WIP: proticdbml output

src/core/identificationgroup.cpp

@@ -166,6 +166,9 @@ void IdentificationGroup::addMsRunSp(MsRunSp ms_run_sp) {
 const std::vector<MsRunSp> & IdentificationGroup::getMsRunSpList() const {
     return _ms_run_list;
 }
+const std::vector<IdentificationDataSource *> & IdentificationGroup::getIdentificationDataSourceList() const {
+    return _id_source_list;
+}
 std::vector<ProteinMatch *> & IdentificationGroup::getProteinMatchList() {
     return _protein_match_list;
 }

src/core/identificationgroup.h

@@ -93,6 +93,7 @@ public:
     void startGrouping (const GroupingType & grouping_type);
 
     const std::vector<MsRunSp> & getMsRunSpList() const;
+    const std::vector<IdentificationDataSource *> & getIdentificationDataSourceList() const;
 
     /** @brief get tab name for qtabwidget
      * */

src/output/proticdbml.cpp

@@ -33,6 +33,7 @@
 #include <pappsomspp/grouping/grpprotein.h>
 #include <pappsomspp/amino_acid/Aa.h>
 #include "../core/msrun.h"
+#include "../config.h"
 
 ProticdbMl::ProticdbMl(const QString & out_filename)
 {
@@ -149,7 +150,7 @@ void ProticdbMl::writeSequence(ProteinMatch * p_protein_match) {
 }
 
 void ProticdbMl::writeProject() {
-qDebug() << "ProticdbMl::writeProject begin";
+    qDebug() << "ProticdbMl::writeProject begin";
     _output_stream->writeStartElement("project");
     _output_stream->writeAttribute("name", "");
     _output_stream->writeAttribute("id", "p1");
@@ -178,101 +179,66 @@ qDebug() << "ProticdbMl::writeProject begin";
     _output_stream->writeEndDocument();
 
 
-qDebug() << "ProticdbMl::writeProject end duration = " << duracel << "ms";
+    qDebug() << "ProticdbMl::writeProject end duration = " << duracel << "ms";
 }
 
 void ProticdbMl::writeIdentMethod() {
-        // Ajout des méthodes
-        _output_stream->writeStartElement("identMeth");
-        _output_stream->writeAttribute("name", "");
-        _output_stream->writeAttribute("id", "m1");
-        _output_stream->writeEndElement();
+    // Ajout des méthodes
+    _output_stream->writeStartElement("identMeth");
+    _output_stream->writeAttribute("name", "");
+    _output_stream->writeAttribute("id", "m1");
+    _output_stream->writeEndElement();
 
-        // Ajout des base de données
-        _output_stream->writeStartElement("customDb");
-        _output_stream->writeAttribute("name", "");
-        _output_stream->writeAttribute("id", "customdb0");
-        _output_stream->writeEndElement();
+    // Ajout des base de données
+    _output_stream->writeStartElement("customDb");
+    _output_stream->writeAttribute("name", "");
+    _output_stream->writeAttribute("id", "customdb0");
+    _output_stream->writeEndElement();
 
 
 }
 
 void ProticdbMl::writeSamples() {
-        _output_stream->writeStartElement("samples");
-        for (std::vector<MsRunSp> msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
-                _output_stream->writeStartElement("sample");
-                QString id_samp = "samp" + pappso::Utils::getLexicalOrderedString(sample_to_id.size());
-                QString id_msrun = msrun_sp.get()->getXmlId();
-                QString name = msrun_sp.get()->getSampleName();
-                // balise sample
-                _output_stream->writeAttribute("name", name);
-                _output_stream->writeAttribute("id", id_samp);
-                _output_stream->writeEmptyElement("description");
-                _sample_to_id.insert(std::pair<QString, QString>( name, id_samp));
-
-                // Element spectrumList = doc.createElement("spectrumList");
-                // msRun.appendChild(spectrumList);
-
-                //msrun_to_id.put(samp.getSampleName(), id_msrun);
-                _output_stream->writeEndElement();// sample
-            
-        }
-        _output_stream->writeEndElement();// samples
+    _output_stream->writeStartElement("samples");
+    for (std::vector<MsRunSp> msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
+        _output_stream->writeStartElement("sample");
+        QString id_samp = "samp" + pappso::Utils::getLexicalOrderedString(sample_to_id.size());
+        QString id_msrun = msrun_sp.get()->getXmlId();
+        QString name = msrun_sp.get()->getSampleName();
+        // balise sample
+        _output_stream->writeAttribute("name", name);
+        _output_stream->writeAttribute("id", id_samp);
+        _output_stream->writeEmptyElement("description");
+        _sample_to_id.insert(std::pair<QString, QString>( name, id_samp));
+
+        // Element spectrumList = doc.createElement("spectrumList");
+        // msRun.appendChild(spectrumList);
+
+        //msrun_to_id.put(samp.getSampleName(), id_msrun);
+        _output_stream->writeEndElement();// sample
+
+    }
+    _output_stream->writeEndElement();// samples
 }
 
