sax parser for xpip file

src/CMakeLists.txt

@@ -12,7 +12,7 @@
 #FIND_PACKAGE(Boost REQUIRED)
 #INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS})
 
-FIND_PACKAGE( Qt4 COMPONENTS QTCORE QTGUI QTSVG REQUIRED )
+FIND_PACKAGE( Qt4 COMPONENTS QTCORE QTGUI QTSVG QTXML REQUIRED )
 
 
 FIND_PACKAGE( Odsstream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
@@ -54,6 +54,7 @@ SET(CPP_FILES
   utils/readspectrum.cpp
   core/project.cpp
   files/xpipfile.cpp
+  input/xpipsaxhandler.cpp
 )
 
 set(QTLIBS ${Qt5Xml_LIBRARIES} ${Qt5Gui_LIBRARIES}  ${Qt5Svg_LIBRARIES})
@@ -92,15 +93,17 @@ MESSAGE("XTPCPP_SRCS:  ${XTPCPP_SRCS}")
 
 
 ADD_EXECUTABLE(xtpcpp main.cpp ${CPP_FILES} ${XTPCPP_SRCS} ${GUI_UI_HDRS} ${XTPCPP_MOC_SRCS})
-target_include_directories (xtpcpp PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR} ${QT_QTGUI_INCLUDE_DIR} ${QT_QTSVG_INCLUDE_DIR})
+target_include_directories (xtpcpp PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR} ${QT_QTGUI_INCLUDE_DIR} ${QT_QTSVG_INCLUDE_DIR} ${QT_QTXML_INCLUDE_DIR})
   SET_TARGET_PROPERTIES(xtpcpp
     PROPERTIES OUTPUT_NAME xtpcpp
     CLEAN_DIRECT_OUTPUT 1
     COMPILE_DEFINITIONS "${QT_DEFINITIONS}"
     #INCLUDE_DIRECTORIES "${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}"
     )
-TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_QT4_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTREAM_QT4_LIBRARY} ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY} ${QT_QTSVG_LIBRARY})
+TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_QT4_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTREAM_QT4_LIBRARY} ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY} ${QT_QTSVG_LIBRARY} ${QT_QTXML_LIBRARY})
 
 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/project.cpp

@@ -21,6 +21,7 @@
 *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
 ******************************************************************************/
 #include "project.h"
+#include "../input/xpipsaxhandler.h"
 
 Project::Project()
 {
@@ -33,5 +34,45 @@ Project::~Project()
 }
 
 ProjectSp Project::makeProjectSp() const {
-  return std::make_shared<Project>(*this);
-}
\ No newline at end of file
+    return std::make_shared<Project>(*this);
+}
+
+
+void Project::readXpipFile(QFileInfo xpip_fileinfo) {
+    
+    
+    XpipSaxHandler * parser = new XpipSaxHandler();
+
+    QXmlSimpleReader simplereader;
+    simplereader.setContentHandler(parser);
+    simplereader.setErrorHandler(parser);
+
+    qDebug() << "Read XPIP XML result file '" << xpip_fileinfo.absoluteFilePath() << "'";
+
+    QFile qfile(xpip_fileinfo.absoluteFilePath());
+    QXmlInputSource xmlInputSource(&qfile);
+
+    if (simplereader.parse(xmlInputSource)) {
+    } 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();
+
+
+    std::list<GrpProteinSp> protein_list;
+    grpExperiment.getGroupedProteinSpList(protein_list);
+    */
+
+}

src/core/project.h

@@ -24,6 +24,8 @@
 #define PROJECT_H
 
 #include<memory>
+#include <pappsomspp/grouping/grpexperiment.h>
+#include <QFileInfo>
 
 class Project;
 typedef std::shared_ptr<Project> ProjectSp;
@@ -35,6 +37,9 @@ public:
     ~Project();
     
     ProjectSp makeProjectSp() const;
+    void readXpipFile(QFileInfo xpip_source);
+    
+    pappso::GrpExperiment * _p_grp_experiment= nullptr; 
 };
 
