From cd76de95cd7483c2872fa511acbfee6e41425d70 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Sun, 23 Apr 2017 23:08:51 +0200
Subject: [PATCH] new peptide counting method : peptide+mass+sample
---
src/core/identificationgroup.cpp | 35 ++++++++++++++++----
src/core/identificationgroup.h | 46 +++++++++++++++-----------
src/core/peptidematch.cpp | 4 +++
src/core/peptidematch.h | 1 +
src/core/proteinmatch.cpp | 9 +++++
src/core/proteinmatch.h | 4 +++
src/gui/project_view/project_view.ui | 5 ++-
src/gui/project_view/projectwindow.cpp | 8 +++--
8 files changed, 82 insertions(+), 30 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index d0334bb28..3e98431bd 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -42,17 +42,40 @@ IdentificationGroup::~IdentificationGroup()
}
- const GroupStore & IdentificationGroup::getGroupStore() const {
- return _group_store;
+const GroupStore & IdentificationGroup::getGroupStore() const {
+ return _group_store;
+}
+
+unsigned int IdentificationGroup::countPeptideMassSample(ValidationState state) const {
+ std::vector<std::size_t> count_peptide_mass_sample;
+ for (auto & p_protein_match : _protein_match_list) {
+ p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+ }
+ std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
+ auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
+ return std::distance(count_peptide_mass_sample.begin(),last);
+}
+
+unsigned int IdentificationGroup::countDecoyPeptideMassSample(ValidationState state) const {
+ std::vector<std::size_t> count_peptide_mass_sample;
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
+ p_protein_match->countPeptideMassSample(count_peptide_mass_sample, state);
+ }
}
+ std::sort(count_peptide_mass_sample.begin(), count_peptide_mass_sample.end());
+ auto last = std::unique(count_peptide_mass_sample.begin(),count_peptide_mass_sample.end());
+ return std::distance(count_peptide_mass_sample.begin(),last);
+}
+
unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
unsigned int i=0;
for (auto & p_protein_match : _protein_match_list) {
//if (p_protein_match->getValidationState() == state) {
- if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
- i+=p_protein_match->countPeptideMatch(state);
- }
+ if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
+ i+=p_protein_match->countPeptideMatch(state);
+ }
//}
}
return i;
@@ -72,7 +95,7 @@ unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const
unsigned int i=0;
for (auto & p_protein_match : _protein_match_list) {
//if (p_protein_match->getValidationState() >= state) {
- i+=p_protein_match->countPeptideMatch(state);
+ i+=p_protein_match->countPeptideMatch(state);
//}
}
return i;
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index ee430508a..e8393d41d 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -50,54 +50,60 @@ public:
std::vector<ProteinMatch *> & getProteinMatchList();
void addMsRunSp(MsRunSp ms_run_sp);
- /** @brief count groups
- * */
+ /** @brief count groups
+ * */
std::size_t countGroup()const;
- /** @brief count subgroups
- * */
+ /** @brief count subgroups
+ * */
std::size_t countSubGroup()const;
-
+
/** @brief count proteins
- * */
+ * */
unsigned int countProteinMatch(ValidationState state) const;
/** @brief count decoy proteins
- * */
- unsigned int countDecoyProteinMatch(ValidationState state) const;
- /** @brief count peptide match
- * */
+ * */
+ unsigned int countDecoyProteinMatch(ValidationState state) const;
+ /** @brief count peptide match (peptide spectrum match + protein match)
+ * */
unsigned int countPeptideMatch(ValidationState state) const;
/** @brief count decoy peptide match
- * */
+ * */
unsigned int countDecoyPeptideMatch(ValidationState state) const;
+ /** @brief count peptide (peptide+mass+sample)
+ * */
+ unsigned int countPeptideMassSample(ValidationState state) const;
+ /** @brief count peptide (peptide+mass+sample) included by decoy proteins
+ * */
+ unsigned int countDecoyPeptideMassSample(ValidationState state) const;
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
+
void startGrouping (const GroupingType & grouping_type);
-
- const std::vector<MsRunSp> & getMsRunSpList() const;
-
+
+ const std::vector<MsRunSp> & getMsRunSpList() const;
+
/** @brief get tab name for qtabwidget
- * */
+ * */
const QString getTabName() const;
-
+
bool contains (const MsRun * p_msrun) const;
-
+
void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
private :
GroupingExperiment * _p_grp_experiment= nullptr;
Project * _p_project;
-
+
GroupStore _group_store;
std::vector<ProteinMatch *> _protein_match_list;
