WIP : xtandem sax parser

src/CMakeLists.txt

@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
 
 #sudo apt-get install libpappsomspp-dev
 #FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
- SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
  SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
  SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
 

src/core/identification_sources/identificationxtandemfile.cpp

@@ -50,16 +50,40 @@ pappso::SpectrumSp IdentificationXtandemFile::getSpectrumSp(unsigned int scan_nu
 
 
 void IdentificationXtandemFile::parseTo(Project* p_project) {
-      qDebug() << "Project::readXpipFile begin";
+    qDebug() << "Project::readXpipFile begin";
 
-    XtandemSaxHandler * parser = new XtandemSaxHandler(p_project);
+    qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
+
+    MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_xtandem_file).baseName());
+    setMsRunSp(msrun_sp);
+    std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+    IdentificationGroup * identification_group_p = nullptr;
+    if (p_project->isCombineMode()) {
+        if (identification_list.size() == 0) {
+            identification_group_p = p_project->newIdentificationGroup();
+        }
+        else {
+            identification_group_p = identification_list[0];
+        }
+    }
+    else {
+        for (IdentificationGroup * identification_p_flist : identification_list) {
+            if (identification_p_flist->contains(msrun_sp.get())) {
+                identification_group_p = identification_p_flist;
+                break;
+            }
+        }
+        if (identification_group_p == nullptr) {
+            identification_group_p = p_project->newIdentificationGroup();
+        }
+    }
+    
+    XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p);
 
     QXmlSimpleReader simplereader;
     simplereader.setContentHandler(parser);
     simplereader.setErrorHandler(parser);
 
-    qDebug() << "Read X!Tandem XML result file '" << _xtandem_file.absoluteFilePath() << "'";
-
     QFile qfile(_xtandem_file.absoluteFilePath());
     QXmlInputSource xmlInputSource(&qfile);
 

src/core/identificationgroup.cpp

@@ -24,6 +24,7 @@
 #include "identificationgroup.h"
 #include "project.h"
 #include "../utils/groupstore.h"
+#include <pappsomspp/pappsoexception.h>
 
 
 IdentificationGroup::IdentificationGroup(Project * project)
@@ -49,9 +50,36 @@ void IdentificationGroup::updateAutomaticFilters(const AutomaticFilterParameters
     }
 
 }
+ProteinMatch * IdentificationGroup::getProteinMatch(const QString accession) {
+    if (accession.isEmpty()) {
+        throw pappso::PappsoException(QObject::tr("Error protein match not found : accession is empty"));
+    }
+    for (ProteinMatch * p_protein_match : _protein_match_list) {
+        if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+            return p_protein_match;
+        }
+    }
+    return nullptr;
+}
 void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
+    QString accession = protein_match->getProteinXtpSp().get()->getAccession();
+    if (accession.isEmpty()) {
+        throw pappso::PappsoException(QObject::tr("Error adding protein match : accession is empty"));
+    }
+    for (ProteinMatch * p_protein_match : _protein_match_list) {
+        if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+            throw pappso::PappsoException(QObject::tr("Error adding protein match : accession %1 already registered").arg(accession));
+        }
+    }
     _protein_match_list.push_back(protein_match);
 }
+
+bool IdentificationGroup::contains (const MsRun * p_msrun) const {
+    for (const MsRunSp & msrun: _ms_run_list) {
+        if (msrun.get() == p_msrun) return true;
+    }
+    return false;
+}
 void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
     _ms_run_list.push_back(ms_run_sp);
 }

src/core/identificationgroup.h

@@ -43,6 +43,7 @@ public:
     IdentificationGroup(Project * project);
     ~IdentificationGroup();
 
