From 35f50c953a41201e072f87cd33e36a24f582896d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 9 Apr 2017 07:42:05 +0200
Subject: [PATCH] new group functions
---
src/core/identificationgroup.cpp | 4 ++++
src/core/identificationgroup.h | 1 +
src/grouping/groupinggroup.cpp | 5 +++++
src/grouping/groupinggroup.h | 5 +++++
src/output/masschroqml.cpp | 22 ++++++++++++++++------
src/output/masschroqml.h | 2 ++
src/utils/groupstore.cpp | 3 +++
src/utils/groupstore.h | 2 ++
8 files changed, 38 insertions(+), 6 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 2bb1162f6..c66ab899c 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -42,6 +42,10 @@ IdentificationGroup::~IdentificationGroup()
}
+ const GroupStore & IdentificationGroup::getGroupStore() const {
+ return _group_store;
+ }
+
unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
unsigned int i=0;
for (auto & p_protein_match : _protein_match_list) {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 74ba6ab90..ee430508a 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -45,6 +45,7 @@ public:
~IdentificationGroup();
ProteinMatch * getProteinMatchInstance(const QString accession);
+ const GroupStore & getGroupStore() const;
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
void addMsRunSp(MsRunSp ms_run_sp);
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index f5da520f6..8c13cad3d 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -137,6 +137,11 @@ std::size_t GroupingGroup::countSpecificSequence(const ProteinMatch * p_protein_
return count;
}
+
+ QString GroupingGroup::getProteinGroupingIdOfSubgroup(unsigned int subgroup_number) const {
+ return QString("%1%2a1").arg(pappso::Utils::getLexicalOrderedString(_group_number)).arg(pappso::Utils::getLexicalOrderedString(subgroup_number));
+ }
+
void GroupingGroup::add(const ProteinMatch * p_protein_match) {
_group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
if (p_protein_match->getGrpProteinSp().get()->getRank() == 1) {
diff --git a/src/grouping/groupinggroup.h b/src/grouping/groupinggroup.h
index 5d740da7e..a84980b9a 100644
--- a/src/grouping/groupinggroup.h
+++ b/src/grouping/groupinggroup.h
@@ -57,6 +57,11 @@ public:
* */
const QStringList getSubgroupIdList(const PeptideMatch * p_peptide_match) const;
+ /** @brief give the protein group id of the representant of a subgroup
+ * */
+ QString getProteinGroupingIdOfSubgroup(unsigned int subgroup_number) const;
+
+
const std::vector<std::pair<unsigned int, const PeptideMatch *>> & getPairSgNumberPeptideMatchList() const;
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index b60f05983..49f5186d9 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -339,23 +339,33 @@ void MassChroQml::writeIsotopeLabelList() {
void MassChroQml::writePeptideList() {
//<peptide_list>
_output_stream->writeStartElement("peptide_list");
+ const std::map<unsigned int, GroupingGroupSp> & group_store = _p_identification_group->getGroupStore().getGroupMap();
+
+ for (auto & group_pair :group_store) {
+ writePeptideListInGroup(group_pair.second.get());
+ }
+}
+
+void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
+
+ const std::vector<std::pair<unsigned int, const PeptideMatch *>> & sg_peptide_match_list = p_group->getPairSgNumberPeptideMatchList();
std::vector<McqPeptide> mcq_peptide_list;
- for (ProteinMatch * p_protein_match :_p_identification_group->getProteinMatchList()) {
- if (!p_protein_match->isGrouped()) continue;
- for (PeptideMatch * peptide_match :p_protein_match->getPeptideMatchList()) {
- if (!peptide_match->isGrouped()) continue;
+
+ for (auto & sg_peptide_pair :sg_peptide_match_list) {
+ unsigned int sg_number = sg_peptide_pair.first;
+ const PeptideMatch * peptide_match = sg_peptide_pair.second;
McqPeptide mcq_peptide;
mcq_peptide.id = peptide_match->getGrpPeptideSp().get()->getGroupingId();
mcq_peptide.mods << peptide_match->getPeptideXtpSp().get()->getModifString();
- mcq_peptide.prot_ids << p_protein_match->getGrpProteinSp().get()->getGroupingId();
+ mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(sg_number);
mcq_peptide.seq = peptide_match->getPeptideXtpSp().get()->getSequence();
mcq_peptide.native_peptide = peptide_match->getPeptideXtpSp().get()->getNativePeptideP();
mcq_peptide.data.push_back(peptide_match->getMsRunP()->getXmlId());
mcq_peptide.scan.push_back(peptide_match->getScan());
mcq_peptide.charge.push_back(peptide_match->getCharge());
mcq_peptide_list.push_back(mcq_peptide);
- }
+
}
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index ff291ffc0..8eeeb559f 100644
--- a/src/output/masschroqml.h
+++ b/src/output/masschroqml.h
@@ -48,12 +48,14 @@ private:
void writeGroups();
void writeProteinList();
void writePeptideList();
+ void writePeptideListInGroup(const GroupingGroup * p_group);
void writeIsotopeLabelList();
void writeAlignments();
void writeQuantificationMethods();
void writeQuantificationResults();
void writeQuantificationTraces();
void writeQuantify();
+
private :
QFile * _output_file;
QXmlStreamWriter * _output_stream;
diff --git a/src/utils/groupstore.cpp b/src/utils/groupstore.cpp
index 17c46e71f..6371c5fc2 100644
--- a/src/utils/groupstore.cpp
+++ b/src/utils/groupstore.cpp
@@ -57,6 +57,9 @@ std::size_t GroupStore::countSubGroup() const {
return count;
}
+ const std::map<unsigned int, GroupingGroupSp> & GroupStore::getGroupMap() const {
+ return _map_group;
+ }
GroupingGroupSp GroupStore::getInstance(unsigned int group_number) {
diff --git a/src/utils/groupstore.h b/src/utils/groupstore.h
index 7ed6182cf..98db1ce54 100644
--- a/src/utils/groupstore.h
+++ b/src/utils/groupstore.h
@@ -41,6 +41,8 @@ public:
GroupStore();
~GroupStore();
GroupingGroupSp getInstance(unsigned int group_number);
+ const std::map<unsigned int, GroupingGroupSp> & getGroupMap() const;
+
void clear();
std::size_t countGroup() const;
std::size_t countSubGroup() const;
--
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