std::vector<MsRunSp> _ms_run_list;
-
+
std::map<QString, ProteinMatch *> _cache_accession_protein_match;
};
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 5761314c3..05085bd33 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -47,6 +47,10 @@ void PeptideMatch::setEvalue(pappso::pappso_double evalue) {
}
+std::size_t PeptideMatch::getHashPeptideMassSample() const {
+ return PeptideMatch::_hash_fn (QString("%1 %2").arg(_peptide_sp.get()->getLiAbsoluteString()).arg(_msrunid_sp->getXmlId()).toStdString());
+}
+
std::size_t PeptideMatch::getHashSampleScan() const {
return _hash_sample_scan;
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 6d885f715..42bcbabfe 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -36,6 +36,7 @@ class PeptideMatch
public :
PeptideMatch(MsRun * msrunid_sp, unsigned int scan);
std::size_t getHashSampleScan() const;
+ std::size_t getHashPeptideMassSample() const;
void setRetentionTime(pappso::pappso_double rt);
void setEvalue(pappso::pappso_double evalue);
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index d44f1fe72..07c97cf88 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -176,6 +176,15 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
}
+void ProteinMatch::countPeptideMassSample(std::vector<size_t> & count_peptide_mass_sample, ValidationState state) const {
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match->getValidationState() >= state) {
+ count_peptide_mass_sample.push_back(p_peptide_match->getHashPeptideMassSample());
+ }
+ }
+}
+
+
unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch * p_peptide_match) {
if (p_peptide_match->getValidationState() >= state) {
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index fb125d15d..c1cf06876 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -77,6 +77,10 @@ public:
ValidationState getValidationState() const;
unsigned int countPeptideMatch(ValidationState state) const;
+
+ /** @brief count peptide (peptide+mass+sample)
+ */
+ void countPeptideMassSample(std::vector<size_t> & count_peptide_mass_sample, ValidationState state) const;
/** @brief count unique identified sequences (from valid and cheked spectrums)
* */
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index f45e0bde2..9313cbdae 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -24,7 +24,7 @@
<string/>
</property>
<property name="currentIndex">
- <number>2</number>
+ <number>0</number>
</property>
<widget class="QWidget" name="identifications">
<attribute name="title">
@@ -52,6 +52,9 @@
<string>Contaminants</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_6">
+ <item>
+ <widget class="QListView" name="contaminant_database_listview"/>
+ </item>
<item>
<widget class="QLineEdit" name="contaminant_protein_regexp_line_edit">
<property name="placeholderText">
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 780eaa948..29e125688 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -45,6 +45,7 @@ ProjectWindow::ProjectWindow(MainWindow *parent):
_p_fasta_str_li = new QStandardItemModel();
ui->decoy_database_listview->setModel(_p_fasta_str_li);
+ ui->contaminant_database_listview->setModel(_p_fasta_str_li);
_p_automatic_filter_widget = new AutomaticFilterWidget(this);
ui->filter_parameter_layout->addWidget(_p_automatic_filter_widget);
@@ -153,8 +154,10 @@ void ProjectWindow::computeFdr() {
for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
total_prot += identification_group->countProteinMatch(state);
false_prot += identification_group->countDecoyProteinMatch(state);
- total_peptide += identification_group->countPeptideMatch(state);
- false_peptide += identification_group->countDecoyPeptideMatch(state);
+ //total_peptide += identification_group->countPeptideMatch(state);
+ //false_peptide += identification_group->countDecoyPeptideMatch(state);
+ total_peptide += identification_group->countPeptideMassSample(state);
+ false_peptide += identification_group->countDecoyPeptideMassSample(state);
}
ui->protein_fdr_label->setText(QString("%1 %").arg(QString::number((false_prot/total_prot)*100.0,'f',10)));
ui->peptide_fdr_label->setText(QString("%1 %").arg(QString::number((false_peptide/total_peptide)*100.0,'f',10)));
@@ -353,7 +356,6 @@ void ProjectWindow::setProjectSp(ProjectSp project_sp) {
qDebug() << "ProjectWindow::setProjectSp begin " << _project_sp.get()->getFastaFileStore().getFastaFileList().size() ;
_fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
-
for (FastaFileSp fasta_file : _fastafile_list ) {
QStandardItem *item;
--
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