+    ProteinMatch * getProteinMatch(const QString accession);
     void addProteinMatch(ProteinMatch * protein_match);
     std::vector<ProteinMatch *> & getProteinMatchList();
     void addMsRunSp(MsRunSp ms_run_sp);
@@ -79,6 +80,8 @@ public:
     /** @brief get tab name for qtabwidget
      * */   
     const QString getTabName() const;
+    
+    bool contains (const MsRun * p_msrun) const;
 private :
     GroupingExperiment * _p_grp_experiment= nullptr;
 

src/core/project.cpp

@@ -46,7 +46,10 @@ void Project::readResultFile(QString filename) {
     ident_source.get()->parseTo(this);
 }
 
-void Project::setCombine(bool is_combine_mode) {
+    bool Project::isCombineMode() const {
+        return _is_combine_mode;
+    }
+void Project::setCombineMode(bool is_combine_mode) {
     _is_combine_mode = is_combine_mode;
 }
 std::vector<IdentificationGroup *> Project::getIdentificationGroupList() {

src/core/project.h

@@ -62,7 +62,8 @@ public:
     const GroupingType getGroupingType() const;
 
     std::vector<IdentificationGroup *> getIdentificationGroupList();
-    void setCombine(bool is_combine_mode);
+    void setCombineMode(bool is_combine_mode);
+    bool isCombineMode() const;
     void readResultFile(QString filename);
 
 private :

src/core/proteinmatch.cpp

@@ -99,9 +99,6 @@ void ProteinMatch::updateAutomaticFilters(const AutomaticFilterParameters & auto
 const ProteinXtpSp & ProteinMatch::getProteinXtpSp() const {
     return _protein_sp;
 }
-void ProteinMatch::setEvalue(pappso::pappso_double evalue) {
-    _evalue = evalue;
-}
 
 void ProteinMatch::setProteinXtpSp(ProteinXtpSp protein_sp) {
     _protein_sp = protein_sp;

src/core/proteinmatch.h

@@ -44,7 +44,6 @@ public:
     ~ProteinMatch();
 
     const ProteinXtpSp & getProteinXtpSp() const;
-    void setEvalue(pappso::pappso_double evalue);
 
     /** @brief compute protein Evalue within samples
       * */
@@ -109,16 +108,15 @@ private :
     unsigned int countValidAndCheckedPeptideMassCharge(const MsRun * sp_msrun_id) const;
 
 private:
-  static QColor _color_peptide_background;
-  static QColor _color_highlighted_peptide_background;
-  
-  
+    static QColor _color_peptide_background;
+    static QColor _color_highlighted_peptide_background;
+
+
     pappso::GrpProteinSp _sp_grp_protein;
     GroupingGroupSp _sp_group;
 
     std::vector<PeptideMatch *> _peptide_match_list;
     ProteinXtpSp _protein_sp = nullptr;
-    pappso::pappso_double _evalue=0;
     /** @brief manually checked by user (true by default)
      */
     bool _checked = true;

src/core/proteinxtp.cpp

@@ -50,7 +50,13 @@ ProteinXtpSp ProteinXtp::makeProteinXtpSp() const {
     return std::make_shared<ProteinXtp>(*this);
 }
 
-
+void ProteinXtp::setCompleteDescription(const QString & full_description) {
+    setAccession (full_description.simplified().section(" ", 0,0));
+    setDescription (full_description.simplified().section(" ", 1));
+    
+    
+        
+}
 void ProteinXtp::setIsContaminant(bool conta) {
     _is_contaminant = conta;
 }

src/core/proteinxtp.h

@@ -44,6 +44,8 @@ public:
 
     ProteinXtpSp makeProteinXtpSp() const;
     
