From 77693a1a2ec81ebe9e368aca4e2a923bd31ab819 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 21 Mar 2017 12:06:58 +0100
Subject: [PATCH] valid and checked design
---
src/CMakeLists.txt | 3 +-
src/core/identificationgroup.cpp | 7 ++--
src/core/identificationgroup.h | 6 +--
src/core/peptidematch.cpp | 17 ++++++++
src/core/peptidematch.h | 8 ++++
src/core/project.cpp | 21 +++-------
src/core/project.h | 16 +-------
src/core/proteinmatch.cpp | 41 +++++++++++++++++++
src/core/proteinmatch.h | 9 ++++
.../peptide_list_view/peptidetablemodel.cpp | 2 +-
.../protein_list_view/proteintablemodel.cpp | 2 +-
src/input/xpipsaxhandler.cpp | 11 ++---
src/input/xpipsaxhandler.h | 1 +
13 files changed, 101 insertions(+), 43 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ade8d7f8f..21b70805f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -53,9 +53,10 @@ configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/c
# File list
SET(CPP_FILES
+ core/automaticfilterparameters.cpp
core/identificationgroup.cpp
core/peptidematch.cpp
- core/project.cpp
+ ./core/project.cpp
core/proteinmatch.cpp
core/identification_sources/identificationdatasource.cpp
core/identification_sources/identificationxtandemfile.cpp
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index f251e0bb2..3a7cea893 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -38,11 +38,12 @@ IdentificationGroup::~IdentificationGroup()
}
}
-bool IdentificationGroup::isValid(ProteinMatch* p_protein_match) const {
- return _p_project->isValid(p_protein_match);
+void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+ for (auto & p_protein_match : _protein_match_list) {
+ p_protein_match->updateAutomaticFilters(automatic_filter_parameters);
+ }
}
-
void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
_protein_match_list.push_back(protein_match);
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 71d591286..dc448a6d7 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -47,9 +47,9 @@ public:
void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
- /** @brief is it valid regarding threshold and project rules
- */
- bool isValid(ProteinMatch* p_protein_match) const;
+ /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+ * */
+ void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
pappso::GrpExperiment * _p_grp_experiment= nullptr;
private :
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index 75c753f69..718d2e025 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -28,6 +28,13 @@ PeptideMatch::PeptideMatch(pappso::MsRunIdSp msrunid_sp, unsigned int scan) {
_scan = scan;
}
+void PeptideMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+ _proxy_valid = false;
+
+ if (_evalue <= automatic_filter_parameters.getFilterPeptideEvalue()) {
+ _proxy_valid = true;
+ }
+}
void PeptideMatch::setRetentionTime(pappso::pappso_double rt) {
_rt = rt;
}
@@ -56,10 +63,16 @@ void PeptideMatch::setChecked(bool arg1) {
_checked = arg1;
}
+bool PeptideMatch::isValid() const {
+ return _proxy_valid;
+}
bool PeptideMatch::isChecked() const {
return _checked;
}
+bool PeptideMatch::isValidAndChecked() const{
+ return _proxy_valid && _checked;
+}
void PeptideMatch::setIdentificationDataSource(IdentificationDataSource* identification_source) {
_p_identification_source = identification_source;
}
@@ -79,3 +92,7 @@ unsigned int PeptideMatch::getCharge() const {
pappso::PeptideSp PeptideMatch::getPeptideSp() const {
return _peptide_sp;
}
+
+const pappso::MsRunIdSp & PeptideMatch::getMsRunIdSp() const {
+ return _msrunid_sp;
+}
\ No newline at end of file
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index 92b42b92d..8d8f26641 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -27,6 +27,7 @@
#include <pappsomspp/types.h>
#include <pappsomspp/peptide/peptide.h>
#include "identification_sources/identificationdatasource.h"
+#include "automaticfilterparameters.h"
class PeptideMatch
{
@@ -42,7 +43,10 @@ public :
void setIdentificationDataSource(IdentificationDataSource* identification_source);
void setChecked(bool arg1);
