * peptide evidence for target Sequences
+ * @param delta_list list of mass delta
+ * @param unit precision unit, ppm or dalton
+ * @param state validation state of the peptides to collect
*/
void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
pappso::PrecisionUnit unit,
ValidationState state) const;
+ /** @brief collect mass delta between theoretical mass and observed mass
+ *
+ * each peptide evidence is only counted once it counts target or decoy
+ * peptide evidence
+ * @param delta_list list of mass delta
+ * @param unit precision unit, ppm or dalton
+ * @param state validation state of the peptides to collect
+ */
+ void collectTargetDecoyMhDelta(std::vector<pappso::pappso_double> &delta_list,
+ pappso::PrecisionUnit unit,
+ ValidationState state) const;
+
+
/** @brief look for a peptide in the same XIC
* @param peptide_evidence_list the peptide evidence list to build
* @param p_msrun MSrun to look for
--
GitLab