+    void setCompleteDescription(const QString & full_description);
+    
     void setIsContaminant(bool conta);
     void setIsDecoy(bool conta);
     bool isContaminant() const;

src/gui/mainwindow.cpp

@@ -58,7 +58,7 @@ void XtpLoaderThread::doLoadingResults(bool is_individual, AutomaticFilterParame
     qDebug() << "XtpLoaderThread::doLoadingResults begin ";
     try {
         ProjectSp project_sp = Project().makeProjectSp();
-	project_sp.get()->setCombine(!is_individual);
+	project_sp.get()->setCombineMode(!is_individual);
 
         for (QString filename : file_list) {
             project_sp.get()->readResultFile(filename);

src/gui/peptide_list_view/peptide_view.ui

@@ -16,7 +16,14 @@
   <widget class="QWidget" name="centralwidget">
    <layout class="QVBoxLayout" name="verticalLayout">
     <item>
-     <widget class="QLabel" name="proteinLabel">
+     <widget class="QLabel" name="accession_label">
+      <property name="text">
+       <string>TextLabel</string>
+      </property>
+     </widget>
+    </item>
+    <item>
+     <widget class="QLabel" name="description_label">
       <property name="text">
        <string>TextLabel</string>
       </property>
@@ -25,7 +32,6 @@
       </property>
      </widget>
     </item>
-    
     <item>
      <layout class="QHBoxLayout" name="horizontalLayoutcb">
       <item>
@@ -69,14 +75,13 @@
      <x>0</x>
      <y>0</y>
      <width>826</width>
-     <height>31</height>
+     <height>25</height>
     </rect>
    </property>
   </widget>
   <widget class="QStatusBar" name="statusbar"/>
  </widget>
  <resources/>
- 
  <connections>
   <connection>
    <sender>hideNotValidCheckBox</sender>

src/gui/peptide_list_view/peptidelistwindow.cpp

@@ -108,7 +108,8 @@ void PeptideListWindow::setProteinMatch(IdentificationGroup * p_identification_g
         _p_protein_match = p_protein_match;
         _peptide_table_model_p->setProteinMatch( p_protein_match);
         _p_proxy_model->setSourceModel(_peptide_table_model_p);
-        ui->proteinLabel->setText(p_protein_match->getProteinXtpSp().get()->getDescription());
+        ui->description_label->setText(p_protein_match->getProteinXtpSp().get()->getDescription());
+        ui->accession_label->setText(p_protein_match->getProteinXtpSp().get()->getAccession());
     }
 
 }

src/gui/project_view/automatic_filter_widget/automatic_filter_widget.ui

@@ -50,13 +50,13 @@
      <item row="0" column="1">
       <widget class="QDoubleSpinBox" name="peptide_evalue_spinbox">
        <property name="decimals">
-        <number>3</number>
+        <number>6</number>
        </property>
        <property name="maximum">
         <double>1.000000000000000</double>
        </property>
        <property name="singleStep">
-        <double>0.010000000000000</double>
+        <double>0.001000000000000</double>
        </property>
        <property name="value">
         <double>0.050000000000000</double>

src/gui/protein_view/protein_detail_view.ui

@@ -20,7 +20,7 @@
       <item>
        <layout class="QHBoxLayout" name="horizontalLayout">
         <item>
-         <widget class="QLabel" name="descriptionLabel">
+         <widget class="QLabel" name="accession_label">
           <property name="sizePolicy">
            <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
             <horstretch>0</horstretch>
@@ -72,6 +72,16 @@
         </item>
        </layout>
       </item>
+      <item>
+       <widget class="QLabel" name="description_label">
+        <property name="text">
+         <string>TextLabel</string>
+        </property>
+        <property name="wordWrap">
+         <bool>true</bool>
+        </property>
+       </widget>
+      </item>
       <item>
        <widget class="QTextEdit" name="sequenceTextEdit">
         <property name="lineWrapMode">

src/gui/protein_view/proteinwindow.cpp

@@ -73,8 +73,8 @@ void ProteinWindow::updateDisplay() {
     try {
         ui->validCheckBox->setCheckState(Qt::Unchecked);
         if (_p_protein_match->isValid()) ui->validCheckBox->setCheckState(Qt::Checked);
-        ui->descriptionLabel->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
-        //ui->sequenceLabel->setText(_p_protein_match->getProteinXtpSp().get()->getSequence());
+        ui->accession_label->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
+        ui->description_label->setText(_p_protein_match->getProteinXtpSp().get()->getDescription());
         ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
         ui->coverage_label->setText(QString("%1 %").arg(_p_protein_match->getCoverage()*100));
         pappso::Peptide peptide(_p_protein_match->getProteinXtpSp().get()->getSequence());

