From d73fcb8b9c157f45fe361391750436141a24f84d Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 19 Aug 2016 18:19:43 +0200
Subject: [PATCH] sax parser for xpip file
---
src/CMakeLists.txt | 9 +-
src/core/project.cpp | 45 +++++-
src/core/project.h | 5 +
src/files/xpipfile.cpp | 7 +-
.../protein_list_view/proteintablemodel.cpp | 6 +-
src/input/xpipsaxhandler.cpp | 136 ++++++++++++++++++
src/input/xpipsaxhandler.h | 60 ++++++++
7 files changed, 258 insertions(+), 10 deletions(-)
create mode 100644 src/input/xpipsaxhandler.cpp
create mode 100644 src/input/xpipsaxhandler.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index e39188a50..67d010994 100644
--- a/src/CMakeLists.txt
+++ b/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
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 7a92c3fb5..4f51f107c 100644
--- a/src/core/project.cpp
+++ b/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);
+ */
+
+}
diff --git a/src/core/project.h b/src/core/project.h
index 31ff6dc68..d5d72c686 100644
--- a/src/core/project.h
+++ b/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
diff --git a/src/files/xpipfile.cpp b/src/files/xpipfile.cpp
index 4d13bf011..e5e55f04a 100644
--- a/src/files/xpipfile.cpp
+++ b/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
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 24a87a25d..7ef7e8e9a 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/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");
}
}
}
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
new file mode 100644
index 000000000..804b5a009
--- /dev/null
+++ b/src/input/xpipsaxhandler.cpp
@@ -0,0 +1,136 @@
+/*******************************************************************************
+* 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;
+}
+
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
new file mode 100644
index 000000000..55ca5e4cb
--- /dev/null
+++ b/src/input/xpipsaxhandler.h
@@ -0,0 +1,60 @@
+/*******************************************************************************
+* 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
--
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