WIP : proticdbml writer, test xpip

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;

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()) {

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;
 };

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") {

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)");

src/output/proticdbml.h

@@ -55,6 +55,7 @@ private :
     void writeIdentMethod();
     void writeSamples();
     void writeMsRuns();
+    void writeIdentificationRun(IdentificationGroup * p_identification);
     
 private :
     QFile * _output_file;