new peptidextp object, collection of modifications in peptide store

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")
 
@@ -56,6 +56,7 @@ SET(CPP_FILES
   core/automaticfilterparameters.cpp
   core/identificationgroup.cpp
   core/peptidematch.cpp
+  core/peptidextp.cpp
   ./core/project.cpp
   core/proteinmatch.cpp
   core/proteinxtp.cpp

src/core/peptidextp.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 "peptidextp.h"
+
+PeptideXtp::PeptideXtp(const QString & pepstr):pappso::Peptide(pepstr)
+{
+
+}
+
+PeptideXtp::PeptideXtp(const PeptideXtp& other):pappso::Peptide(other)
+{
+
+}
+
+PeptideXtp::~PeptideXtp()
+{
+
+}
+
+PeptideXtpSp PeptideXtp::makePeptideXtpSp() const {
+    return std::make_shared<PeptideXtp>(*this);
+}

src/core/peptidextp.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
+******************************************************************************/
+
+#ifndef PEPTIDEXTP_H
+#define PEPTIDEXTP_H
+
+#include <pappsomspp/peptide/peptide.h>
+
+class PeptideXtp;
+
+/** \brief shared pointer on a Peptide object
+ */
+typedef std::shared_ptr<PeptideXtp> PeptideXtpSp;
+
+class PeptideXtp : public pappso::Peptide 
+{
+public:
+    PeptideXtp(const QString & pepstr);
+    PeptideXtp(const PeptideXtp& other);
+    ~PeptideXtp();
+    
+    PeptideXtpSp makePeptideXtpSp() const;
+
+};
+
+#endif // PEPTIDEXTP_H

src/input/xpipsaxhandler.cpp

@@ -236,7 +236,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
     //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
 //</modifs>
     qDebug() << "startElement_peptide ";
-    _current_peptide_sp = pappso::Peptide(attributes.value("sequence").simplified()).makeNoConstPeptideSp();
+    _current_peptide_sp = PeptideXtp(attributes.value("sequence").simplified()).makePeptideXtpSp();
     pappso::MsRunIdSp ms_run_id = _map_msrunid[attributes.value("sample").simplified()];
     _p_peptide_match = new PeptideMatch(ms_run_id, attributes.value("scan").simplified().toUInt());
     _p_peptide_match->setRetentionTime(attributes.value("RT").simplified().toDouble());
@@ -278,7 +278,7 @@ bool XpipSaxHandler::startElement_modif(QXmlAttributes attributes) {
 bool XpipSaxHandler::endElement_peptide() {
     qDebug() << "endElement_peptide ";
 
-    pappso::PeptideSp peptide_const = pappso::Peptide(*(_current_peptide_sp.get())).makePeptideSp();
+    PeptideXtpSp peptide_const = PeptideXtp(*(_current_peptide_sp.get())).makePeptideXtpSp();
     peptide_const = _p_project->getPeptideStore().getInstance(peptide_const);
     _p_peptide_match->setPeptideSp(peptide_const);
     return true;

src/input/xpipsaxhandler.h

@@ -26,7 +26,7 @@
 #include <QXmlDefaultHandler>
 #include <pappsomspp/pappsoexception.h>
 #include "../core/proteinxtp.h"
-#include <pappsomspp/peptide/peptide.h>
+#include "../core/peptidextp.h"
 #include <pappsomspp/amino_acid/aamodification.h>
 #include "../core/project.h"
 #include "../core/proteinmatch.h"
@@ -83,7 +83,7 @@ private:
     ProteinMatch * _p_protein_match;
     PeptideMatch * _p_peptide_match;
     ProteinXtp _current_protein;
-    pappso::NoConstPeptideSp _current_peptide_sp;
+    PeptideXtpSp _current_peptide_sp;
     IdentificationGroup * _current_identification_group_p;
     
     QMap<QString, pappso::AaModificationP> _map_massstr_aamod;

src/utils/peptidestore.cpp

@@ -28,6 +28,7 @@
  ******************************************************************************/
 
 #include "peptidestore.h"
+#include <pappsomspp/amino_acid/Aa.h>
 
 PeptideStore::PeptideStore()
 {
@@ -39,14 +40,21 @@ PeptideStore::~PeptideStore()
 
 }
 
-pappso::PeptideSp & PeptideStore::getInstance(pappso::PeptideSp & peptide_in) {
-    std::size_t sequence_li_crc = _hash_fn ( peptide_in.get()->getLiAbsoluteString().toStdString());
+PeptideXtpSp & PeptideStore::getInstance(PeptideXtpSp & peptide_in) {
+    std::size_t sequence_crc = _hash_fn ( peptide_in.get()->toAbsoluteString().toStdString());
 
     //QByteArray source = peptide_in.get()->getLiAbsoluteString().toUtf8();
     //quint16 sequence_li_crc = qChecksum(source.data(), source.length());
 
-    std::pair<std::unordered_map< std::size_t, pappso::PeptideSp>::iterator,bool> ret = _map_crc_peptide_list.insert(std::pair<std::size_t, pappso::PeptideSp>(sequence_li_crc,peptide_in));
-    
+    std::pair<std::unordered_map< std::size_t, PeptideXtpSp>::iterator,bool> ret = _map_crc_peptide_list.insert(std::pair<std::size_t, PeptideXtpSp>(sequence_crc,peptide_in));
+    if (ret.second) {
+        //if new peptide in store
+
+        for (auto && aa : *(ret.first->second.get())) {
+            std::list<pappso::AaModificationP> mod_list = aa.getModificationList();
+	    _modification_collection.insert(mod_list.begin(), mod_list.end());
+        }
+    }
     return ret.first->second;
 
 }

src/utils/peptidestore.h

@@ -30,8 +30,9 @@
 #ifndef PEPTIDESTORE_H
 #define PEPTIDESTORE_H
 
-#include <pappsomspp/peptide/peptide.h>
+#include "../core/peptidextp.h"
 #include <unordered_map>
+#include <set>
 
 class PeptideStore
 {
@@ -39,12 +40,13 @@ public:
     PeptideStore();
     ~PeptideStore();
 
-    pappso::PeptideSp & getInstance(pappso::PeptideSp & peptide_in);
+    PeptideXtpSp & getInstance(PeptideXtpSp & peptide_in);
 
 private :
   
     std::hash<std::string> _hash_fn;
-    std::unordered_map<std::size_t, pappso::PeptideSp> _map_crc_peptide_list;
+    std::unordered_map<std::size_t, PeptideXtpSp> _map_crc_peptide_list;
+    std::set<pappso::AaModificationP> _modification_collection;
 };
 
 #endif // PEPTIDESTORE_H