wip : lot of xpip features

src/CMakeLists.txt

@@ -53,6 +53,7 @@ configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/c
 
 # File list
 SET(CPP_FILES
+  core/identificationgroup.cpp
   core/peptidematch.cpp
   core/project.cpp
   core/proteinmatch.cpp

src/core/identificationgroup.cpp

+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp is free software: you can redistribute it and/or modify
+*     it under the terms of the GNU General Public License as published by
+*     the Free Software Foundation, either version 3 of the License, or
+*     (at your option) any later version.
+*
+*     XTPcpp is distributed in the hope that it will be useful,
+*     but WITHOUT ANY WARRANTY; without even the implied warranty of
+*     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*     GNU General Public License for more details.
+*
+*     You should have received a copy of the GNU General Public License
+*     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "identificationgroup.h"
+
+IdentificationGroup::IdentificationGroup(Project * project)
+{
+    _p_project = project;
+}
+
+IdentificationGroup::~IdentificationGroup()
+{
+    auto it = _protein_match_list.begin();
+    while (it != _protein_match_list.end()) {
+        delete (*it);
+        it++;
+    }
+}
+
+bool IdentificationGroup::isValid(ProteinMatch* p_protein_match) const {
+    return true;
+}
+
+void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
+    _protein_match_list.push_back(protein_match);
+}
+void IdentificationGroup::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
+    _ms_run_list.push_back(ms_run_sp);
+}
+std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
+    return _protein_match_list;
+}

src/core/identificationgroup.h

+
+/*******************************************************************************
+* Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp is free software: you can redistribute it and/or modify
+*     it under the terms of the GNU General Public License as published by
+*     the Free Software Foundation, either version 3 of the License, or
+*     (at your option) any later version.
+*
+*     XTPcpp is distributed in the hope that it will be useful,
+*     but WITHOUT ANY WARRANTY; without even the implied warranty of
+*     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*     GNU General Public License for more details.
+*
+*     You should have received a copy of the GNU General Public License
+*     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+*     Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+#include <memory>
+#include <pappsomspp/grouping/grpexperiment.h>
+#include <QFileInfo>
+#include "proteinmatch.h"
+#include <pappsomspp/msrun/msrunid.h>
+
+
+#ifndef IDENTIFICATIONGROUP_H
+#define IDENTIFICATIONGROUP_H
+
+
+class Project;
+
+/** @brief an identification group contains one or more sample to consider for grouping
+ */
+class IdentificationGroup
+{
+
+public:
+    IdentificationGroup(Project * project);
+    ~IdentificationGroup();
+
+    void addProteinMatch(ProteinMatch * protein_match);
+    std::vector<ProteinMatch *> & getProteinMatchList();
+    void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
+
+
+    /** @brief is it valid regarding threshold and project rules
+     */
+    bool isValid(ProteinMatch* p_protein_match) const;
+
+    pappso::GrpExperiment * _p_grp_experiment= nullptr;
+private :
+    Project * _p_project;
+
+    std::vector<ProteinMatch *> _protein_match_list;
+
+    std::vector<pappso::MsRunIdSp> _ms_run_list;
+};
+
+#endif // IDENTIFICATIONGROUP_H

src/core/peptidematch.cpp

@@ -48,3 +48,10 @@ void PeptideMatch::setCharge(unsigned int charge) {
 void PeptideMatch::setPeptideSp (pappso::PeptideSp peptide) {
     _peptide_sp = peptide;
 }
+
+void PeptideMatch::setChecked(bool arg1) {
+    _checked = arg1;
+}
+void PeptideMatch::setIdentificationDataSource(IdentificationDataSource* identification_source) {
+    _p_identification_source = identification_source;
+}

src/core/peptidematch.h

@@ -39,6 +39,8 @@ public :
     void setStart(unsigned int start);
     void setCharge(unsigned int charge);
     void setPeptideSp (pappso::PeptideSp peptide);
+    void setIdentificationDataSource(IdentificationDataSource* identification_source);
+    void setChecked(bool arg1);
 
 
 private :
@@ -50,6 +52,15 @@ private :
     pappso::pappso_double _exp_mass;
     unsigned int _start;
     unsigned int _charge;
+    IdentificationDataSource* _p_identification_source = nullptr;
+    
+    /** @brief manually checked by user (true by default)
+     */
+    bool _checked = true;
+    
+    /** @brief automatic filter result (false by default)
+     */
+    bool _proxy_valid = false;
 };
 
