| OpenMS 2.5.0

IdXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/METADATA/ProteinIdentification.h>
39 #include <OpenMS/METADATA/PeptideIdentification.h>
40 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
41 #include <OpenMS/FORMAT/XMLFile.h>
42
43 #include <vector>
44
45 namespace OpenMS
46 {
63 class OPENMS_DLLAPI IdXMLFile :
64 protected Internal::XMLHandler,
65 public Internal::XMLFile,
66 public ProgressLogger
67 {
68 public:
69 // both ConsensusXMLFile and FeatureXMLFile use some protected IdXML helper functions to parse identifications without code duplication
70 friend class ConsensusXMLFile;
71 friend class FeatureXMLFile;
72
74 IdXMLFile();
75
85 void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);
86
96 void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, String& document_id);
97
105 void store(const String& filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id = "");
106
107
108 protected:
109 // Docu in base class
110 void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
111
112 // Docu in base class
113 void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
114
118 void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
119 const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id, XMLHandler::ActionMode mode);
120
122 void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
123
128 static std::ostream& createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
129
134 static std::ostream& createPositionXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
135
136
140 static void writeFragmentAnnotations_(const String & tag_name, std::ostream & os,
141 const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent);
142
146 static void parseFragmentAnnotation_(const String& s, std::vector<PeptideHit::PeakAnnotation> & annotations);
147
148
150
151 std::vector<ProteinIdentification>* prot_ids_;
154 std::vector<PeptideIdentification>* pep_ids_;
156 MetaInfoInterface* last_meta_;
158 std::map<String, ProteinIdentification::SearchParameters> parameters_;
160 ProteinIdentification::SearchParameters param_;
162 String id_;
164 ProteinIdentification prot_id_;
166 PeptideIdentification pep_id_;
168 ProteinHit prot_hit_;
170 PeptideHit pep_hit_;
172 PeptideHit::PepXMLAnalysisResult current_analysis_result_;
174 std::vector<PeptideEvidence> peptide_evidences_;
176 std::unordered_map<std::string, String> proteinid_to_accession_;
178 String* document_id_;
180 bool prot_id_in_run_;
182 };
183
184 } // namespace OpenMS
185
OpenMS::Internal::XMLHandler::ActionMode
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:169
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OpenMS::IdXMLFile::parameters_
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id")
Definition: IdXMLFile.h:158
OpenMS::IdXMLFile::pep_ids_
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:154
XMLHandler.h
OpenMS::IdXMLFile::last_meta_
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:156
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
OpenMS::IdXMLFile::pep_hit_
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:170
OpenMS::IdXMLFile::pep_id_
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:166
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::IdXMLFile::id_
String id_
Temporary id.
Definition: IdXMLFile.h:162
OpenMS::IdXMLFile::param_
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:160
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
OpenMS::IdXMLFile::peptide_evidences_
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: IdXMLFile.h:174
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::IdXMLFile::proteinid_to_accession_
std::unordered_map< std::string, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:176
ProgressLogger.h
OpenMS::PeptideHit::PepXMLAnalysisResult
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:210
OpenMS::IdXMLFile::prot_id_
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:164
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IdXMLFile::current_analysis_result_
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Temporary analysis result instance.
Definition: IdXMLFile.h:172
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::IdXMLFile::prot_hit_
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:168
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::IdXMLFile::prot_id_in_run_
bool prot_id_in_run_
true if a prot id is contained in the current run
Definition: IdXMLFile.h:180
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::IdXMLFile::document_id_
String * document_id_
Document identifier.
Definition: IdXMLFile.h:178
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63