From cc4bc995c96807ec192106bebbd6e13e2a41fa8c Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Wed, 17 May 2017 16:47:51 +0200
Subject: [PATCH] WIP : proticdbml writer, test xpip
---
.../identificationxtandemfile.cpp | 2 +-
src/core/identificationgroup.cpp | 8 ++++
src/core/identificationgroup.h | 6 ++-
src/input/xpipsaxhandler.cpp | 3 +-
src/output/proticdbml.cpp | 39 ++++++++++---------
src/output/proticdbml.h | 1 +
6 files changed, 37 insertions(+), 22 deletions(-)
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index dd394f345..1555984d0 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -80,7 +80,7 @@ void IdentificationXtandemFile::parseTo(Project* p_project) {
}
}
- identification_group_p->addMsRunSp(msrun_sp);
+ identification_group_p->addIdentificationDataSourceP(this);
XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p, this);
QXmlSimpleReader simplereader;
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 944f41fa5..78e09767a 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -149,6 +149,14 @@ bool IdentificationGroup::contains (const MsRun * p_msrun) const {
}
return false;
}
+
+ void IdentificationGroup::addIdentificationDataSourceP(IdentificationDataSource * p_identification_source) {
+ addMsRunSp(p_identification_source->getMsRunSp());
+ auto it = std::find (_id_source_list.begin() ,_id_source_list.end(),p_identification_source);
+ if (it == _id_source_list.end()) {
+ _id_source_list.push_back(p_identification_source);
+ }
+ }
void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
auto it = std::find (_ms_run_list.begin() ,_ms_run_list.end(),ms_run_sp);
if (it == _ms_run_list.end()) {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 53c1f6949..0d5de141e 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -48,7 +48,7 @@ public:
const GroupStore & getGroupStore() const;
void addProteinMatch(ProteinMatch * protein_match);
std::vector<ProteinMatch *> & getProteinMatchList();
- void addMsRunSp(MsRunSp ms_run_sp);
+ void addIdentificationDataSourceP(IdentificationDataSource * p_identification_source);
/** @brief count groups
* */
@@ -102,6 +102,9 @@ public:
void collectMhDelta(std::vector< pappso::pappso_double> & delta_list, pappso::PrecisionUnit unit, ValidationState state) const;
private :
+
+ void addMsRunSp(MsRunSp ms_run_sp);
+private :
GroupingExperiment * _p_grp_experiment= nullptr;
Project * _p_project;
@@ -111,6 +114,7 @@ private :
std::vector<ProteinMatch *> _protein_match_list;
std::vector<MsRunSp> _ms_run_list;
+ std::vector<IdentificationDataSource *> _id_source_list;
std::map<QString, ProteinMatch *> _cache_accession_protein_match;
};
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 411c8227f..739fc8ac2 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -189,7 +189,7 @@ bool XpipSaxHandler::startElement_sample(QXmlAttributes attributes) {
MsRunSp ms_run = _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
ms_run.get()->setFilename(attributes.value("value").simplified());
- _current_identification_group_p->addMsRunSp(ms_run);
+ //_current_identification_group_p->addMsRunSp(ms_run);
qDebug() << "startElement_sample end" ;
return true;
}
@@ -255,6 +255,7 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
}
+ _current_identification_group_p->addIdentificationDataSourceP(p_identification_data_source);
p_identification_data_source->addFastaFile(_current_fasta_file_sp);
_p_peptide_match->setChecked(false);
if (attributes.value("validate").simplified().toLower() == "true") {
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index cf80947e1..06ba2c163 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -270,12 +270,12 @@ void ProticdbMl::writeMsRuns() {
}
-void ProticdbMl::writeIdentificationRun(Identification identification) {
- writer.writeAttribute("ident_method_id", "m1");
- writer.writeAttribute("customdb_id", "customdb0");
+void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification) {
+ _output_stream->writeAttribute("ident_method_id", "m1");
+ _output_stream->writeAttribute("customdb_id", "customdb0");
- writer.writeStartElement("description");
- writer.writeStartElement("admin");
+ _output_stream->writeStartElement("description");
+ _output_stream->writeStartElement("admin");
// writer.writeStartElement("contact");
// writer.writeStartElement("email");
// writer.writeCharacters("valot@moulon.inra.fr");
@@ -285,24 +285,25 @@ void ProticdbMl::writeIdentificationRun(Identification identification) {
// writer.writeCharacters("Valot Benoit");
// writer.writeEndElement();// name
// writer.writeEndElement();// contact
+ /*
this.xpipFile = XtandemPipelineSession.getInstance()
.getCurrentXpipFile();
- writer.writeStartElement("sourceFile");
- writer.writeStartElement("nameOfFile");
+ _output_stream->writeStartElement("sourceFile");
+ _output_stream->writeStartElement("nameOfFile");
// TODO
// get the loaded xpip file name
- writer.writeCharacters(this.xpipFile.getName());
- writer.writeEndElement();// nameOfFile
- writer.writeStartElement("pathToFile");
- writer.writeCharacters(this.xpipFile.getAbsolutePath());
- writer.writeEndElement();// pathToFile
- writer.writeStartElement("fileType");
- writer.writeCharacters("XPIP file");
- writer.writeEndElement();// fileType
- writer.writeEndElement();// sourceFile
-
- writer.writeEndElement();// admin
+ _output_stream->writeCharacters(this.xpipFile.getName());
+ _output_stream->writeEndElement();// nameOfFile
+ _output_stream->writeStartElement("pathToFile");
+ _output_stream->writeCharacters(this.xpipFile.getAbsolutePath());
+ _output_stream->writeEndElement();// pathToFile
+ _output_stream->writeStartElement("fileType");
+ _output_stream->writeCharacters("XPIP file");
+ _output_stream->writeEndElement();// fileType
+ _output_stream->writeEndElement();// sourceFile
+*/
+ _output_stream->writeEndElement();// admin
// if we can retrieve original informations in xml xtandem results
HashSet<IdentificationXtandemFile> xtSourceFiles = Utils
@@ -345,7 +346,7 @@ void ProticdbMl::writeIdentificationRun(Identification identification) {
writer.writeStartElement("processingMethod");
// cvParams
- this.writeCvParam("PROTICdbO:0000323", ""
+ writeCvParam("PROTICdbO:0000323", ""
+ XtandemPipelineSession.getInstance().getConfig()
.get_protein_evalue(),
"X!TandemPipeline filter on protein evalue (log)");
diff --git a/src/output/proticdbml.h b/src/output/proticdbml.h
index f2b6837ef..b3364df62 100644
--- a/src/output/proticdbml.h
+++ b/src/output/proticdbml.h
@@ -55,6 +55,7 @@ private :
void writeIdentMethod();
void writeSamples();
void writeMsRuns();
+ void writeIdentificationRun(IdentificationGroup * p_identification);
private :
QFile * _output_file;
--
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