bool isChecked() const;
+ bool isValid() const;
+ bool isValidAndChecked() const;
+ const pappso::MsRunIdSp & getMsRunIdSp() const;
IdentificationDataSource* getIdentificationDataSource () const;
unsigned int getScan() const;
pappso::pappso_double getRetentionTime() const;
@@ -50,6 +54,10 @@ public :
pappso::PeptideSp getPeptideSp() const;
pappso::pappso_double getEvalue() const;
+ /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+ * */
+ void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+
private :
pappso::MsRunIdSp _msrunid_sp;
unsigned int _scan;
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 4cdc329c1..3e6a0955d 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -39,7 +39,12 @@ Project::~Project()
}
}
-void Project::updateAutomaticFilters() {
+void Project::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+ _automatic_filter_parameters = automatic_filter_parameters;
+ for (auto & p_id_group : _identification_goup_list) {
+ p_id_group->updateAutomaticFilters(_automatic_filter_parameters);
+ }
+
}
ProjectSp Project::makeProjectSp() const {
return std::make_shared<Project>(*this);
@@ -83,17 +88,3 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
return _p_current_identification_group;
}
-
-bool Project::isValid(PeptideMatch* p_peptide_match) const {
- if (p_peptide_match->getEvalue() > _filter_minimum_peptide_evalue) {
- return false;
- }
- return true;
-}
-
-bool Project::isValid(ProteinMatch* p_protein_match) const {
- if (p_protein_match->getEvalue() > _filter_minimum_protein_evalue) {
- return false;
- }
- return true;
-}
diff --git a/src/core/project.h b/src/core/project.h
index b97e74130..b5ddcdf6a 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -33,9 +33,8 @@ typedef std::shared_ptr<Project> ProjectSp;
class PeptideMatch;
class ProteinMatch;
-class Project : public QObject
+class Project
{
- Q_OBJECT
public:
Project();
~Project();
@@ -44,22 +43,11 @@ public:
void readXpipFile(QFileInfo xpip_source);
IdentificationGroup* newIdentificationGroup();
IdentificationGroup* getCurrentIdentificationGroupP() const;
- /** @brief is it valid regarding threshold and project rules
- */
- bool isValid(PeptideMatch* p_peptide_match) const;
- /** @brief is it valid regarding threshold and project rules
- */
- bool isValid(ProteinMatch* p_protein_match) const;
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
- signals:
- /** @brief signal when automatic filters are applied and project is ready
- * */
- void projectReady();
-
+
private :
std::vector<IdentificationGroup *> _identification_goup_list;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index fb14cd1b4..f72acb9d2 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -22,6 +22,7 @@
******************************************************************************/
#include "proteinmatch.h"
+#include <pappsomspp/msrun/msrunid.h>
ProteinMatch::ProteinMatch()
@@ -38,6 +39,37 @@ ProteinMatch::~ProteinMatch()
}
}
+void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters) {
+ _proxy_valid = false;
+ unsigned int _number_of_valid_peptides =0;
+ std::map<const pappso::MsRunId*, unsigned int> _count_per_msrun;
+ bool cross_sample = automatic_filter_parameters.getFilterCrossSamplePeptideNumber();
+
+ for (auto & p_peptide_match : _peptide_match_list) {
+ p_peptide_match->updateAutomaticFilters(automatic_filter_parameters);
+ //count valid and checked peptides :
+ if (p_peptide_match->isValidAndChecked()) {
+ if (cross_sample) {
+ _number_of_valid_peptides++;
+ }
+ else {
+ std::pair<std::map<const pappso::MsRunId*, unsigned int>::iterator,bool> ret = _count_per_msrun.insert(std::pair<const pappso::MsRunId*, unsigned int>(p_peptide_match->getMsRunIdSp().get(),0));
+ ret.first->second +=1;
+ if (ret.first->second > _number_of_valid_peptides) {
+ _number_of_valid_peptides = ret.first->second;
+ }
+ }
+ }
+ }
+
+
+ if (_number_of_valid_peptides >= automatic_filter_parameters.getFilterMinimumPeptidePerMatch()) {
+ if (_evalue <= automatic_filter_parameters.getFilterProteinEvalue()) {
+ _proxy_valid = true;
+ }
+ }
