new identification data source object

src/CMakeLists.txt

@@ -26,11 +26,11 @@ 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")
+FIND_PACKAGE( Pappsomspp REQUIRED )
+#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}/build/src/libpappsomspp-qt4.so")
+ #SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+ #SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/build/src/libpappsomspp-qt4.so")
 
 INCLUDE_DIRECTORIES( ${PAPPSOMSPP_INCLUDE_DIR} )
 
@@ -53,6 +53,9 @@ configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/c
 SET(CPP_FILES
   utils/readspectrum.cpp
   core/project.cpp
+  core/match.cpp
+  core/identification_sources/identificationdatasource.cpp
+  core/identification_sources/identificationxtandemfile.cpp
   files/xpipfile.cpp
   input/xpipsaxhandler.cpp
 )
@@ -105,5 +108,3 @@ TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_QT4_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTRE
 INSTALL(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/xtpcpp DESTINATION bin)
 
 #configure_file (${CMAKE_SOURCE_DIR}/templates/share/applications/pt-peptideviewer.desktop.cmake ${CMAKE_BINARY_DIR}/templates/share/applications/pt-peptideviewer.desktop)
-
-add_subdirectory(input)
\ No newline at end of file

src/core/identification_sources/identificationdatasource.cpp

+
+/*******************************************************************************
+* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+#include "identificationdatasource.h"
+
+IdentificationDataSource::IdentificationDataSource(pappso::MsRunIdSp & ms_run_sp)
+{
+    _ms_run_sp = ms_run_sp;
+}
+
+IdentificationDataSource::IdentificationDataSource(const IdentificationDataSource& other)
+{
+    _ms_run_sp = other._ms_run_sp;
+    _resource_name = other._resource_name;
+}
+
+IdentificationDataSource::~IdentificationDataSource()
+{
+
+}
+
+bool IdentificationDataSource::operator==(const IdentificationDataSource& other) const
+{
+
+}
+
+
+const QString & IdentificationDataSource::getResourceName () const {
+    return _resource_name;
+}
+
+
+pappso::MsRunIdSp IdentificationDataSource::getMsRunSp () const {
+    return (_ms_run_sp);
+}

src/core/identification_sources/identificationdatasource.h

+
+/*******************************************************************************
+* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+#ifndef IDENTIFICATIONDATASOURCE_H
+#define IDENTIFICATIONDATASOURCE_H
+
+
+#include <pappsomspp/msrun/msrunid.h>
+class IdentificationDataSource
+{
+public:
+    IdentificationDataSource(pappso::MsRunIdSp & ms_run_sp);
+    IdentificationDataSource(const IdentificationDataSource& other);
+    ~IdentificationDataSource();
+    bool operator==(const IdentificationDataSource& other) const;
+    
+    const QString & getResourceName () const;
+    pappso::MsRunIdSp getMsRunSp () const;
+
+protected :
+    QString _resource_name;
+private :
+    pappso::MsRunIdSp _ms_run_sp = nullptr;
+};
+
+#endif // IDENTIFICATIONDATASOURCE_H

src/core/identification_sources/identificationxtandemfile.cpp

+
+/*******************************************************************************
+* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+#include "identificationxtandemfile.h"
+
+IdentificationXtandemFile::IdentificationXtandemFile(pappso::MsRunIdSp & ms_run_sp, const QFileInfo & xtandem_file) : IdentificationDataSource(ms_run_sp), _xtandem_file(xtandem_file)
+{
+  _resource_name = _xtandem_file.absoluteFilePath();
+}
+
+IdentificationXtandemFile::IdentificationXtandemFile(const IdentificationXtandemFile& other) : IdentificationDataSource(other),_xtandem_file (other._xtandem_file)
+{ 
+}
+
+IdentificationXtandemFile::~IdentificationXtandemFile()
+{
+
+}
+
+bool IdentificationXtandemFile::operator==(const IdentificationXtandemFile& other) const
+{
+
+}

src/core/identification_sources/identificationxtandemfile.h

+
+/*******************************************************************************
+* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+#ifndef IDENTIFICATIONXTANDEMFILE_H
+#define IDENTIFICATIONXTANDEMFILE_H
+
+#include "identificationdatasource.h"
+#include <QFileInfo>
+
+class IdentificationXtandemFile: public IdentificationDataSource
+{
+public:
+    IdentificationXtandemFile(pappso::MsRunIdSp & ms_run_sp, const QFileInfo & xtandem_file);
+    IdentificationXtandemFile(const IdentificationXtandemFile& other);
+    ~IdentificationXtandemFile();
+    bool operator==(const IdentificationXtandemFile& other) const;
+    
+private:
+  const QFileInfo _xtandem_file;
+};
+
+#endif // IDENTIFICATIONXTANDEMFILE_H

src/core/match.cpp

+
+/*******************************************************************************
+* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+#include "match.h"
+
+Match::Match()
+{
+
+}
+
+Match::~Match()
+{
+
+}