 #endif // PEPTIDEMATCH_H

src/core/project.cpp

@@ -30,8 +30,8 @@ Project::Project()
 
 Project::~Project()
 {
-    auto it = _protein_match_list.begin();
-    while (it != _protein_match_list.end()) {
+    auto it = _identification_goup_list.begin();
+    while (it != _identification_goup_list.end()) {
         delete (*it);
         it++;
     }
@@ -42,6 +42,11 @@ ProjectSp Project::makeProjectSp() const {
 }
 
 
+IdentificationGroup* Project::newIdentificationGroup() {
+    _p_current_identification_group =  new IdentificationGroup(this);
+    _identification_goup_list.push_back(_p_current_identification_group);
+    return _p_current_identification_group;
+}
 void Project::readXpipFile(QFileInfo xpip_fileinfo) {
 
 
@@ -57,37 +62,21 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
     QXmlInputSource xmlInputSource(&qfile);
 
     if (simplereader.parse(xmlInputSource)) {
+
+        qfile.close();
     } else {
         qDebug() << parser->errorString();
         // throw PappsoException(
         //    QObject::tr("error reading tandem XML result file :\n").append(
         //         parser->errorString()));
-    }
-    qfile.close();
-
-    /*
-        GrpGroupingMonitor monitor;
-        GrpExperiment grpExperiment(monitor);
-        PeptideReader peptideReader(grpExperiment);
-        FastaReader reader(peptideReader);
-        reader.parse(&fastaFile);
-        fastaFile.close();
-        grpExperiment.startGrouping();
 
+        qfile.close();
 
-        std::list<GrpProteinSp> protein_list;
-        grpExperiment.getGroupedProteinSpList(protein_list);
-        */
+        throw pappso::PappsoException(QObject::tr("Error reading %1 XPIP file :\n %2").arg(xpip_fileinfo.absoluteFilePath()).arg(parser->errorString()));
+    }
 
 }
 
-
-void Project::addProteinMatch(ProteinMatch * protein_match) {
-    _protein_match_list.push_back(protein_match);
-}
-void Project::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
-    _ms_run_list.push_back(ms_run_sp);
-}
-std::vector<ProteinMatch *> & Project::getProteinMatchList() {
-    return _protein_match_list;
+IdentificationGroup* Project::getCurrentIdentificationGroupP() const {
+    return _p_current_identification_group;
 }

src/core/project.h

@@ -24,10 +24,7 @@
 #define PROJECT_H
 
 #include<memory>
-#include <pappsomspp/grouping/grpexperiment.h>
-#include <QFileInfo>
-#include "proteinmatch.h"
-#include <pappsomspp/msrun/msrunid.h>
+#include "identificationgroup.h"
 
 class Project;
 typedef std::shared_ptr<Project> ProjectSp;
@@ -40,15 +37,11 @@ public:
 
     ProjectSp makeProjectSp() const;
     void readXpipFile(QFileInfo xpip_source);
-    void addProteinMatch(ProteinMatch * protein_match);
-    std::vector<ProteinMatch *> & getProteinMatchList();
-    void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
-
-    pappso::GrpExperiment * _p_grp_experiment= nullptr;
+    IdentificationGroup* newIdentificationGroup();
+    IdentificationGroup* getCurrentIdentificationGroupP() const;
 private :
-    std::vector<ProteinMatch *> _protein_match_list;
-
-    std::vector<pappso::MsRunIdSp> _ms_run_list;
+    std::vector<IdentificationGroup *> _identification_goup_list;
+    IdentificationGroup* _p_current_identification_group = nullptr;
 };
 