src/input/xpipsaxhandler.cpp

@@ -215,9 +215,7 @@ bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
                 <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
               </protein>
               */
-    _p_protein_match->setEvalue(std::pow ((double) 10.0, attributes.value("evalue").toDouble()));
-    _current_protein.setDescription(attributes.value("description").simplified());
-    _current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
+    _current_protein.setCompleteDescription(attributes.value("description"));
     qDebug() << "startElement_protein end" ;
     return true;
 }

src/input/xtandemsaxhandler.cpp

@@ -35,9 +35,9 @@
 #include "../utils/peptidestore.h"
 #include "../utils/proteinstore.h"
 
-XtandemSaxHandler::XtandemSaxHandler(Project * p_project):_p_project(p_project)
+XtandemSaxHandler::XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group):_p_project(p_project)
 {
-
+    _p_identification_group = p_identification_group;
 }
 
 XtandemSaxHandler::~XtandemSaxHandler()
@@ -54,36 +54,31 @@ bool XtandemSaxHandler::startElement(const QString & namespaceURI, const QString
 
     try {
         //startElement_group
-        if (qName == "match") {
-            is_ok = startElement_match(attributes);
+        if (qName == "group") {
+            is_ok = startElement_group(attributes);
         } else if (qName == "protein") {
             is_ok = startElement_protein(attributes);
-        } else if (qName == "identification") {
-            is_ok = startElement_identification(attributes);
+        } else if (qName == "note") {
+            is_ok = startElement_note(attributes);
         }
-        //<sample value="P6_08_10"/>
-        else if (qName == "sample") {
-            is_ok = startElement_sample(attributes);
+        else if (qName == "file") {
+            is_ok = startElement_file(attributes);
         } else if (qName == "peptide") {
             is_ok = startElement_peptide(attributes);
-        } else if (qName == "modifs_mass") {
-            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);
+        } else if (qName == "aa") {
+            is_ok = startElement_aa(attributes);
+        } else if (qName == "domain") {
+            is_ok = startElement_domain(attributes);
         }
 
         _current_text.clear();
     }
     catch (pappso::PappsoException exception_pappso) {
-        _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
+        _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
         return false;
     }
     catch (std::exception exception_std) {
-        _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
+        _errorStr = QObject::tr("ERROR in XtandemSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
         return false;
     }
     return is_ok;
@@ -95,21 +90,9 @@ bool XtandemSaxHandler::endElement(const QString & namespaceURI, const QString &
     bool is_ok = true;
     // endElement_peptide_list
     try {
-        if (qName == "protein")
+        if (qName == "note")
         {
-            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();
+            is_ok = endElement_note();
         }
 
         // end of detection_moulon
@@ -117,11 +100,11 @@ bool XtandemSaxHandler::endElement(const QString & namespaceURI, const QString &
         //         (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
     }
     catch (pappso::PappsoException exception_pappso) {
-        _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
+        _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
         return false;
     }
     catch (std::exception exception_std) {
-        _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
+        _errorStr = QObject::tr("ERROR in XtandemSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
         return false;
     }
 
@@ -143,91 +126,61 @@ bool XtandemSaxHandler::startElement_group(QXmlAttributes attrs) {
         _scan = attrs.value("id").toUInt();
         _mhplus_obser = attrs.value("mh").toDouble();
         _charge = attrs.value("z").toUInt();
-        _RT = attrs.value("rt");
+        //_retention_time = attrs.value("rt");
     }
 }
 
