OpenMS  3.0.0
IdXMLFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
41 #include <OpenMS/FORMAT/XMLFile.h>
42 
43 #include <vector>
44 
45 namespace OpenMS
46 {
47  namespace Internal
48  {
49  class FeatureXMLHandler;
50  class ConsensusXMLHandler;
51  }
68  class OPENMS_DLLAPI IdXMLFile :
69  protected Internal::XMLHandler,
70  public Internal::XMLFile,
71  public ProgressLogger
72  {
73 public:
74  // both ConsensusXMLFile and FeatureXMLFile use some protected IdXML helper functions to parse identifications without code duplication
77 
79  IdXMLFile();
80 
90  void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);
91 
101  void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, String& document_id);
102 
111  void store(const String& filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id = "");
112 
113 
114 protected:
115  // Docu in base class
116  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
117 
118  // Docu in base class
119  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
120 
124  void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
125  const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id, XMLHandler::ActionMode mode);
126 
128  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
129 
134  static std::ostream& createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
135 
140  static std::ostream& createPositionXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
141 
142 
146  static void writeFragmentAnnotations_(const String & tag_name, std::ostream & os,
147  const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent);
148 
152  static void parseFragmentAnnotation_(const String& s, std::vector<PeptideHit::PeakAnnotation> & annotations);
153 
154 
156 
157  std::vector<ProteinIdentification>* prot_ids_;
160  std::vector<PeptideIdentification>* pep_ids_;
164  std::map<String, ProteinIdentification::SearchParameters> parameters_;
180  std::vector<PeptideEvidence> peptide_evidences_;
182  std::unordered_map<std::string, String> proteinid_to_accession_;
188  };
189 
190 } // namespace OpenMS
191 
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
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:186
FileHandler.h
OpenMS::IdXMLFile::current_analysis_result_
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Temporary analysis result instance.
Definition: IdXMLFile.h:178
XMLFile.h
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::Internal::ConsensusXMLHandler
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLHandler.h:64
OpenMS::IdXMLFile::store
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.
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::FeatureMap::Iterator
Base::iterator Iterator
Definition: FeatureMap.h:144
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::PeptideHit::PepXMLAnalysisResult
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:175
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::IdXMLFile::peptide_evidences_
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: IdXMLFile.h:180
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:150
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
IdXMLFile.h
FeatureXMLFile.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::Internal::FeatureXMLHandler
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLHandler.h:71
XMLHandler.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::ExperimentalSettings::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
returns a const reference to the protein ProteinIdentification vector
OpenMS::IdXMLFile::document_id_
String * document_id_
Document identifier.
Definition: IdXMLFile.h:184
OpenMS::IdXMLFile::param_
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:166
OpenMS::IdXMLFile::id_
String id_
Temporary id.
Definition: IdXMLFile.h:168
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MSExperiment::Iterator
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:104
OpenMS::IdXMLFile::prot_id_
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:170
OpenMS::IdXMLFile::last_meta_
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:162
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::IdXMLFile::parameters_
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id")
Definition: IdXMLFile.h:164
ProgressLogger.h
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
ProteinIdentification.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::ConsensusMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::FeatureMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IdXMLFile::proteinid_to_accession_
std::unordered_map< std::string, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:182
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::Exception::RequiredParameterNotGiven
A required parameter was not given.
Definition: TOPPBase.h:114
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::Internal::XMLHandler::ActionMode
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:341
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:160
OpenMS::ConsensusMap::Iterator
std::vector< ConsensusFeature >::iterator Iterator
Mutable iterator.
Definition: ConsensusMap.h:166
OpenMS::IdXMLFile::pep_ids_
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:160
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::IdXMLFile::pep_hit_
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:176
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::IdXMLFile::prot_hit_
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:174
PeptideIdentification.h
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::DataProcessing::FILTERING
Data filtering or extraction.
Definition: DataProcessing.h:71
OpenMS::IdXMLFile::pep_id_
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:172
TOPPBase.h
OpenMS::FeatureMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55