 #endif // PROJECT_H

src/core/proteinmatch.cpp

@@ -48,6 +48,12 @@ void ProteinMatch::setProteinSp(pappso::ProteinSp protein_sp) {
     _protein_sp = protein_sp;
 }
 
+bool ProteinMatch::isChecked() const {
+    return _checked;
+}
+void ProteinMatch::setChecked(bool arg1) {
+    _checked = arg1;
+}
 void ProteinMatch::addPeptideMatch(PeptideMatch * peptide_match) {
     _peptide_match_list.push_back(peptide_match);
 }

src/core/proteinmatch.h

@@ -40,10 +40,19 @@ public:
     void setProteinSp(pappso::ProteinSp protein_sp);
     void addPeptideMatch(PeptideMatch * peptide_match);
     std::vector<PeptideMatch *> & getPeptideMatchList();
+    void setChecked(bool arg1);
+    bool isChecked() const;
 private:
     std::vector<PeptideMatch *> _peptide_match_list;
     pappso::ProteinSp _protein_sp = nullptr;
     pappso::pappso_double _evalue=0;
+    /** @brief manually checked by user (true by default)
+     */
+    bool _checked = true;
+    
+    /** @brief automatic filter result (false by default)
+     */
+    bool _proxy_valid = false;
 
 };
 

src/gui/mainwindow.cpp

@@ -92,6 +92,6 @@ void MainWindow::selectXpipFile() {
     XpipFile xpip_file(new_xpip_file);
     
     _project_sp = xpip_file.getProjectSp();
-    _protein_list_window->setProject(_project_sp.get());
+    _protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
     
 }

src/gui/protein_list_view/proteinlistwindow.cpp

@@ -53,7 +53,7 @@ ProteinListWindow::ProteinListWindow(QWidget *parent):
     _protein_table_model_p = new ProteinTableModel(0);
 
 
-    _p_proxy_model = new ProteinTableProxyModel(this);
+    _p_proxy_model = new ProteinTableProxyModel(this, _protein_table_model_p);
     _p_proxy_model->setSourceModel(_protein_table_model_p);
     _p_proxy_model->setDynamicSortFilter(true);
     ui->tableView->setModel( _p_proxy_model );
@@ -68,8 +68,9 @@ ProteinListWindow::~ProteinListWindow()
 }
 
 
-void ProteinListWindow::setProject(Project* project_p) {
-    _protein_table_model_p->setProject(project_p);
-     _p_proxy_model->setSourceModel(_protein_table_model_p);
+void ProteinListWindow::setIdentificationGroup(IdentificationGroup * p_identification_group) {
+    _protein_table_model_p->setIdentificationGroup(p_identification_group);
+    _p_proxy_model->setSourceModel(_protein_table_model_p);
 
 }
+

src/gui/protein_list_view/proteinlistwindow.h

@@ -40,7 +40,7 @@ public:
 
     explicit ProteinListWindow(QWidget * parent = 0);
     ~ProteinListWindow();
-    void setProject(Project* project_p);
+    void setIdentificationGroup(IdentificationGroup * p_identification_group);
 
 public slots:
     //void peptideEdited(QString peptideStr);

src/gui/protein_list_view/proteintablemodel.cpp

@@ -26,14 +26,16 @@
 #include <QDebug>
 
 
-ProteinTableProxyModel::ProteinTableProxyModel(QObject *parent): QSortFilterProxyModel(parent),
+ProteinTableProxyModel::ProteinTableProxyModel(QObject *parent,ProteinTableModel* protein_table_model_p): QSortFilterProxyModel(parent),
     m_minGravity(0.0), m_minDensity(0.0)
 {
+    _protein_table_model_p = protein_table_model_p;
 }
 
 bool ProteinTableProxyModel::filterAcceptsRow(int source_row,
         const QModelIndex &source_parent) const {
-    return true;
+    //return _protein_table_model_p->acceptRow(source_row);
+	  return true;
 }
 
 bool ProteinTableProxyModel::lessThan(const QModelIndex & left, const QModelIndex & right) const {
@@ -81,9 +83,9 @@ ProteinTableModel::ProteinTableModel(QObject *parent)
 }
 
