OpenMS
OMSSAXMLFile.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Andreas Bertsch $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 #include <OpenMS/FORMAT/XMLFile.h>
18 
19 #include <vector>
20 
21 namespace OpenMS
22 {
23  class String;
24  class ModificationsDB;
25 
34  class OPENMS_DLLAPI OMSSAXMLFile :
35  protected Internal::XMLHandler,
36  public Internal::XMLFile
37  {
38 public:
39 
42 
44  ~OMSSAXMLFile() override;
62  void load(const String& filename,
63  ProteinIdentification& protein_identification,
65  bool load_proteins = true,
66  bool load_empty_hits = true);
67 
70 
71 protected:
72  // Docu in base class
73  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
74 
75  // Docu in base class
76  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
77 
78  // Docu in base class
79  void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
80 
81 private:
82 
84 
86 
89 
92 
94 
96 
98 
99  std::vector<PeptideEvidence> actual_peptide_evidences_;
100 
102 
104 
106 
109 
112 
114  std::vector<std::pair<UInt, String> > modifications_;
115 
118 
121 
123  std::map<UInt, std::vector<const ResidueModification*> > mods_map_;
124 
126  std::map<String, UInt> mods_to_num_;
127 
130  };
131 
132 } // namespace OpenMS
133 
char16_t XMLCh
Definition: ClassTest.h:28
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:23
Base class for XML handlers.
Definition: XMLHandler.h:328
Definition: ModificationDefinitionsSet.h:34
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:37
OMSSAXMLFile & operator=(const OMSSAXMLFile &rhs)
std::vector< PeptideEvidence > actual_peptide_evidences_
Definition: OMSSAXMLFile.h:99
PeptideEvidence actual_peptide_evidence_
Definition: OMSSAXMLFile.h:97
void readMappingFile_()
reads the mapping file needed for modifications
ProteinIdentification actual_protein_id_
Definition: OMSSAXMLFile.h:103
PeptideIdentification actual_peptide_id_
Definition: OMSSAXMLFile.h:101
std::map< UInt, std::vector< const ResidueModification * > > mods_map_
modifications mapping file from OMSSA mod num to UniMod accession
Definition: OMSSAXMLFile.h:123
PeptideHit actual_peptide_hit_
Definition: OMSSAXMLFile.h:95
String tag_
Definition: OMSSAXMLFile.h:105
ModificationDefinitionsSet mod_def_set_
modification definitions set of the search, needed to annotate fixed modifications
Definition: OMSSAXMLFile.h:129
std::map< String, UInt > mods_to_num_
modification mapping reverse, from the modification to the mod_num
Definition: OMSSAXMLFile.h:126
OMSSAXMLFile()
Default constructor.
OMSSAXMLFile(const OMSSAXMLFile &rhs)
ProteinHit actual_protein_hit_
Definition: OMSSAXMLFile.h:93
bool load_empty_hits_
should empty peptide identifications be loaded or skipped?
Definition: OMSSAXMLFile.h:120
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:111
void setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)
sets the valid modifications
bool load_proteins_
should protein hits be read from the file?
Definition: OMSSAXMLFile.h:117
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:114
~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:108
PeptideIdentificationList * peptide_identifications_
the identifications (storing the peptide hits)
Definition: OMSSAXMLFile.h:91
Representation of a peptide evidence.
Definition: PeptideEvidence.h:25
Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS).
Definition: PeptideHit.h:50
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum.
Definition: PeptideIdentification.h:63
Representation of a protein hit.
Definition: ProteinHit.h:34
Representation of a protein identification run.
Definition: ProteinIdentification.h:51
A more convenient string class.
Definition: String.h:34
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
void load(const String &filename, ProteinIdentification &protein_identification, PeptideIdentificationList &id_data, bool load_proteins=true, bool load_empty_hits=true)
loads data from a OMSSAXML file
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19