writeSamples added

src/output/proticdbml.cpp

@@ -32,6 +32,7 @@
 #include <pappsomspp/utils.h>
 #include <pappsomspp/grouping/grpprotein.h>
 #include <pappsomspp/amino_acid/Aa.h>
+#include "../core/msrun.h"
 
 ProticdbMl::ProticdbMl(const QString & out_filename)
 {
@@ -196,37 +197,27 @@ void ProticdbMl::writeIdentMethod() {
 
 }
 
-private void writeSamples() throws Exception {
-    try {
-        writer.writeStartElement("samples");
-
-        for (Identification ident : arrayIdentifications) {
-            for (MsRun samp : ident.getMsRunSet()) {
-                writer.writeStartElement("sample");
-                String id_samp = "samp" + sample_to_id.size();
-                String id_msrun = "msr" + msrun_to_id.size();
-                String name = samp.getSampleName();
-                name = name.replaceAll(".xml", "");
+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
-                writer.writeAttribute("name", name);
-                writer.writeAttribute("id", id_samp);
-                writer.writeEmptyElement("description");
-                sample_to_id.put(samp.getSampleName(), id_samp);
+                _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);
-                writer.writeEndElement();// sample
-            }
+                //msrun_to_id.put(samp.getSampleName(), id_msrun);
+                _output_stream->writeEndElement();// sample
+            
         }
-        writer.writeEndElement();// samples
-    } catch (Exception e) {
-        String message = "error writing samples in ProticDbMl \n"
-                         + e.getMessage();
-        logger.error(message);
-        throw new Exception(message);
-    }
+        _output_stream->writeEndElement();// samples
 }
 
 private void writeMsRuns() throws Exception {

src/output/proticdbml.h

@@ -53,6 +53,7 @@ private :
     void writeSequence(ProteinMatch * p_protein_match);
     void writeProject();
     void writeIdentMethod();
+    void writeSamples();
     
 private :
     QFile * _output_file;
@@ -61,6 +62,7 @@ private :
     IdentificationGroup * _p_identification_group;
     QTime _duracel;
     std::map<QString, QString> _map_accession2xmlid;
+    std::map<QString, QString> _sample_to_id;
 };
 
 #endif // PROTICDBML_H