valid and checked design

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

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);
 }

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 :

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

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;

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;
-}

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;

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;
 }

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;

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;

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;

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;
 }
 

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;