From 7e5372d2b776ea8469581b617efce23ff6456f10 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 21:30:24 +0200
Subject: [PATCH] count factorisation
---
src/core/identificationgroup.cpp | 34 ++-----------------
src/core/identificationgroup.h | 16 ++-------
src/core/proteinmatch.cpp | 15 ++------
src/core/proteinmatch.h | 9 +----
src/grouping/groupinggroup.cpp | 4 +--
.../identificationgroupwidget.cpp | 2 +-
src/gui/project_view/projectwindow.cpp | 4 +--
.../protein_list_view/proteinlistwindow.cpp | 2 +-
.../protein_list_view/proteintablemodel.cpp | 4 +--
9 files changed, 15 insertions(+), 75 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 602d9cf02..40646661d 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -53,7 +53,7 @@ unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state)
}
return i;
}
-unsigned int IdentificationGroup::countDecoyProtein(ValidationState state) const {
+unsigned int IdentificationGroup::countDecoyProteinMatch(ValidationState state) const {
return std::count_if (_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)) {
return true;
@@ -74,7 +74,7 @@ unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const
return i;
}
-unsigned int IdentificationGroup::countProtein(ValidationState state) const {
+unsigned int IdentificationGroup::countProteinMatch(ValidationState state) const {
return std::count_if (_protein_match_list.begin(), _protein_match_list.end(), [state](const ProteinMatch * p_protein_match) {
if (p_protein_match->getValidationState() >= state) {
return true;
@@ -134,36 +134,6 @@ std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
return _protein_match_list;
}
-size_t IdentificationGroup::countGrouped()const {
- size_t i=0;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->isGrouped()) {
- i++;
- }
- }
- return i;
-}
-
-size_t IdentificationGroup::countValidAndChecked()const {
- size_t i=0;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->isValidAndChecked()) {
- i++;
- }
- }
- return i;
-}
-
-size_t IdentificationGroup::countValid()const {
- size_t i=0;
- for (auto & p_protein_match : _protein_match_list) {
- if (p_protein_match->isValid()) {
- i++;
- }
- }
- return i;
-}
-
std::size_t IdentificationGroup::countGroup()const {
return _group_store.countGroup();
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 3eaf8565c..9726a01be 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -48,18 +48,6 @@ public:
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
void addMsRunSp(MsRunSp ms_run_sp);
-
- /** @brief count valid proteins
- * */
- std::size_t countValid()const;
-
- /** @brief count valid and manually checked proteins
- * */
- std::size_t countValidAndChecked()const;
-
- /** @brief count grouped proteins
- * */
- std::size_t countGrouped()const;
/** @brief count groups
* */
@@ -71,10 +59,10 @@ public:
/** @brief count proteins
* */
- unsigned int countProtein(ValidationState state) const;
+ unsigned int countProteinMatch(ValidationState state) const;
/** @brief count decoy proteins
* */
- unsigned int countDecoyProtein(ValidationState state) const;
+ unsigned int countDecoyProteinMatch(ValidationState state) const;
/** @brief count peptide match
* */
unsigned int countPeptideMatch(ValidationState state) const;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 799f6ceca..9f097e0f0 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -187,21 +187,10 @@ unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
});
}
-size_t ProteinMatch::countValidSpectrum()const {
- return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * p_peptide_match) {
- return (p_peptide_match->isValid());
- });
-}
-
-size_t ProteinMatch::countValidAndCheckedSpectrum()const {
- return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * p_peptide_match) {
- return (p_peptide_match->isValidAndChecked());
- });
-}
-size_t ProteinMatch::countUniqueSequence()const {
+size_t ProteinMatch::countUniqueSequence(ValidationState state)const {
std::set<QString> sequence_list;
for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->isValidAndChecked()) {
+ if (p_peptide_match->getValidationState() >= state) {
sequence_list.insert(p_peptide_match->getPeptideXtpSp().get()->getSequence());
}
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index b2501074d..35685e991 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -78,16 +78,9 @@ public:
ValidationState getValidationState() const;
unsigned int countPeptideMatch(ValidationState state) const;
- /** @brief count valid spectrums
- * */
- size_t countValidSpectrum()const;
-
- /** @brief count valid and manually checked spectrums
- * */
- size_t countValidAndCheckedSpectrum()const;