 
-void ProteinTableModel::setProject(Project * p_project) {
-    qDebug() << "ProteinTableModel::setProject begin " << p_project->getProteinMatchList().size();
-    _p_project = p_project;
+void ProteinTableModel::setIdentificationGroup(IdentificationGroup * p_identification_group) {
+    qDebug() << "ProteinTableModel::setIdentificationGroup begin " << p_identification_group->getProteinMatchList().size();
+    _p_identification_group = p_identification_group;
 
     QModelIndex topLeft = createIndex(0,0);
     QModelIndex bottomRight = createIndex(rowCount(),columnCount());
@@ -92,9 +94,9 @@ void ProteinTableModel::setProject(Project * p_project) {
 }
 
 int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
-    if (_p_project != nullptr) {
-        qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) " << _p_project->getProteinMatchList().size();
-        return _p_project->getProteinMatchList().size();
+    if (_p_identification_group != nullptr) {
+        qDebug() << "ProteinTableModel::rowCount(const QModelIndex &parent ) " << _p_identification_group->getProteinMatchList().size();
+        return _p_identification_group->getProteinMatchList().size();
     }
     return 0;
 }
@@ -125,21 +127,35 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
     int col = index.column();
     qDebug() << QString("row %1, col%2, role %3")
              .arg(row).arg(col).arg(role);
-    if (role == Qt::DisplayRole)
-    {
+
+    switch(role) {
+    case Qt::CheckStateRole:
+
+        if (col == 0) //add a checkbox to cell(1,0)
+        {
+            if ( _p_identification_group->getProteinMatchList().at(row)->isChecked()) {
+                return Qt::Checked;
+            }
+            else {
+                return Qt::Unchecked;
+            }
+        }
+        break;
+    case Qt::DisplayRole:
         if (col == 0) {
-            if (_p_project != nullptr) {
-                return QVariant ((quint16) _p_project->getProteinMatchList().at(row)->getPeptideMatchList().size());
+            if (_p_identification_group != nullptr) {
+
+                return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->getPeptideMatchList().size());
             }
         }
         if (col == 1) {
-            if (_p_project != nullptr) {
-                return _p_project->getProteinMatchList().at(row)->getProteinSp().get()->getAccession();
+            if (_p_identification_group != nullptr) {
+                return _p_identification_group->getProteinMatchList().at(row)->getProteinSp().get()->getAccession();
             }
         }
         if (col == 2) {
-            if (_p_project != nullptr) {
-                return _p_project->getProteinMatchList().at(row)->getProteinSp().get()->getDescription();
+            if (_p_identification_group != nullptr) {
+                return _p_identification_group->getProteinMatchList().at(row)->getProteinSp().get()->getDescription();
             }
         }
         return QString("Row%1, Column%2")
@@ -148,3 +164,11 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
     }
     return QVariant();
 }
+
+
+bool ProteinTableModel::acceptRow(int source_row) {
+    if (_p_identification_group->isValid(_p_identification_group->getProteinMatchList().at(source_row))) {
+        return true;
+    }
+    return false;
+}

src/gui/protein_list_view/proteintablemodel.h

@@ -28,12 +28,12 @@
 #include <QSortFilterProxyModel>
 #include "../../core/project.h"
 
-
+class ProteinTableModel;
 class ProteinTableProxyModel : public QSortFilterProxyModel
 {
     Q_OBJECT
 public:
-    ProteinTableProxyModel(QObject* parent = 0);
+    ProteinTableProxyModel(QObject* parent,ProteinTableModel* protein_table_model_p);
     bool filterAcceptsRow(int source_row,
                           const QModelIndex &source_parent) const override;
     QVariant headerData(int section, Qt::Orientation orientation,
@@ -46,6 +46,7 @@ public slots:
 private:
     double m_minGravity;
     double m_minDensity;
+    ProteinTableModel* _protein_table_model_p;
 };
 
 class ProteinTableModel: public QAbstractTableModel
@@ -59,10 +60,11 @@ public:
     QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
 
