OpenMS
ConsensusXMLHandler.h
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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: Clemens Groepl, Marc Sturm $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
18 #include <unordered_map>
19 #include <map>
20 
21 namespace OpenMS
22 {
23 namespace Internal
24 {
38  class OPENMS_DLLAPI ConsensusXMLHandler :
39  public Internal::XMLHandler,
40  public ProgressLogger
41  {
42 public:
44  ConsensusXMLHandler(ConsensusMap& map, const String& filename);
45  ConsensusXMLHandler(const ConsensusMap& map, const String& filename);
48 
51 
53 
55  const PeakFileOptions& getOptions() const;
56 
58  void writeTo(std::ostream& os) override;
59 
60 protected:
61 
62  // Docu in base class
63  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
64 
65  // Docu in base class
66  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
67 
68  // Docu in base class
69  void characters(const XMLCh* const chars, const XMLSize_t length) override;
70 
72  void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
73 
77  void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
78  const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id,
79  const String& runid, XMLHandler::ActionMode mode);
80 
82  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
83 
86 
88 
93  double it_;
95 
107  std::vector<PeptideEvidence> peptide_evidences_;
109  std::map<String, String> proteinid_to_accession_;
111  std::unordered_map<std::string, UInt> accession_to_id_;
113  std::map<String, String> identifier_id_;
115  std::map<String, String> id_identifier_;
118 
120  };
121 } // namespace Internal
122 } // namespace OpenMS
123 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:45
A container for consensus elements.
Definition: ConsensusMap.h:66
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLHandler.h:41
const ConsensusMap * cconsensus_map_
Definition: ConsensusXMLHandler.h:90
void addProteinGroups_(MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, const String &runid, XMLHandler::ActionMode mode)
std::map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: ConsensusXMLHandler.h:109
void setOptions(const PeakFileOptions &)
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: ConsensusXMLHandler.h:117
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: ConsensusXMLHandler.h:97
void getProteinGroups_(std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)
Read and store ProteinGroup data.
void writeTo(std::ostream &os) override
Docu in base class XMLHandler::writeTo.
DPosition< 2 > pos_
Definition: ConsensusXMLHandler.h:92
const PeakFileOptions & getOptions() const
Non-mutable access to the options for loading/storing.
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: ConsensusXMLHandler.h:99
PeakFileOptions options_
Options that can be set.
Definition: ConsensusXMLHandler.h:85
ConsensusFeature act_cons_element_
Definition: ConsensusXMLHandler.h:91
std::unordered_map< std::string, UInt > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: ConsensusXMLHandler.h:111
double it_
Definition: ConsensusXMLHandler.h:93
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
ProteinHit prot_hit_
Temporary protein hit.
Definition: ConsensusXMLHandler.h:103
UInt progress_
Definition: ConsensusXMLHandler.h:119
void writePeptideIdentification_(const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level)
Writes a peptide identification to a stream (for assigned/unassigned peptide identifications)
PeptideHit pep_hit_
Temporary peptide hit.
Definition: ConsensusXMLHandler.h:105
ConsensusMap * consensus_map_
Definition: ConsensusXMLHandler.h:89
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: ConsensusXMLHandler.h:107
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
std::map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: ConsensusXMLHandler.h:113
ConsensusXMLHandler(ConsensusMap &map, const String &filename)
Constructor.
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: ConsensusXMLHandler.h:101
std::map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: ConsensusXMLHandler.h:115
ConsensusXMLHandler(const ConsensusMap &map, const String &filename)
void characters(const XMLCh *const chars, const XMLSize_t length) override
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
~ConsensusXMLHandler() override
Destructor.
Base class for XML handlers.
Definition: XMLHandler.h:300
ActionMode
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
Options for loading files containing peak data.
Definition: PeakFileOptions.h:22
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