+}
+
const pappso::ProteinSp & ProteinMatch::getProteinSp() const {
return _protein_sp;
}
@@ -52,9 +84,18 @@ void ProteinMatch::setProteinSp(pappso::ProteinSp protein_sp) {
_protein_sp = protein_sp;
}
+
+bool ProteinMatch::isValid() const {
+ return _proxy_valid;
+}
bool ProteinMatch::isChecked() const {
return _checked;
}
+
+bool ProteinMatch::isValidAndChecked() const{
+ return _proxy_valid && _checked;
+}
+
void ProteinMatch::setChecked(bool arg1) {
_checked = arg1;
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index a0a0f5999..6fba08333 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -28,6 +28,7 @@
#include <pappsomspp/types.h>
#include <pappsomspp/protein/protein.h>
#include "peptidematch.h"
+#include "automaticfilterparameters.h"
class ProteinMatch
{
@@ -42,7 +43,15 @@ public:
void addPeptideMatch(PeptideMatch * peptide_match);
std::vector<PeptideMatch *> & getPeptideMatchList();
void setChecked(bool arg1);
+
bool isChecked() const;
+ bool isValid() const;
+ bool isValidAndChecked() const;
+
+ /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+ * */
+ void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
+
private:
std::vector<PeptideMatch *> _peptide_match_list;
pappso::ProteinSp _protein_sp = nullptr;
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index 3096830a8..f5e88e48c 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -191,7 +191,7 @@ void PeptideTableModel::onTableClicked(const QModelIndex &index)
}
bool PeptideTableModel::acceptRow(int source_row) {
- if (_p_project->isValid(_p_protein_match->getPeptideMatchList().at(source_row))) {
+ if (_p_protein_match->getPeptideMatchList().at(source_row)->isValid()) {
return true;
}
return false;
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index bd7b21d82..5ceaa2609 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -223,7 +223,7 @@ bool ProteinTableModel::acceptRow(int source_row) {
return false;
}
}
- if (_p_identification_group->isValid(protein_match)) {
+ if (protein_match->isValid()) {
return true;
}
return false;
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 2cb9a30c1..ca567de05 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -134,12 +134,12 @@ bool XpipSaxHandler::startElement_filter_params(QXmlAttributes attributes) {
//<filter_params pep_evalue="0.01" prot_evalue="-2.0" pep_number="1" filter_to_all="false" database_filter="contaminants_standarts.fasta"/>
qDebug() << "startElement_filter_params ";
- _p_project->setFilterPeptideEvalue( attributes.value("pep_evalue").simplified().toDouble());
- _p_project->setFilterProteinEvalue( std::pow ((double) 10.0,attributes.value("prot_evalue").simplified().toDouble()));
- _p_project->setFilterMinimumPeptidePerMatch( attributes.value("pep_number").simplified().toUInt());
- _p_project->setFilterCrossSamplePeptideNumber(false);
+ _automatic_filter_parameters.setFilterPeptideEvalue( attributes.value("pep_evalue").simplified().toDouble());
+ _automatic_filter_parameters.setFilterProteinEvalue( std::pow ((double) 10.0,attributes.value("prot_evalue").simplified().toDouble()));
+ _automatic_filter_parameters.setFilterMinimumPeptidePerMatch( attributes.value("pep_number").simplified().toUInt());
+ _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(false);
if (attributes.value("filter_to_all").simplified() == "true") {
- _p_project->setFilterCrossSamplePeptideNumber(true);
+ _automatic_filter_parameters.setFilterCrossSamplePeptideNumber(true);
}
qDebug() << "startElement_filter_params end" ;
return true;
@@ -331,6 +331,7 @@ QString XpipSaxHandler::errorString() const {
bool XpipSaxHandler::endDocument() {
+ _p_project->updateAutomaticFilters(_automatic_filter_parameters);
return true;
}
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index ae9e8ff12..7a6e471f1 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -78,6 +78,7 @@ private:
std::vector<QString> _tag_stack;
QString _errorStr;
QString _current_text;
+ AutomaticFilterParameters _automatic_filter_parameters;
Project * _p_project;
ProteinMatch * _p_protein_match;
--
GitLab