 
-    void setProject(Project * p_project);
+    void setIdentificationGroup(IdentificationGroup * p_identification_group);
+    bool acceptRow(int source_row);
 
 private :
-    Project * _p_project = nullptr;
+    IdentificationGroup * _p_identification_group = nullptr;
 };
 
 #endif // PROTEINTABLEMODEL_H

src/input/xpipsaxhandler.cpp

@@ -43,9 +43,12 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
 
     try {
         //startElement_group
-        if (qName == "protein")
-        {
+        if (qName == "match") {
+            is_ok = startElement_match(attributes);
+        } else if (qName == "protein") {
             is_ok = startElement_protein(attributes);
+        } else if (qName == "identification") {
+            is_ok = startElement_identification(attributes);
         }
         //<sample value="P6_08_10"/>
         else if (qName == "sample") {
@@ -56,7 +59,12 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
             is_ok = startElement_modifs_mass(attributes);
         } else if (qName == "modif") {
             is_ok = startElement_modif(attributes);
+        }  else if (qName == "filter_params") {
+            is_ok = startElement_filter_params(attributes);
+        }  else if (qName == "information") {
+            is_ok = startElement_information(attributes);
         }
+
         _current_text.clear();
     }
     catch (pappso::PappsoException exception_pappso) {
@@ -80,12 +88,18 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
         {
             is_ok = endElement_protein();
         }
+        else if (qName == "identification") {
+            is_ok = endElement_identification();
+        }
         else if (qName == "peptide") {
             is_ok = endElement_peptide();
         }
         else if (qName == "sequence") {
             is_ok = endElement_sequence();
         }
+        else if (qName == "match") {
+            is_ok = endElement_match();
+        }
 
         // end of detection_moulon
         // else if ((_tag_stack.size() > 1) &&
@@ -106,6 +120,31 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
     return is_ok;
 }
 
+bool XpipSaxHandler::startElement_identification(QXmlAttributes attributes) {
+
+    qDebug() << "startElement_identification ";
+    _map_massstr_aamod.clear();
+    _current_identification_group_p = _p_project->newIdentificationGroup();
+    qDebug() << "startElement_identification end" ;
+    return true;
+}
+
+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 ";
+    qDebug() << "startElement_filter_params end" ;
+    return true;
+}
+
+bool XpipSaxHandler::startElement_information(QXmlAttributes attributes) {
+
+//<information Data_Type="indiv" match_number="223"/>
+    qDebug() << "startElement_information ";
+    qDebug() << "startElement_information end" ;
+    return true;
+}
+
 bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
 
     /*
@@ -120,9 +159,9 @@ bool XpipSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
     qDebug() << "startElement_modifs_mass ";
     QString mass_str(attributes.value("modvalue").simplified());
     pappso::mz mass = mass_str.toDouble();
-    
+
     pappso::AaModificationP mod = getAaModificationP(mass);
-    
+
     _map_massstr_aamod[mass_str] = mod;
     qDebug() << "startElement_modifs_mass end" ;
     return true;
@@ -137,25 +176,40 @@ bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
     ms_run.setFilename(attributes.value("value").simplified());
 
     pappso::MsRunIdSp msrunid_sp = ms_run.makeMsRunIdSp();
-    _p_project->addMsRunIdSp(msrunid_sp);
-    
+    _current_identification_group_p->addMsRunIdSp(msrunid_sp);
+
     _map_msrunid[ms_run.getXmlId()] = msrunid_sp;
     qDebug() << "startElement_sample end" ;
     return true;
 }
 
