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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Marc Sturm $
7 // --------------------------------------------------------------------------
9 #pragma once
15 #include <OpenMS/FORMAT/XMLFile.h>
17 #include <vector>
19 namespace OpenMS
20 {
21  namespace Internal
22  {
23  class FeatureXMLHandler;
24  class ConsensusXMLHandler;
25  }
42  class OPENMS_DLLAPI IdXMLFile :
43  protected Internal::XMLHandler,
44  public Internal::XMLFile,
45  public ProgressLogger
46  {
47 public:
48  // both ConsensusXMLFile and FeatureXMLFile use some protected IdXML helper functions to parse identifications without code duplication
64  void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);
75  void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, String& document_id);
85  void store(const String& filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id = "");
88 protected:
89  // Docu in base class
90  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
92  // Docu in base class
93  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
98  void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
99  const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id, XMLHandler::ActionMode mode);
102  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
108  static std::ostream& createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
114  static std::ostream& createPositionXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
120  static void writeFragmentAnnotations_(const String & tag_name, std::ostream & os,
121  const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent);
126  static void parseFragmentAnnotation_(const String& s, std::vector<PeptideHit::PeakAnnotation> & annotations);
131  std::vector<ProteinIdentification>* prot_ids_;
134  std::vector<PeptideIdentification>* pep_ids_;
138  std::map<String, ProteinIdentification::SearchParameters> parameters_;
154  std::vector<PeptideEvidence> peptide_evidences_;
156  std::unordered_map<std::string, String> proteinid_to_accession_;
162  };
164 } // namespace OpenMS
Used to load and store idXML files.
Definition: IdXMLFile.h:46
static std::ostream & createPositionXMLString_(const std::vector< PeptideEvidence > &pes, std::ostream &os)
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:134
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:136
void getProteinGroups_(std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)
Read and store ProteinGroup data.
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:140
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:144
std::unordered_map< std::string, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:156
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Temporary analysis result instance.
Definition: IdXMLFile.h:152
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:148
static std::ostream & createFlankingAAXMLString_(const std::vector< PeptideEvidence > &pes, std::ostream &os)
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
void addProteinGroups_(MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, XMLHandler::ActionMode mode)
static void parseFragmentAnnotation_(const String &s, std::vector< PeptideHit::PeakAnnotation > &annotations)
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:150
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, String &document_id)
Loads the identifications of an idXML file.
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: IdXMLFile.h:154
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
bool prot_id_in_run_
true if a prot id is contained in the current run
Definition: IdXMLFile.h:160
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:146
String * document_id_
Document identifier.
Definition: IdXMLFile.h:158
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id")
Definition: IdXMLFile.h:138
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
static void writeFragmentAnnotations_(const String &tag_name, std::ostream &os, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent)
String id_
Temporary id.
Definition: IdXMLFile.h:142
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLHandler.h:41
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLHandler.h:48
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:300
Action to set the current mode (for error messages)
Definition: XMLHandler.h:317
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:35
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:150
Representation of a peptide hit.
Definition: PeptideHit.h:31
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:39
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
Representation of a protein hit.
Definition: ProteinHit.h:34
Representation of a protein identification run.
Definition: ProteinIdentification.h:50
A more convenient string class.
Definition: String.h:34
unsigned int UInt
Unsigned integer type.
Definition: Types.h:68
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
Search parameters of the DB search.
Definition: ProteinIdentification.h:247