From ee09dcc411581af643a48e69a7273dc2e38507a1 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 18 Oct 2018 21:36:02 +0200
Subject: [PATCH] NSAF indice handles labeling methods
---
src/core/identificationgroup.cpp | 26 ++++++++------
src/core/identificationgroup.h | 10 ++++--
src/core/proteinmatch.cpp | 21 ++++++-----
src/core/proteinmatch.h | 9 +++--
src/output/ods/comparspectrasheet.cpp | 50 ++++++++++++++++++++-------
src/output/ods/comparspectrasheet.h | 2 +-
6 files changed, 80 insertions(+), 38 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 1f805b5e6..5063f0bfb 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -55,14 +55,15 @@ IdentificationGroup::getGroupStore() const
}
pappso::pappso_double
-IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id) const
+IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id,
+ const Label *p_label) const
{
pappso::pappso_double nsaf_sum = 0;
for(auto &p_protein_match : _protein_match_list)
{
if(p_protein_match->getValidationState() >= ValidationState::grouped)
{
- nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id);
+ nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id, p_label);
}
}
return nsaf_sum;
@@ -130,7 +131,8 @@ unsigned int
IdentificationGroup::countDecoyProteinMatch(ValidationState state) const
{
return std::count_if(
- _protein_match_list.begin(), _protein_match_list.end(),
+ _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))
@@ -209,7 +211,8 @@ IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const
unsigned int
IdentificationGroup::countProteinMatch(ValidationState state) const
{
- return std::count_if(_protein_match_list.begin(), _protein_match_list.end(),
+ return std::count_if(_protein_match_list.begin(),
+ _protein_match_list.end(),
[state](const ProteinMatch *p_protein_match) {
if(p_protein_match->getValidationState() >= state)
{
@@ -302,8 +305,8 @@ IdentificationGroup::addIdentificationDataSourceP(
IdentificationDataSource *p_identification_source)
{
addMsRunSp(p_identification_source->getMsRunSp());
- auto it = std::find(_id_source_list.begin(), _id_source_list.end(),
- p_identification_source);
+ auto it = std::find(
+ _id_source_list.begin(), _id_source_list.end(), p_identification_source);
if(it == _id_source_list.end())
{
_id_source_list.push_back(p_identification_source);
@@ -353,7 +356,8 @@ IdentificationGroup::countSubGroup() const
void
IdentificationGroup::collectMhDelta(
- std::vector<pappso::pappso_double> &delta_list, pappso::PrecisionUnit unit,
+ std::vector<pappso::pappso_double> &delta_list,
+ pappso::PrecisionUnit unit,
ValidationState state) const
{
std::set<const PeptideEvidence *> peptide_evidence_list;
@@ -466,7 +470,9 @@ IdentificationGroup::getProteinFdr(ValidationState state) const
void
IdentificationGroup::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
{
if(!contains(p_msrun))
return;
@@ -475,8 +481,8 @@ IdentificationGroup::getSameXicPeptideEvidenceList(
if(p_msrun == p_identification_source->getMsRunSp().get())
{
p_identification_source->getPeptideEvidenceStore()
- .getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun,
- p_peptide, charge);
+ .getSameXicPeptideEvidenceList(
+ peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 43e03e2bd..7ec739ac5 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -62,7 +62,9 @@ class IdentificationGroup
* Warning: this is not NSAF, just a part
* @param p_msrun_id pointer on the msrun to get NSAF.
* */
- pappso::pappso_double computeProtoNsafSum(const MsRun *p_msrun_id) const;
+ pappso::pappso_double
+ computeProtoNsafSum(const MsRun *p_msrun_id,
+ const Label *p_label = nullptr) const;
/** @brief count groups
* */
@@ -152,7 +154,8 @@ class IdentificationGroup
* each peptide evidence is only counted once
*/
void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
- pappso::PrecisionUnit unit, ValidationState state) const;
+ pappso::PrecisionUnit unit,
+ ValidationState state) const;
/** @brief look for a peptide in the same XIC
@@ -163,7 +166,8 @@ class IdentificationGroup
*/
void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
unsigned int charge) const;
private:
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 343155ed6..64149784c 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -434,8 +434,10 @@ ProteinMatch::countPeptideMassCharge(ValidationState state,
{
if(p_label != nullptr)
{
- if(peptide_match.getPeptideEvidence()->getPeptideXtpSp().get()->getLabel() ==
- p_label)
+ if(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getLabel() == p_label)
{
sequence_list.insert(
QString("%1-%2-%3")
@@ -559,7 +561,8 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const
}
pappso::pappso_double
ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
- const MsRun *p_msrun_id) const
+ const MsRun *p_msrun_id,
+ const Label *p_label) const
{
if(proto_nsaf_sum == 0)
{
@@ -568,11 +571,11 @@ ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
"Error computing NSAF for protein %1 :\nproto_nsaf_sum is null")
.arg(this->getProteinXtpSp().get()->getAccession()));
}
- return (getProtoNsaf(p_msrun_id) / proto_nsaf_sum);
+ return (getProtoNsaf(p_msrun_id, p_label) / proto_nsaf_sum);
}
pappso::pappso_double
-ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
+ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id, const Label *p_label) const
{
try
{
@@ -582,8 +585,8 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
QObject::tr("protein has no amino acid sequence"));
}
pappso::pappso_double proto_nsaf =
- (pappso::pappso_double)countSampleScan(ValidationState::validAndChecked,
- sp_msrun_id) /
+ (pappso::pappso_double)countSampleScan(
+ ValidationState::validAndChecked, sp_msrun_id, p_label) /
(pappso::pappso_double)_protein_sp.get()->size();
return proto_nsaf;
}
@@ -617,11 +620,11 @@ ProteinMatch::getPAI(const MsRun *sp_msrun_id, const Label *p_label) const
}
pappso::pappso_double
-ProteinMatch::getEmPAI(const MsRun *sp_msrun_id) const
+ProteinMatch::getEmPAI(const MsRun *sp_msrun_id, const Label *p_label) const
{
// compute emPAI, Ishihama 2005
pappso::pappso_double value =
- std::pow(10.0, getPAI(sp_msrun_id)) - (pappso::pappso_double)1.0;
+ std::pow(10.0, getPAI(sp_msrun_id, p_label)) - (pappso::pappso_double)1.0;
return value;
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index e99e2ef5f..33ff923c7 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -72,7 +72,8 @@ class ProteinMatch
* Warning: this is not NSAF, just a part
* @param p_msrun_id pointer on the msrun to get NSAF.