 #endif // PROJECT_H

src/files/xpipfile.cpp

@@ -30,9 +30,12 @@ XpipFile::~XpipFile()
 {
 
 }
+
 ProjectSp XpipFile::getProjectSp() const {
-  Project project;
+  ProjectSp project_sp = Project().makeProjectSp();
+  
+  project_sp.get()->readXpipFile(QFileInfo(_xpip_source.toLocalFile()));
   
-  return (project.makeProjectSp());
+  return (project_sp);
   
 }
\ No newline at end of file

src/gui/protein_list_view/proteintablemodel.cpp

@@ -49,11 +49,11 @@ QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation,
             switch (section)
             {
             case 0:
-                return QString("first");
+                return QString("group");
             case 1:
-                return QString("second");
+                return QString("subgroup");
             case 2:
-                return QString("third");
+                return QString("protein description");
             }
         }
     }

src/input/xpipsaxhandler.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 "xpipsaxhandler.h"
+
+XpipSaxHandler::XpipSaxHandler()
+{
+
+}
+
+XpipSaxHandler::~XpipSaxHandler()
+{
+
+}
+
+
+bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString & localName,
+                                  const QString & qName, const QXmlAttributes & attributes) {
+    // qDebug() << namespaceURI << " " << localName << " " << qName ;
+    _tag_stack.push_back(qName);
+    bool is_ok = true;
+
+    try {
+        //startElement_group
+        if (qName == "group")
+        {
+            //is_ok = startElement_group(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());
+        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());
+        return false;
+    }
+    return is_ok;
+}
+
+bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & localName,
+                                const QString & qName) {
+
+    bool is_ok = true;
+    // endElement_peptide_list
+    try {
+        if (qName == "group")
+        {
+            //is_ok = endElement_group();
+        }
+
+        // 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());
+        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());
+        return false;
+    }
+
+    _current_text.clear();
+    _tag_stack.pop_back();
+
+    return is_ok;
+}
+
+/*
+bool XpipSaxHandler::endElement_group() {
+    if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 2] == "group")) {
+    }
+    else {
+        // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
+    }
+    return true;
+}
+*/
+
+
+bool XpipSaxHandler::error(const QXmlParseException &exception) {
+    _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                            "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
+                    exception.message());
+
+    return false;
+}
+
+
+bool XpipSaxHandler::fatalError(const QXmlParseException &exception) {
+    _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+                            "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
+                    exception.message());
+    return false;
+}
+
+QString XpipSaxHandler::errorString() const {
+    return _errorStr;
+}
+
+
+bool XpipSaxHandler::endDocument() {
+    return true;
+}
+
+bool XpipSaxHandler::startDocument() {
+    return true;
+}
+
+bool XpipSaxHandler::characters(const QString &str) {
+    _current_text += str;
+    return true;
+}
+

src/input/xpipsaxhandler.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 XPIPSAXHANDLER_H
+#define XPIPSAXHANDLER_H
+
+#include <QXmlDefaultHandler>
+#include <pappsomspp/pappsoexception.h>
+
+using namespace pappso;
+
+class XpipSaxHandler: public QXmlDefaultHandler
+{
+public:
+    XpipSaxHandler();
+    ~XpipSaxHandler();
+
+    bool startElement(const QString & namespaceURI, const QString & localName,
+                      const QString & qName, const QXmlAttributes & attributes);
+
+    bool endElement(const QString & namespaceURI, const QString & localName,
+                    const QString & qName);
+
+    bool startDocument();
+
+    bool endDocument();
+
+    bool characters(const QString &str);
+
+    bool fatalError(const QXmlParseException &exception);
+    bool error(const QXmlParseException &exception);
+
+    QString errorString() const;
+
+private:
+    std::vector<QString> _tag_stack;
+    QString _errorStr;
+    QString _current_text;
+};
+
+#endif // XTANDEMRESULTSHANDLER_H