 void ProticdbMl::writeMsRuns() {
-    
-        _output_stream->writeStartElement("msRuns");
-        for (std::vector<MsRunSp> msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
-
-                QString name = msrun_sp.get()->getSampleName();
-
-                QString id_samp = _sample_to_id.at(name);
-
-                // Element spectrumList = doc.createElement("spectrumList");
-                // msRun.appendChild(spectrumList);
-
-                QString id_msrun = msrun_sp.get()->getXmlId();
-
-                // balise MsRun
-                _output_stream->writeStartElement("msRun");
-                _output_stream->writeAttribute("sample_id", id_samp);
-                _output_stream->writeAttribute("id", id_msrun);
-
-                _output_stream->writeStartElement("description");
-                _output_stream->writeStartElement("admin");
-                // writer.writeStartElement("contact");
-                // writer.writeStartElement("email");
-                // writer.writeCharacters("valot@moulon.inra.fr");
-                // writer.writeEndElement();// email
-
-                // writer.writeStartElement("name");
-                // writer.writeCharacters("Valot Benoit");
-                // writer.writeEndElement();// name
-                // writer.writeEndElement();// contact
-
-                _output_stream->writeStartElement("sourceFile");
-                _output_stream->writeStartElement("nameOfFile");
-                _output_stream->writeCharacters(name + ".RAW");
-                _output_stream->writeEndElement();// nameOfFile
-                _output_stream->writeEndElement();// sourceFile
-
-                _output_stream->writeStartElement("sampleName");
-                _output_stream->writeCharacters(name);
-                _output_stream->writeEndElement();// sampleName
-                _output_stream->writeEndElement();// admin
-                _output_stream->writeEndElement();// description
-
-                _output_stream->writeEndElement();// msRun
-            
-        }
-        _output_stream->writeEndElement();// msRuns
-}
 
+    _output_stream->writeStartElement("msRuns");
+    for (std::vector<MsRunSp> msrun_sp : _sp_project.get()->getMsRunStore().getMsRunList()) {
 
-void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification) {
-        _output_stream->writeAttribute("ident_method_id", "m1");
-        _output_stream->writeAttribute("customdb_id", "customdb0");
+        QString name = msrun_sp.get()->getSampleName();
+
+        QString id_samp = _sample_to_id.at(name);
+
+        // Element spectrumList = doc.createElement("spectrumList");
+        // msRun.appendChild(spectrumList);
+
+        QString id_msrun = msrun_sp.get()->getXmlId();
+
+        // balise MsRun
+        _output_stream->writeStartElement("msRun");
+        _output_stream->writeAttribute("sample_id", id_samp);
+        _output_stream->writeAttribute("id", id_msrun);
 
         _output_stream->writeStartElement("description");
         _output_stream->writeStartElement("admin");
@@ -285,108 +251,163 @@ void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification)
         // writer.writeCharacters("Valot Benoit");
         // writer.writeEndElement();// name
         // writer.writeEndElement();// contact
-        /*
-        this.xpipFile = XtandemPipelineSession.getInstance()
-        .getCurrentXpipFile();
 
         _output_stream->writeStartElement("sourceFile");
         _output_stream->writeStartElement("nameOfFile");
-        // TODO
-        // get the loaded xpip file name
-        _output_stream->writeCharacters(this.xpipFile.getName());
+        _output_stream->writeCharacters(name + ".RAW");
         _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->writeStartElement("sampleName");
+        _output_stream->writeCharacters(name);
+        _output_stream->writeEndElement();// sampleName
         _output_stream->writeEndElement();// admin
+        _output_stream->writeEndElement();// description
 