-bool XtandemSaxHandler::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);
+bool XtandemSaxHandler::startElement_note(QXmlAttributes attributes) {
+//<note label="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</note>
+    _is_protein_description = false;
+    if (attributes.value("label") == "description") {
+        if (_tag_stack[_tag_stack.size() - 2] == "protein") {
+            _is_protein_description = true;
+        }
     }
-    qDebug() << "startElement_match end" ;
-    return true;
 }
 
 bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) {
 //<protein expect="-704.6" id="1976.1" uid="195701" label="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC..." sumI="9.36" >
 
     qDebug() << "startElement_protein ";
-    _p_protein_match->setEvalue(std::pow ((double) 10.0, attributes.value("expect").toDouble()));
-    _current_protein.setDescription(attributes.value("label").simplified());
-    _current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
-    qDebug() << "startElement_protein end" ;
-    return true;
-}
+    QString accession = attributes.value("label").simplified().split(" ", QString::SkipEmptyParts).at(0);
+    ProteinMatch * p_protein_match = _p_identification_group->getProteinMatch(accession);
 
-bool XtandemSaxHandler::startElement_file(QXmlAttributes attributes) {
-    if (attrs.getValue("type").equals("peptide"))
-        prot_.setDatabase(identification_.getDatabaseSet().getInstance(
-                              attrs.getValue("URL")));
-}
+    _current_protein.setAccession(accession);
+    if (p_protein_match == nullptr) {
+        _p_protein_match = new ProteinMatch();
+        _p_protein_match->setChecked(false);
 
-bool XtandemSaxHandler::startElement_identification(QXmlAttributes attributes) {
-
-    qDebug() << "startElement_identification ";
-    _map_massstr_aamod.clear();
-    _current_identification_group_p = _p_project->newIdentificationGroup();
-    qDebug() << "startElement_identification end" ;
+    }
+    ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
+    p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
+    qDebug() << "startElement_protein end" ;
     return true;
 }
 
-bool XtandemSaxHandler::startElement_information(QXmlAttributes attributes) {
-
-//<information Data_Type="indiv" match_number="223"/>
-    qDebug() << "startElement_information ";
-    qDebug() << "startElement_information end" ;
-    return true;
-}
 
-bool XtandemSaxHandler::startElement_modifs_mass(QXmlAttributes attributes) {
-
-    /*
-    <modifs_list_mass><modifs_mass modvalue="-18.01056"/>
-    <modifs_mass modvalue="-17.02655"/>
-    <modifs_mass modvalue="15.99491"/>
-    <modifs_mass modvalue="42.01057"/>
-    <modifs_mass modvalue="42.01056"/>
-    <modifs_mass modvalue="57.02146"/>
-    </modifs_list_mass>
-    */
-    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;
+bool XtandemSaxHandler::startElement_file(QXmlAttributes attributes) {
+    //<file type="peptide" URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/>
+    if (attributes.value("type") == "peptide") {
+        //prot_.setDatabase(identification_.getDatabaseSet().getInstance(
+         //                     attrs.getValue("URL")));
+    }
 }
 
-//<sample value="P6_21_23"/>
-bool XtandemSaxHandler::startElement_sample(QXmlAttributes attributes) {
+bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
+//<domain id="1976.1.1" start="620" end="629" expect="9.7e-04" mh="1120.5307" delta="-0.0012" hyperscore="29.9"
+    //nextscore="10.2" y_score="10.4" y_ions="7" b_score="11.2" b_ions="3" pre="QLYR" post="RYGV"
+    //seq="AQEEMAQVAK" missed_cleavages="0">
 
-    qDebug() << "startElement_sample ";
+    qDebug() << "startElement_domain ";
 
     MsRunSp ms_run =  _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
     ms_run.get()->setXmlId(attributes.value("value").simplified());
     ms_run.get()->setFilename(attributes.value("value").simplified());
-    _current_identification_group_p->addMsRunSp(ms_run);
-    qDebug() << "startElement_sample end" ;
+    _p_identification_group->addMsRunSp(ms_run);
+    qDebug() << "startElement_domain end" ;
     return true;
 }
 bool XtandemSaxHandler::startElement_peptide(QXmlAttributes attributes) {
@@ -270,52 +223,25 @@ bool XtandemSaxHandler::startElement_peptide(QXmlAttributes attributes) {
     return true;
 }
 