* */
- pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id) const;
+ pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id,
+ const Label *p_label = nullptr) const;
/** @brief compute NSAF within msrun : normalized spectral abundance factor
* (NSAF) Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing
@@ -84,7 +85,8 @@ class ProteinMatch
* @param p_msrun_id pointer on the msrun to get NSAF
* */
pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum,
- const MsRun *p_msrun_id) const;
+ const MsRun *p_msrun_id,
+ const Label *p_label = nullptr) const;
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
@@ -95,7 +97,8 @@ class ProteinMatch
/** @brief compute emPAI within sample
* Ishihama 2005
* */
- pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr) const;
+ pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr,
+ const Label *p_label = nullptr) const;
void setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(const PeptideMatch &peptide_match);
diff --git a/src/output/ods/comparspectrasheet.cpp b/src/output/ods/comparspectrasheet.cpp
index b2fe6ae6f..b9ee4cc32 100644
--- a/src/output/ods/comparspectrasheet.cpp
+++ b/src/output/ods/comparspectrasheet.cpp
@@ -110,7 +110,7 @@ ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label)
{
qDebug() << "ComparEmpaiSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
+ _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun, p_label));
qDebug() << "ComparEmpaiSheet::writeComparValue end";
}
@@ -130,21 +130,47 @@ ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
{
qDebug() << "ComparNsafSheet::writeComparValue begin";
pappso::pappso_double proto_nsaf_sum = 0;
- std::pair<std::map<const MsRun *, pappso::pappso_double>::iterator, bool>
- ret = _map_proto_nsaf_sum_by_msrun.insert(
- std::pair<const MsRun *, pappso::pappso_double>(p_msrun, 0));
- if(ret.second == false)
+
+ if(_label_list.size() > 0)
{
- //"element 'z' already existed";
- proto_nsaf_sum = ret.first->second;
+ std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
+ _map_proto_nsaf_sum_by_msrun.insert(
+ std::pair<QString, pappso::pappso_double>(
+ QString("%1--%2").arg(p_msrun->getXmlId()).arg(p_label->getXmlId()),
+ 0));
+ if(ret.second == false)
+ {
+ //"element 'z' already existed";
+ proto_nsaf_sum = ret.first->second;
+ }
+ else
+ {
+ proto_nsaf_sum = _p_current_identification_group->computeProtoNsafSum(
+ p_msrun, p_label);
+ ret.first->second = proto_nsaf_sum;
+ }
+
+ _p_writer->writeCell(
+ p_protein_match->getNsaf(proto_nsaf_sum, p_msrun, p_label));
}
else
{
- proto_nsaf_sum =
- _p_current_identification_group->computeProtoNsafSum(p_msrun);
- ret.first->second = proto_nsaf_sum;
+ std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
+ _map_proto_nsaf_sum_by_msrun.insert(
+ std::pair<QString, pappso::pappso_double>(p_msrun->getXmlId(), 0));
+ if(ret.second == false)
+ {
+ //"element 'z' already existed";
+ proto_nsaf_sum = ret.first->second;
+ }
+ else
+ {
+ proto_nsaf_sum =
+ _p_current_identification_group->computeProtoNsafSum(p_msrun);
+ ret.first->second = proto_nsaf_sum;
+ }
+
+ _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
}
-
- _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
qDebug() << "ComparNsafSheet::writeComparValue end";
}
diff --git a/src/output/ods/comparspectrasheet.h b/src/output/ods/comparspectrasheet.h
index 737af6c1e..d129f71f7 100644
--- a/src/output/ods/comparspectrasheet.h
+++ b/src/output/ods/comparspectrasheet.h
@@ -104,7 +104,7 @@ class ComparNsafSheet : public ComparBaseSheet
const Label *p_label = nullptr) override;
private:
- std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
+ std::map<QString, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
};
#endif // COMPARSPECTRASHEET_H
--
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