From 05666e515a81e52bcbc36e2e261be020f9fa9770 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 19 Aug 2016 18:51:46 +0200
Subject: [PATCH] WIP parsing XPIP
---
src/CMakeLists.txt | 8 ++++----
src/core/project.cpp | 32 ++++++++++++++++++--------------
src/core/project.h | 2 ++
src/input/xpipsaxhandler.cpp | 29 +++++++++++++++++++++++++----
src/input/xpipsaxhandler.h | 13 ++++++++++++-
5 files changed, 61 insertions(+), 23 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 67d010994..31f62f99d 100644
--- a/src/CMakeLists.txt
+++ b/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} )
diff --git a/src/core/project.cpp b/src/core/project.cpp
index 4f51f107c..2d848022c 100644
--- a/src/core/project.cpp
+++ b/src/core/project.cpp
@@ -39,9 +39,9 @@ ProjectSp Project::makeProjectSp() const {
void Project::readXpipFile(QFileInfo xpip_fileinfo) {
-
-
- XpipSaxHandler * parser = new XpipSaxHandler();
+
+
+ XpipSaxHandler * parser = new XpipSaxHandler(this);
QXmlSimpleReader simplereader;
simplereader.setContentHandler(parser);
@@ -61,18 +61,22 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
}
qfile.close();
-/*
- GrpGroupingMonitor monitor;
- GrpExperiment grpExperiment(monitor);
- PeptideReader peptideReader(grpExperiment);
- FastaReader reader(peptideReader);
- reader.parse(&fastaFile);
- fastaFile.close();
- grpExperiment.startGrouping();
+ /*
+ 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);
+ */
+
+}
- std::list<GrpProteinSp> protein_list;
- grpExperiment.getGroupedProteinSpList(protein_list);
- */
+void Project::addProteinSp(pappso::ProteinSp makeProteinSp) {
}
diff --git a/src/core/project.h b/src/core/project.h
index d5d72c686..49338ace7 100644
--- a/src/core/project.h
+++ b/src/core/project.h
@@ -26,6 +26,7 @@
#include<memory>
#include <pappsomspp/grouping/grpexperiment.h>
#include <QFileInfo>
+#include <pappsomspp/protein/protein.h>
class Project;
typedef std::shared_ptr<Project> ProjectSp;
@@ -38,6 +39,7 @@ public:
ProjectSp makeProjectSp() const;
void readXpipFile(QFileInfo xpip_source);
+ void addProteinSp(pappso::ProteinSp makeProteinSp);
pappso::GrpExperiment * _p_grp_experiment= nullptr;
};
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 804b5a009..38d82c6d3 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -22,7 +22,7 @@
#include "xpipsaxhandler.h"
-XpipSaxHandler::XpipSaxHandler()
+XpipSaxHandler::XpipSaxHandler(Project * p_project):_p_project(p_project)
{
}
@@ -89,15 +89,36 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
}
/*
-bool XpipSaxHandler::endElement_group() {
- if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 2] == "group")) {
+ * <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"/>
+ <protein_evalue evalue="-384.54382" sample="20120906_balliau_extract_1_A01_urnb-1"/>
+ <sequence>MASTKAPGPGEKHHSIDAQLRQLVPGKVSEDDKLIEYDALLVDRFLNILQDLHGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVASSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEETLKRLVSEVGKSPEEVFEALKNQTVDLVFTAHPTQSARRSLLQKNARIRNCLTQLNAKDITDDDKQELDEALQREIQAAFRTDEIRRAQPTPQDEMRYGMSYIHETVWKGVPKFLRRVDTALKNIGINERLPYNVSLIRFSSWMGGDRDGNPRVTPEVTRDVCLLARMMAANLYIDQIEELMFELSMWRCNDELRVRAEELHSSSGSKVTKYYIEFWKQIPPNEPYRVILGHVRDKLYNTRERARHLLASGVSEISAESSFTSIEEFLEPLELCYKSLCDCGDKAIADGSLLDLLRQVFTFGLSLVKLDIRQESERHTDVIDAITTHLGIGSYREWPEDKRQEWLLSELRGKRPLLPPDLPQTDEIADVIGAFHVLAELPPDSFGPYIISMATAPSDVLAVELLQRECGVRQPLPVVPLFERLADLQSAPASVERLFSVDWYMDRIKGKQQVMVGYSDSGKDAGRLSAAWQLYRAQEEMAQVAKRYGVKLTLFHGRGGTVGRGGGPTHLAILSQPPDTINGSIRVTVQGEVIEFCFGEEHLCFQTLQRFTAATLEHGMHPPVSPKPEWRKLMDEMAVVATEEYRSVVVKEARFVEYFRSATPETEYGRMNIGSRPAKRRPGGGITTLRAIPWIFSWTQTRFHLPVWLGVGAAFKFAIDKDVRNFQVLKEMYNEWPFFRVTLDLLEMVFAKGDPGIAGLYDELLVAEELKPFGKQLRDKYVETQQLLLQIAGHKDILEGDPFLKQGLVLRNPYITTLNVFQAYTLKRIRDPNFKVTPQPPLSKEFADENKPAGLVKLNPASEYPPGLEDTLILTMKGIAAGMQNTG</sequence>
+ </protein>
+ */
+
+bool XpipSaxHandler::startElement_protein(QXmlAttributes attributes) {
+
+ qDebug() << "startElement_protein ";
+ _current_protein.setDescription(attributes.value("description").simplified());
+ _current_protein.setAccession(_current_protein.getDescription().split(" ").at(0));
+ qDebug() << "startElement_protein end" ;
+ return true;
+}
+
+bool XpipSaxHandler::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 XpipSaxHandler::endElement_protein() {
+ _p_project->addProteinSp(_current_protein.makeProteinSp());
+ return true;
+}
+
bool XpipSaxHandler::error(const QXmlParseException &exception) {
diff --git a/src/input/xpipsaxhandler.h b/src/input/xpipsaxhandler.h
index 55ca5e4cb..860584e06 100644
--- a/src/input/xpipsaxhandler.h
+++ b/src/input/xpipsaxhandler.h
@@ -25,13 +25,15 @@
#include <QXmlDefaultHandler>
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/protein/protein.h>
+#include "../core/project.h"
using namespace pappso;
class XpipSaxHandler: public QXmlDefaultHandler
{
public:
- XpipSaxHandler();
+ XpipSaxHandler(Project * p_project);
~XpipSaxHandler();
bool startElement(const QString & namespaceURI, const QString & localName,
@@ -51,10 +53,19 @@ public:
QString errorString() const;
+
+private:
+ bool startElement_protein(QXmlAttributes attributes);
+ bool endElement_sequence();
+ bool endElement_protein();
+
private:
std::vector<QString> _tag_stack;
QString _errorStr;
QString _current_text;
+
+ Project * _p_project;
+ Protein _current_protein;
};
#endif // XTANDEMRESULTSHANDLER_H
--
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