| OpenMS 2.5.0

ConsensusXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Clemens Groepl, Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
39 #include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
40 #include <OpenMS/FORMAT/XMLFile.h>
41 #include <OpenMS/KERNEL/ConsensusMap.h>
42 #include <OpenMS/METADATA/PeptideEvidence.h>
43 #include <OpenMS/METADATA/ProteinIdentification.h>
44 #include <OpenMS/METADATA/PeptideIdentification.h>
45
46 namespace OpenMS
47 {
61 class OPENMS_DLLAPI ConsensusXMLFile :
62 public Internal::XMLHandler,
63 public Internal::XMLFile,
64 public ProgressLogger
65 {
66 public:
68 ConsensusXMLFile();
70 ~ConsensusXMLFile() override;
71
72
80 void load(const String& filename, ConsensusMap& map);
81
89 void store(const String& filename, const ConsensusMap& consensus_map);
90
92 PeakFileOptions& getOptions();
93
95 const PeakFileOptions& getOptions() const;
96
97 protected:
98
99 // Docu in base class
100 void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
101
102 // Docu in base class
103 void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
104
105 // Docu in base class
106 void characters(const XMLCh* const chars, const XMLSize_t length) override;
107
108
110 void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
111
112
114 PeakFileOptions options_;
115
117
118 ConsensusMap* consensus_map_;
119 ConsensusFeature act_cons_element_;
120 DPosition<2> pos_;
121 double it_;
123
125 MetaInfoInterface* last_meta_;
127 ProteinIdentification prot_id_;
129 PeptideIdentification pep_id_;
131 ProteinHit prot_hit_;
133 PeptideHit pep_hit_;
135 std::vector<PeptideEvidence> peptide_evidences_;
137 Map<String, String> proteinid_to_accession_;
139 Map<String, Size> accession_to_id_;
141 Map<String, String> identifier_id_;
143 Map<String, String> id_identifier_;
145 ProteinIdentification::SearchParameters search_param_;
146
147 UInt progress_;
148
149 };
150 } // namespace OpenMS
151
152
OpenMS::ConsensusXMLFile::identifier_id_
Map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: ConsensusXMLFile.h:141
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OpenMS::ConsensusXMLFile::prot_hit_
ProteinHit prot_hit_
Temporary protein hit.
Definition: ConsensusXMLFile.h:131
XMLHandler.h
OpenMS::ConsensusXMLFile::proteinid_to_accession_
Map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: ConsensusXMLFile.h:137
OpenMS::ConsensusXMLFile::progress_
UInt progress_
Definition: ConsensusXMLFile.h:147
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
OpenMS::ConsensusXMLFile::pos_
DPosition< 2 > pos_
Definition: ConsensusXMLFile.h:120
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
PeptideEvidence.h
ConsensusMap.h
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::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
ProgressLogger.h
OpenMS::ConsensusXMLFile::last_meta_
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: ConsensusXMLFile.h:125
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
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::ConsensusXMLFile::id_identifier_
Map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: ConsensusXMLFile.h:143
OpenMS::ConsensusXMLFile::prot_id_
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: ConsensusXMLFile.h:127
OpenMS::ConsensusXMLFile::consensus_map_
ConsensusMap * consensus_map_
Definition: ConsensusXMLFile.h:118
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::DPosition< 2 >
OpenMS::ConsensusXMLFile::pep_id_
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: ConsensusXMLFile.h:129
OpenMS::ConsensusXMLFile::options_
PeakFileOptions options_
Options that can be set.
Definition: ConsensusXMLFile.h:114
OpenMS::ConsensusXMLFile::pep_hit_
PeptideHit pep_hit_
Temporary peptide hit.
Definition: ConsensusXMLFile.h:133
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
PeakFileOptions.h
OpenMS::ConsensusXMLFile::accession_to_id_
Map< String, Size > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: ConsensusXMLFile.h:139
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::ConsensusXMLFile::peptide_evidences_
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: ConsensusXMLFile.h:135
OpenMS::ConsensusXMLFile::it_
double it_
Definition: ConsensusXMLFile.h:121
OpenMS::ConsensusXMLFile::search_param_
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: ConsensusXMLFile.h:145
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
OpenMS::ConsensusXMLFile::act_cons_element_
ConsensusFeature act_cons_element_
Definition: ConsensusXMLFile.h:119
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60