OpenMS
ProtXMLFile.h
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34 
35 #pragma once
36 
40 #include <OpenMS/FORMAT/XMLFile.h>
41 
42 #include <vector>
43 
44 namespace OpenMS
45 {
70  class OPENMS_DLLAPI ProtXMLFile :
71  protected Internal::XMLHandler,
72  public Internal::XMLFile
73  {
74 public:
75 
78 
81 
91  void load(const String & filename, ProteinIdentification & protein_ids, PeptideIdentification & peptide_ids);
92 
101  void store(const String & filename, const ProteinIdentification & protein_ids, const PeptideIdentification & peptide_ids, const String & document_id = "");
102 
103 protected:
104 
107 
109  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
110 
112  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
113 
115  void registerProtein_(const String & protein_name);
116 
129  void matchModification_(const double mass, const String & origin, String & modification_description);
130 
132 
133  ProteinIdentification * prot_id_;
141 
142 
144  };
145 
146 } // namespace OpenMS
147 
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
Base class for XML handlers.
Definition: XMLHandler.h:326
Representation of a peptide hit.
Definition: PeptideHit.h:57
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
Used to load (storing not supported, yet) ProtXML files.
Definition: ProtXMLFile.h:73
void store(const String &filename, const ProteinIdentification &protein_ids, const PeptideIdentification &peptide_ids, const String &document_id="")
[not implemented yet!] Stores the data in an ProtXML file
ProteinIdentification::ProteinGroup ProteinGroup
A protein group (set of indices into ProteinIdentification)
Definition: ProtXMLFile.h:77
ProtXMLFile()
Constructor.
PeptideHit * pep_hit_
Temporary peptide hit.
Definition: ProtXMLFile.h:138
void registerProtein_(const String &protein_name)
Creates a new protein entry (if not already present) and appends it to the current group.
void matchModification_(const double mass, const String &origin, String &modification_description)
find modification name given a modified AA mass
void load(const String &filename, ProteinIdentification &protein_ids, PeptideIdentification &peptide_ids)
Loads the identifications of an ProtXML file without identifier.
PeptideIdentification * pep_id_
Pointer to peptide identification.
Definition: ProtXMLFile.h:136
ProteinGroup protein_group_
protein group
Definition: ProtXMLFile.h:140
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
Docu in base class.
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
Docu in base class.
void resetMembers_()
reset members after reading/writing
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:131
Representation of a protein identification run.
Definition: ProteinIdentification.h:76
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48