-        // if we can retrieve original informations in xml xtandem results
-        HashSet<IdentificationXtandemFile> xtSourceFiles = Utils
-        .getXtandemFileList(identification);
-        if (xtSourceFiles != null) {
-            //
-            for (IdentificationXtandemFile xtFile : xtSourceFiles) {
-                xtFile.writeProticDbMlDataProcessing(this.writer);
-            }
-        } else {
-            writer.writeStartElement("dataProcessing");
-            writer.writeStartElement("software");
-            writer.writeStartElement("name");
-            writer.writeAttribute("acc", "PROTICdbO:0000283");
-            writer.writeCharacters("X!Tandem");
-            writer.writeEndElement();// name
-            writer.writeStartElement("version");
-            writer.writeCharacters(XtandemPipelineSession.getInstance()
-            .getConfig().getXtandemVersion());
-            writer.writeEndElement();// version
-            writer.writeEndElement();// software
-            writer.writeStartElement("processingMethod");
-            writer.writeEndElement();// processingMethod
-            writer.writeEndElement();// dataProcessing
-        }
+        _output_stream->writeEndElement();// msRun
 
-        // id: PROTICdbO:0000316
-        // name: X!TandemPipeline
-
-        writer.writeStartElement("dataProcessing");
-        writer.writeStartElement("software");
-        writer.writeStartElement("name");
-        writer.writeAttribute("acc", "PROTICdbO:0000316");
-        writer.writeCharacters("X!TandemPipeline");
-        writer.writeEndElement();// name
-        writer.writeStartElement("version");
-        writer.writeCharacters(XtandemPipelineMain.version);
-        writer.writeEndElement();// version
-        writer.writeEndElement();// software
-        writer.writeStartElement("processingMethod");
-        // cvParams
-
-        writeCvParam("PROTICdbO:0000323", ""
-        + XtandemPipelineSession.getInstance().getConfig()
-        .get_protein_evalue(),
-        "X!TandemPipeline filter on protein evalue (log)");
-
-        // indi
-        // combine
-        // phospho
-        xtpExperimentType = XtandemPipelineSession.getInstance()
-        .getDataTypeBase().getType();
-        if (xtpExperimentType.equals("indiv")) {
-            this.writeCvParam("PROTICdbO:0000319", xtpExperimentType, "");
-        }
-        if (xtpExperimentType.equals("combi")) {
-            this.writeCvParam("PROTICdbO:0000320", xtpExperimentType, "");
-        }
-        if (xtpExperimentType.equals("phospho")) {
-            this.writeCvParam("PROTICdbO:0000321", xtpExperimentType, "");
-        }
+    }
+    _output_stream->writeEndElement();// msRuns
+}
+
+void ProticdbMl::writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source) {
+
+
+    _output_stream->writeStartElement("dataProcessing");
+    _output_stream->writeStartElement("software");
+    _output_stream->writeStartElement("name");
+    if (p_identification_data_source->getIdentificationEngine() == IdentificationEngine::XTandem) {
+        _output_stream->writeAttribute("acc", "PROTICdbO:0000283");
+    }
+    _output_stream->writeCharacters(p_identification_data_source->getIdentificationEngineName());
+
+    _output_stream->writeEndElement();// name
+    _output_stream->writeStartElement("version");
+    _output_stream->writeCharacters(p_identification_data_source->getIdentificationEngineVersion());
+    _output_stream->writeEndElement();// version
+    _output_stream->writeEndElement();// software
+    _output_stream->writeStartElement("processingMethod");
+    // mzXml source file name
+    writeCvParam("PROTICdbO:0000343",p_identification_data_source->getMsRunSp().get()->getFilename(),
+                 "MS/MS data source file name");
+    if (p_identification_data_source->getIdentificationEngine() == IdentificationEngine::XTandem) {
+        // model file name
+        writeCvParam("PROTICdbO:0000342", p_identification_data_source->getIdentificationEngineParam(IdentificationEngineParam::tandem_param).toString(),
+                     "X!tandem xml model file name");
+        // xtandem result file name
+        writeCvParam("PROTICdbO:0000341", p_identification_data_source->getResourceName(),
+                     "X!tandem xml result file name");
+    }
+    _output_stream->writeEndElement();// processingMethod
+    _output_stream->writeEndElement();// dataProcessing
+    /*
+    _output_stream->writeStartElement("dataProcessing");
+    _output_stream->writeStartElement("software");
+    _output_stream->writeStartElement("name");
+    _output_stream->writeAttribute("acc", "PROTICdbO:0000283");
+    _output_stream->writeCharacters("X!Tandem");
+    _output_stream->writeEndElement();// name
+    _output_stream->writeStartElement("version");
+    _output_stream->writeCharacters(XtandemPipelineSession.getInstance()
+                           .getConfig().getXtandemVersion());
+    _output_stream->writeEndElement();// version
+    _output_stream->writeEndElement();// software
+    _output_stream->writeStartElement("processingMethod");
+    _output_stream->writeEndElement();// processingMethod
+    _output_stream->writeEndElement();// dataProcessing
+    */
+}
+
+void ProticdbMl::writeIdentificationRun(IdentificationGroup * p_identification) {
+    _output_stream->writeAttribute("ident_method_id", "m1");
+    _output_stream->writeAttribute("customdb_id", "customdb0");
+
+    _output_stream->writeStartElement("description");
+    _output_stream->writeStartElement("admin");
+    // writer.writeStartElement("contact");
+    // writer.writeStartElement("email");
+    // writer.writeCharacters("valot@moulon.inra.fr");
+    // writer.writeEndElement();// email
+
+    // writer.writeStartElement("name");
+    // writer.writeCharacters("Valot Benoit");
+    // writer.writeEndElement();// name
+    // writer.writeEndElement();// contact
+    /*
+    this.xpipFile = XtandemPipelineSession.getInstance()
+    .getCurrentXpipFile();
+
+    _output_stream->writeStartElement("sourceFile");
+    _output_stream->writeStartElement("nameOfFile");
+    // TODO
+    // get the loaded xpip file name
+    _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
+    //
+    for (IdentificationDataSource * p_identification_data_source : p_identification->getIdentificationDataSourceList()) {
+        writeIdentificationDataSource(p_identification_data_source);
+    }
+
+// id: PROTICdbO:0000316
+// name: X!TandemPipeline
+
+    _output_stream->writeStartElement("dataProcessing");
+    _output_stream->writeStartElement("software");
+    _output_stream->writeStartElement("name");
+    _output_stream->writeAttribute("acc", "PROTICdbO:0000316");
+    _output_stream->writeCharacters("X!TandemPipeline");
+    _output_stream->writeEndElement();// name
+    _output_stream->writeStartElement("version");
+    _output_stream->writeCharacters(XTPCPP_VERSION);
+    _output_stream->writeEndElement();// version
+    _output_stream->writeEndElement();// software
+    _output_stream->writeStartElement("processingMethod");
+// cvParams
+
+    writeCvParam("PROTICdbO:0000323", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterProteinEvalue()),
+                 "X!TandemPipeline filter on protein evalue (log)");
+
+// indi
+// combine
+// phospho
+    if (_sp_project.get()->isCombineMode()) {
+        writeCvParam("PROTICdbO:0000320", "combine", "");
+    }
+    else {
+        writeCvParam("PROTICdbO:0000319", "indiv", "");
+    }
+    //if (xtpExperimentType.equals("phospho")) {
+    //    this.writeCvParam("PROTICdbO:0000321", xtpExperimentType, "");
+    //}
 
