OpenMS  3.0.0
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 
80  ProtXMLFile();
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 
106  void resetMembers_();
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 
OpenMS::ProtXMLFile
Used to load (storing not supported, yet) ProtXML files.
Definition: ProtXMLFile.h:70
XMLFile.h
OpenMS::ProtXMLFile::protein_group_
ProteinGroup protein_group_
protein group
Definition: ProtXMLFile.h:140
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::ProtXMLFile::pep_id_
PeptideIdentification * pep_id_
Pointer to peptide identification.
Definition: ProtXMLFile.h:136
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLHandler.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
ProteinIdentification.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::ProtXMLFile::ProteinGroup
ProteinIdentification::ProteinGroup ProteinGroup
A protein group (set of indices into ProteinIdentification)
Definition: ProtXMLFile.h:77
OpenMS::ProtXMLFile::pep_hit_
PeptideHit * pep_hit_
Temporary peptide hit.
Definition: ProtXMLFile.h:138
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
PeptideIdentification.h
OpenMS::ProteinIdentification::ProteinGroup
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:117
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55