/** @brief count unique identified sequences (from valid and cheked spectrums)
* */
- size_t countUniqueSequence()const;
+ size_t countUniqueSequence(ValidationState state)const;
const pappso::GrpProteinSp & getGrpProteinSp() const;
diff --git a/src/grouping/groupinggroup.cpp b/src/grouping/groupinggroup.cpp
index 7dd05b0af..b27c25706 100644
--- a/src/grouping/groupinggroup.cpp
+++ b/src/grouping/groupinggroup.cpp
@@ -83,7 +83,7 @@ unsigned int GroupingGroup::countSubgroupPresence(const PeptideMatch * p_peptide
std::size_t GroupingGroup::countSpecificSpectrum(const ProteinMatch * p_protein_match) const {
if (_number_of_subgroup == 1) {
- return p_protein_match->countValidAndCheckedSpectrum();
+ return p_protein_match->countPeptideMatch(ValidationState::validAndChecked);
}
std::set<QString> spectrum_list_in;
for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
@@ -111,7 +111,7 @@ std::size_t GroupingGroup::countSpecificSpectrum(const ProteinMatch * p_protein_
std::size_t GroupingGroup::countSpecificSequence(const ProteinMatch * p_protein_match) const {
if (_number_of_subgroup == 1) {
- return p_protein_match->countUniqueSequence();
+ return p_protein_match->countUniqueSequence(ValidationState::validAndChecked);
}
std::set<QString> sequence_list_in;
for (auto && p_peptide_match :p_protein_match->getPeptideMatchList()) {
diff --git a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
index 8fb21db15..df8ff2f8d 100644
--- a/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
+++ b/src/gui/project_view/identification_group_widget/identificationgroupwidget.cpp
@@ -68,6 +68,6 @@ void IdentificationGroupWidget::doIdentificationGroupGrouped(IdentificationGroup
ui->group_number_display->setText(QString("%1").arg(_p_identification_group->countGroup()));
ui->subgroup_number_display->setText(QString("%1").arg(_p_identification_group->countSubGroup()));
- ui->protein_number_display->setText(QString("%1").arg(_p_identification_group->countGrouped()));
+ ui->protein_number_display->setText(QString("%1").arg(_p_identification_group->countProteinMatch(ValidationState::grouped)));
}
}
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index f9c63fed0..5311738fe 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -142,8 +142,8 @@ void ProjectWindow::computeFdr(ValidationState state) {
pappso::pappso_double total_prot=0;
pappso::pappso_double false_prot=0;
for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
- total_prot += identification_group->countProtein(state);
- false_prot += identification_group->countDecoyProtein(state);
+ total_prot += identification_group->countProteinMatch(state);
+ false_prot += identification_group->countDecoyProteinMatch(state);
}
ui->protein_fdr_label->setText(QString("%1 %").arg(false_prot/total_prot));
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 0392a9296..8515a4d98 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -227,7 +227,7 @@ void ProteinListWindow::updateStatusBar() {
if (_p_identification_group == nullptr) {
}
else {
- ui->statusbar->showMessage(tr("proteins %1 valid, %2 checked, %3 displayed").arg(_p_identification_group->countValid()).arg(_p_identification_group->countValidAndChecked()).arg(_p_proxy_model->rowCount()));
+ ui->statusbar->showMessage(tr("proteins %1 valid, %2 checked, %3 displayed").arg(_p_identification_group->countProteinMatch(ValidationState::valid)).arg(_p_identification_group->countProteinMatch(ValidationState::validAndChecked)).arg(_p_proxy_model->rowCount()));
}
}
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 85b9831b8..904fa910d 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -170,7 +170,7 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getEvalue());
}
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::spectrum ) {
- return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countValidAndCheckedSpectrum());
+ return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countPeptideMatch(ValidationState::validAndChecked));
}
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::specific_spectrum ) {
@@ -181,7 +181,7 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
}
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::sequence ) {
- return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countUniqueSequence());
+ return QVariant ((qreal) _p_identification_group->getProteinMatchList().at(row)->countUniqueSequence(ValidationState::validAndChecked));
}
if (_column_assignment[col] == (std::int8_t) ProteinListColumn::specific_sequence ) {
GroupingGroup * p_groupin_group = _p_identification_group->getProteinMatchList().at(row)->getGroupingGroupSp().get();
--
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