+bool XpipSaxHandler::startElement_match(QXmlAttributes attributes) {
+
+    qDebug() << "startElement_match ";
+    /*
+     * <match_list><match validate="true">
+              */
+    _p_protein_match = new ProteinMatch();
+    _p_protein_match->setChecked(false);
+    if (attributes.value("validate").simplified().toLower() == "true") {
+        _p_protein_match->setChecked(true);
+    }
+    qDebug() << "startElement_match end" ;
+    return true;
+}
 bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
 
+    qDebug() << "startElement_protein ";
     /*
-     * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta" description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
+     * <protein peptide_number="268" evalue="-432.77353" URL="Genome_Z_mays_5a.fasta" 
+     * description="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC 4.1.1.31) 
+     * seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01; parent_gene=GRMZM2G083841">
                 <protein_evalue evalue="-399.36093" sample="20120906_balliau_extract_1_A02_urzb-1"/>
                 <protein_evalue evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
                 <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
               </protein>
               */
-    _p_protein_match = new ProteinMatch();
     _p_protein_match->setEvalue(attributes.value("evalue").toDouble());
-    qDebug() << "startElement_protein ";
     _current_protein.setDescription(attributes.value("description").simplified());
     _current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
     qDebug() << "startElement_protein end" ;
@@ -181,7 +235,21 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
     _p_peptide_match->setExperimentalMass(exp_mass);
     _p_peptide_match->setStart(attributes.value("start").simplified().toUInt());
     _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
-    
+
+    _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
+
+    IdentificationDataSource* p_identification_data_source = IdentificationDataSource::getInstance(attributes.value("sample_file").simplified());
+    _p_peptide_match->setIdentificationDataSource( p_identification_data_source);
+    if (p_identification_data_source->getMsRunSp().get() == nullptr) {
+        p_identification_data_source->setMsRunSp(ms_run_id);
+    }
+    if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
+        throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
+    }
+    _p_peptide_match->setChecked(false);
+    if (attributes.value("validate").simplified().toLower() == "true") {
+        _p_peptide_match->setChecked(true);
+    }
     _p_protein_match->addPeptideMatch(_p_peptide_match);
     qDebug() << "startElement_peptide end" ;
     return true;
@@ -217,10 +285,20 @@ bool XpipSaxHandler::endElement_sequence() {
 }
 bool XpipSaxHandler::endElement_protein() {
     _p_protein_match->setProteinSp(_current_protein.makeProteinSp());
-    _p_project->addProteinMatch(_p_protein_match);
+
+    return true;
+}
+
+bool XpipSaxHandler::endElement_identification() {
+
     return true;
 }
 
+bool XpipSaxHandler::endElement_match() {
+    _current_identification_group_p->addProteinMatch(_p_protein_match);
+    _p_protein_match = nullptr;
+    return true;
+}
 
 
 bool XpipSaxHandler::error(const QXmlParseException &exception) {

src/input/xpipsaxhandler.h

@@ -57,14 +57,20 @@ public:
 
 
 private:
+    bool startElement_filter_params(QXmlAttributes attributes);
+    bool startElement_information(QXmlAttributes attributes);
+    bool startElement_identification(QXmlAttributes attributes);
+    bool startElement_match(QXmlAttributes attributes);
     bool startElement_peptide(QXmlAttributes attributes);
     bool startElement_protein(QXmlAttributes attributes);
     bool startElement_sample(QXmlAttributes attributes);
     bool startElement_modifs_mass(QXmlAttributes attributes);
     bool startElement_modif(QXmlAttributes attributes);
+    bool endElement_identification();
     bool endElement_sequence();
     bool endElement_protein();
     bool endElement_peptide();
+    bool endElement_match();
     
     pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
 
@@ -78,6 +84,7 @@ private:
     PeptideMatch * _p_peptide_match;
     pappso::Protein _current_protein;
     pappso::NoConstPeptideSp _current_peptide_sp;
+    IdentificationGroup * _current_identification_group_p;
     
     PeptideStore _peptide_store;
     QMap<QString, pappso::AaModificationP> _map_massstr_aamod;