-bool XtandemSaxHandler::startElement_modif(QXmlAttributes attributes) {
-
-    //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
-    qDebug() << "startElement_modif ";
+bool XtandemSaxHandler::startElement_aa(QXmlAttributes attributes) {
+//<aa type="M" at="624" modified="15.99491" />
+    qDebug() << "startElement_aa ";
     pappso::AaModificationP modif = _map_massstr_aamod[attributes.value("modvalue").simplified()];
     unsigned int position = attributes.value("posi").simplified().toUInt();
     _current_peptide_sp.get()->addAaModification(modif, position-1);
-    qDebug() << "startElement_modif end" ;
-    return true;
-}
-bool XtandemSaxHandler::endElement_peptide() {
-    qDebug() << "endElement_peptide ";
-
-    PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
-    peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
-    _p_peptide_match->setPeptideXtpSp(peptide_const);
-    return true;
-}
-
-bool XtandemSaxHandler::endElement_sequence() {
-    //if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
-    _current_protein.setSequence(_current_text);
-    //}
-    //else {
-    // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
-    //}
-    return true;
-}
-bool XtandemSaxHandler::endElement_protein() {
-    ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
-
-    _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
-
+    qDebug() << "startElement_aa end" ;
     return true;
 }
 
-bool XtandemSaxHandler::endElement_identification() {
-
+bool XtandemSaxHandler::endElement_note() {
+//<note label="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</note>
+    if (_is_protein_description) {
+        _p_protein_match->getProteinXtpSp().get()->setDescription(_current_text.section(" ",1));
+    }
     return true;
 }
 
-bool XtandemSaxHandler::endElement_match() {
-    _current_identification_group_p->addProteinMatch(_p_protein_match);
-    _p_protein_match = nullptr;
-    return true;
-}
 
 
 bool XtandemSaxHandler::error(const QXmlParseException &exception) {
@@ -340,7 +266,6 @@ QString XtandemSaxHandler::errorString() const {
 
 
 bool XtandemSaxHandler::endDocument() {
-    _p_project->updateAutomaticFilters(_automatic_filter_parameters);
     return true;
 }
 

src/input/xtandemsaxhandler.h

@@ -43,7 +43,7 @@
 class XtandemSaxHandler: public QXmlDefaultHandler
 {
 public:
-    XtandemSaxHandler(Project * p_project);
+    XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group);
     ~XtandemSaxHandler();
 
     bool startElement(const QString & namespaceURI, const QString & localName,
@@ -66,21 +66,13 @@ public:
 
 private:
   bool startElement_group(QXmlAttributes attrs);
-  
-    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();
+    bool startElement_note(QXmlAttributes attributes);
+    bool startElement_file(QXmlAttributes attributes);
+    bool startElement_aa(QXmlAttributes attributes);
+    bool startElement_domain(QXmlAttributes attributes);
+    bool endElement_note();
     
     pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
 
@@ -90,19 +82,22 @@ private:
     QString _current_text;
 
     Project * _p_project;
+    IdentificationGroup * _p_identification_group;
+    
     ProteinMatch * _p_protein_match;
     PeptideMatch * _p_peptide_match;
     ProteinXtp _current_protein;
     PeptideXtpSp _current_peptide_sp;
-    IdentificationGroup * _current_identification_group_p;
     
     QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+    
     QString _current_group_label;
     QString _current_group_type;
-    uint _scan;
-    double _mhplus_obser;
-    uint _charge;
-    getValue _RT;
+    unsigned int _scan;
+    pappso::pappso_double _mhplus_obser;
+    unsigned int _charge;
+    pappso::pappso_double _retention_time;
+    bool _is_protein_description = false;
 };
 
 #endif // XTANDEMSAXHANDLER_H