-        this.writeCvParam("PROTICdbO:0000325", ""
-        + XtandemPipelineSession.getInstance().getConfig()
-        .get_peptide_number(),
-        "X!TandemPipeline filter on minimal number of peptide per protein");
+    writeCvParam("PROTICdbO:0000325", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterMinimumPeptidePerMatch()),
+                      "X!TandemPipeline filter on minimal number of peptide per protein");
 
-        this.writeCvParam("PROTICdbO:0000324", ""
-        + XtandemPipelineSession.getInstance().getConfig()
-        .get_peptide_evalue(),
-        "X!TandemPipeline filter on peptide evalue");
+    writeCvParam("PROTICdbO:0000324", QString("%1").arg(_sp_project.get()->getAutomaticFilterParameters().getFilterPeptideEvalue()),
+                      "X!TandemPipeline filter on peptide evalue");
 
-        // TODO write database filter
-        // this.writeCvParam("PROTICdbO:0000324", ""
-        // +
-        // XtandemPipelineSession.getInstance().getConfig().get_database_filter(),
-        // "X!TandemPipeline filter on peptide evalue");
+// TODO write database filter
+// this.writeCvParam("PROTICdbO:0000324", ""
+// +
+// XtandemPipelineSession.getInstance().getConfig().get_database_filter(),
+// "X!TandemPipeline filter on peptide evalue");
 
-        writer.writeEndElement();// processingMethod
+    _output_stream->writeEndElement();// processingMethod
 
-        writer.writeEndElement();// dataProcessing
+    _output_stream->writeEndElement();// dataProcessing
 
-        writer.writeEndElement();// description
+    _output_stream->writeEndElement();// description
 }
 
 private void writePeptideHit(Peptide pep, Group group,

src/output/proticdbml.h

@@ -56,6 +56,7 @@ private :
     void writeSamples();
     void writeMsRuns();
     void writeIdentificationRun(IdentificationGroup * p_identification);
+    void writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source);
     
 private :
     QFile * _output_file;