OpenMS  2.8.0
OMSSAXMLFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/XMLFile.h>
44 
45 #include <vector>
46 
47 namespace OpenMS
48 {
49  class String;
50  class ModificationsDB;
51 
60  class OPENMS_DLLAPI OMSSAXMLFile :
61  protected Internal::XMLHandler,
62  public Internal::XMLFile
63  {
64 public:
65 
68 
70  ~OMSSAXMLFile() override;
88  void load(const String& filename,
89  ProteinIdentification& protein_identification,
90  std::vector<PeptideIdentification>& id_data,
91  bool load_proteins = true,
92  bool load_empty_hits = true);
93 
96 
97 protected:
98  // Docu in base class
99  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
100 
101  // Docu in base class
102  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
103 
104  // Docu in base class
105  void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
106 
107 private:
108 
110 
112 
115 
117  std::vector<PeptideIdentification>* peptide_identifications_;
118 
120 
122 
124 
125  std::vector<PeptideEvidence> actual_peptide_evidences_;
126 
128 
130 
132 
135 
138 
140  std::vector<std::pair<UInt, String> > modifications_;
141 
144 
147 
150 
153 
156  };
157 
158 } // namespace OpenMS
159 
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:325
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:59
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:63
OMSSAXMLFile & operator=(const OMSSAXMLFile &rhs)
std::vector< PeptideEvidence > actual_peptide_evidences_
Definition: OMSSAXMLFile.h:125
PeptideEvidence actual_peptide_evidence_
Definition: OMSSAXMLFile.h:123
void readMappingFile_()
reads the mapping file needed for modifications
ProteinIdentification actual_protein_id_
Definition: OMSSAXMLFile.h:129
PeptideIdentification actual_peptide_id_
Definition: OMSSAXMLFile.h:127
PeptideHit actual_peptide_hit_
Definition: OMSSAXMLFile.h:121
std::vector< PeptideIdentification > * peptide_identifications_
the identifications (storing the peptide hits)
Definition: OMSSAXMLFile.h:117
String tag_
Definition: OMSSAXMLFile.h:131
ModificationDefinitionsSet mod_def_set_
modification definitions set of the search, needed to annotate fixed modifications
Definition: OMSSAXMLFile.h:155
OMSSAXMLFile()
Default constructor.
OMSSAXMLFile(const OMSSAXMLFile &rhs)
ProteinHit actual_protein_hit_
Definition: OMSSAXMLFile.h:119
bool load_empty_hits_
should empty peptide identifications be loaded or skipped?
Definition: OMSSAXMLFile.h:146
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
String actual_mod_type_
type of the modification
Definition: OMSSAXMLFile.h:137
void setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)
sets the valid modifications
Map< String, UInt > mods_to_num_
modification mapping reverse, from the modification to the mod_num
Definition: OMSSAXMLFile.h:152
bool load_proteins_
should protein hits be read from the file?
Definition: OMSSAXMLFile.h:143
void characters(const XMLCh *const chars, const XMLSize_t) override
std::vector< std::pair< UInt, String > > modifications_
modifications of the peptide defined by site and type
Definition: OMSSAXMLFile.h:140
Map< UInt, std::vector< const ResidueModification * > > mods_map_
modifications mapping file from OMSSA mod num to UniMod accession
Definition: OMSSAXMLFile.h:149
~OMSSAXMLFile() override
Destructor.
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
UInt actual_mod_site_
site of the actual modification (simple position in the peptide)
Definition: OMSSAXMLFile.h:134
Representation of a peptide evidence.
Definition: PeptideEvidence.h:51
Representation of a peptide hit.
Definition: PeptideHit.h:57
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
Representation of a protein hit.
Definition: ProteinHit.h:60
Representation of a protein identification run.
Definition: ProteinIdentification.h:72
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
loads data from a OMSSAXML file
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Returns a pointer to a modified residue given a residue and a pointer to a modification from the.