WIP: writing proticdbml

src/core/peptidematch.h

@@ -46,19 +46,19 @@ public :
      */
     pappso::pappso_double getExperimentalMass() const;
 
-        /** @brief get experimental mz of this peptide
-     * @return the real mass measured (precuror mass) by the spectrometer
-     */
+    /** @brief get experimental mz of this peptide
+    * @return the real mass measured (precuror mass) by the spectrometer
+    */
     pappso::pappso_double getExperimentalMz() const;
 
-    
+
     /** @brief set experimental mass of this peptide
      * @arg exp_mass the computed mass given the precursor measured mass and the deduced peptide charge
      */
     void setExperimentalMass(pappso::pappso_double exp_mass);
-    
-    
-        
+
+
+
     /** \brief set specific parameter value
      */
     virtual void setParam(PeptideMatchParam param, const QVariant& value);
@@ -66,14 +66,14 @@ public :
      */
     virtual const QVariant getParam(PeptideMatchParam param) const;
 
-    
-/** @brief set start position of this peptide inside the protein sequence
-     * @param start position in the protein amino acid sequence (starts at 0)
-     * */
+
+    /** @brief set start position of this peptide inside the protein sequence
+         * @param start position in the protein amino acid sequence (starts at 0)
+         * */
     void setStart(unsigned int start);
-/** @brief get start position of this peptide inside the protein sequence
-     * @return start position in the protein amino acid sequence (starts at 0)
-     * */
+    /** @brief get start position of this peptide inside the protein sequence
+         * @return start position in the protein amino acid sequence (starts at 0)
+         * */
     unsigned int getStart() const;
     void setCharge(unsigned int charge);
     void setPeptideXtpSp (PeptideXtpSp peptide);
@@ -91,19 +91,19 @@ public :
     unsigned int getCharge() const;
     const PeptideXtpSp & getPeptideXtpSp() const;
     pappso::pappso_double getEvalue() const;
-    
+
     void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
     const pappso::GrpPeptideSp & getGrpPeptideSp() const;
 
-           /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
-     * */
+    /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
+    * */
     void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-    
+
     /** @brief get delta between theoretical mhplus mass and mhplus experimental mass
      * theoretical mhplus mass - mhplus experimental mass
       */
     pappso::mz getDeltaMass() const;
-    
+
     ValidationState getValidationState() const;
 
 private :

src/output/proticdbml.h

@@ -38,6 +38,8 @@
 #include "../core/project.h"
 #include "../grouping/groupinggroup.h"
 
+struct ProticPeptideHit;
+
 class ProticdbMl
 {
     public:
@@ -59,6 +61,9 @@ private :
     void writeIdentificationDataSource(IdentificationDataSource * p_identification_data_source);
     void writepeptideHits(IdentificationGroup * p_identification);
     void writepeptideHitsbyGroup(GroupingGroup * p_group);
+    void writePeptideHit(QString xml_id, ProticPeptideHit & protic_peptide_hit);
+    void writePtms(PeptideXtp * p_peptide);
+    void writeMatchs(IdentificationGroup * p_identification);
     
 private :
     QFile * _output_file;

src/utils/utils.cpp

@@ -7,6 +7,9 @@ const QUrl Utils::getOlsUrl(QString psimod_accession) {
     return url;
 }
 
+const QString Utils::getXmlDouble(pappso::pappso_double number){
+    return QString::number(number,'g',6);
+}
 
 const QString Utils::getDatabaseName(ExternalDatabase database) {
     QString database_name;

src/utils/utils.h

@@ -31,6 +31,7 @@ class Utils
 public:
     static const QUrl getOlsUrl(QString modification);
     static const QString getDatabaseName(ExternalDatabase database);
+    static const QString getXmlDouble(pappso::pappso_double number);
 };
 
 #endif // UTILS_H