src/core/match.h

+
+/*******************************************************************************
+* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+#ifndef MATCH_H
+#define MATCH_H
+
+#include <pappsomspp/protein/protein.h>
+
+class Match
+{
+public:
+    Match();
+    ~Match();
+
+private:
+    pappso::ProteinSp _protein_sp = nullptr;
+};
+
+#endif // MATCH_H

src/core/project.cpp

@@ -81,7 +81,9 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
 void Project::addProteinSp(pappso::ProteinSp protein_sp) {
   _protein_list.push_back(protein_sp);
 }
-
+void Project::addMsRunIdSp(pappso::MsRunIdSp ms_run_sp) {
+  _ms_run_list.push_back(ms_run_sp);
+}
     std::vector<pappso::ProteinSp> & Project::getProteinList() {
       return _protein_list;
     }
\ No newline at end of file

src/core/project.h

@@ -27,6 +27,7 @@
 #include <pappsomspp/grouping/grpexperiment.h>
 #include <QFileInfo>
 #include <pappsomspp/protein/protein.h>
+#include <pappsomspp/msrun/msrunid.h>
 
 class Project;
 typedef std::shared_ptr<Project> ProjectSp;
@@ -41,10 +42,13 @@ public:
     void readXpipFile(QFileInfo xpip_source);
     void addProteinSp(pappso::ProteinSp protein_sp);
     std::vector<pappso::ProteinSp> & getProteinList();
+    void addMsRunIdSp(pappso::MsRunIdSp ms_run_sp);
     
     pappso::GrpExperiment * _p_grp_experiment= nullptr;
 private :
   std::vector<pappso::ProteinSp> _protein_list;
+  
+  std::vector<pappso::MsRunIdSp> _ms_run_list;
 };
 
 #endif // PROJECT_H

src/input/xpipsaxhandler.cpp

@@ -21,6 +21,7 @@
 ******************************************************************************/
 
 #include "xpipsaxhandler.h"
+#include <pappsomspp/msrun/msrunid.h>
 
 XpipSaxHandler::XpipSaxHandler(Project * p_project):_p_project(p_project)
 {
@@ -45,14 +46,18 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
         {
             is_ok = startElement_protein(attributes);
         }
+        //<sample value="P6_08_10"/>
+        else if (qName == "sample") {
+            is_ok = startElement_sample(attributes);
+        }
         _current_text.clear();
     }
     catch (PappsoException exception_pappso) {
-        _errorStr = QObject::tr("ERROR in XtandemResultsHandler::startElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
+        _errorStr = QObject::tr("ERROR in XpipSaxHandler::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 XtandemResultsHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
+        _errorStr = QObject::tr("ERROR in XpipSaxHandler::startElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
         return false;
     }
     return is_ok;
@@ -69,19 +74,19 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
             is_ok = endElement_protein();
         }
         else if (qName == "sequence") {
-	  is_ok = endElement_sequence();
-	}
+            is_ok = endElement_sequence();
+        }
 
         // end of detection_moulon
         // else if ((_tag_stack.size() > 1) &&
         //         (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
     }
     catch (PappsoException exception_pappso) {
-        _errorStr = QObject::tr("ERROR in XtandemResultsHandler::endElement tag %1, PAPPSO exception:\n%2").arg(qName).arg(exception_pappso.qwhat());
+        _errorStr = QObject::tr("ERROR in XpipSaxHandler::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 XtandemResultsHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
+        _errorStr = QObject::tr("ERROR in XpipSaxHandler::endElement tag %1, std exception:\n%2").arg(qName).arg(exception_std.what());
         return false;
     }
 
@@ -91,6 +96,19 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
     return is_ok;
 }
 
+//<sample value="P6_21_23"/>
+bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
+
+    qDebug() << "startElement_sample ";
+    MsRunId ms_run;
+    ms_run.setXmlId(attributes.value("value").simplified());
+    ms_run.setFilename(attributes.value("value").simplified());
+    
+    _p_project->addMsRunIdSp(ms_run.makeMsRunIdSp());
+    qDebug() << "startElement_sample end" ;
+    return true;
+}
+
 /*
  * <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"/>
@@ -98,7 +116,6 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
             <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
           </protein>
           */
-
 bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
 
     qDebug() << "startElement_protein ";
@@ -110,7 +127,7 @@ bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
 
 bool XpipSaxHandler::endElement_sequence() {
     if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
-      _current_protein.setSequence(_current_text);
+        _current_protein.setSequence(_current_text);
     }
     else {
         // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);

src/input/xpipsaxhandler.h

@@ -56,6 +56,7 @@ public:
     
 private:
   bool startElement_protein(QXmlAttributes attributes);
+  bool startElement_sample(QXmlAttributes attributes);
   bool endElement_sequence();
   bool endElement_protein();