OpenMS  3.0.0
TraMLHandler.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Andreas Bertsch, Hannes Roest $
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34 
35 #pragma once
36 
43 
44 #include <iosfwd>
45 #include <map>
46 
47 namespace OpenMS
48 {
49  namespace Internal
50  {
51 
57  class OPENMS_DLLAPI TraMLHandler :
58  public XMLHandler
59  {
60 public:
61 
62  TraMLHandler() = delete;
63  TraMLHandler(const TraMLHandler & rhs) = delete;
64  TraMLHandler & operator=(const TraMLHandler & rhs) = delete;
65 
66  typedef std::vector<ReactionMonitoringTransition::Product> ProductListType;
67  typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType;
68 
71  TraMLHandler(const TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);
73 
75  TraMLHandler(TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);
76 
78  ~TraMLHandler() override;
80 
81 
82  // Docu in base class
83  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
84 
85  // Docu in base class
86  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
87 
88  // Docu in base class
89  void characters(const XMLCh * const chars, const XMLSize_t length) override;
90 
91  //Docu in base class
92  void writeTo(std::ostream & os) override;
93 
94 protected:
95 
98 
101 
103 
105 
107 
109 
111 
113 
115 
117 
119 
121 
123 
125 
127 
129 
131 
133 
134  std::vector<ReactionMonitoringTransition::Product> actual_intermediate_products_;
135 
137 
139 
141 
143  void handleCVParam_(const String & parent_parent_tag, const String & parent_tag, const CVTerm & cv_term);
144 
146  void handleUserParam_(const String & parent_parent_tag, const String & parent_tag, const String & name, const String & type, const String & value);
147 
149  void writeUserParam_(std::ostream & os, const MetaInfoInterface & meta, UInt indent) const;
150 
151  void writeUserParams_(std::ostream & os, const std::vector<MetaInfoInterface> & meta, UInt indent) const;
152 
153  void writeCVParams_(std::ostream & os, const CVTermList & cv_terms, UInt indent) const;
154  void writeCVParams_(std::ostream & os, const CVTermListInterface & cv_terms, UInt indent) const;
155 
156  void writeCVList_(std::ostream & os, const std::map<String, std::vector<CVTerm>> & cv_terms, UInt indent) const;
157 
158  // subfunctions of write
159  void writeTarget_(std::ostream & os, const std::vector<IncludeExcludeTarget>::const_iterator & it) const;
160 
161  void writeRetentionTime_(std::ostream& os, const TargetedExperimentHelper::RetentionTime& rt) const;
162 
163  void writeProduct_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Product>::const_iterator & prod_it) const;
164 
165  void writeConfiguration_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Configuration>::const_iterator & cit) const;
166 
168  ControlledVocabulary::CVTerm getChildWithName_(const String & parent_accession, const String & name) const;
169 
171  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
172 
173  };
174  } // namespace Internal
175 } // namespace OpenMS
176 
177 
OpenMS::Software
Description of the software used for processing.
Definition: Software.h:48
OpenMS::TargetedExperimentHelper::Instrument
Definition: TargetedExperimentHelper.h:461
TargetedExperiment.h
OpenMS::Internal::TraMLHandler::exp_
TargetedExperiment * exp_
Definition: TraMLHandler.h:104
OpenMS::Internal::TraMLHandler::actual_software_
Software actual_software_
Definition: TraMLHandler.h:116
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:358
ControlledVocabulary.h
OpenMS::Internal::TraMLHandler::cexp_
const TargetedExperiment * cexp_
Definition: TraMLHandler.h:106
OpenMS::Internal::TraMLHandler::actual_peptide_
TargetedExperiment::Peptide actual_peptide_
Definition: TraMLHandler.h:122
OpenMS::TargetedExperimentHelper::Contact
Definition: TargetedExperimentHelper.h:427
OpenMS::Internal::TraMLHandler::actual_contact_
TargetedExperiment::Contact actual_contact_
Definition: TraMLHandler.h:110
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::TraMLHandler::ProductListType
std::vector< ReactionMonitoringTransition::Product > ProductListType
Definition: TraMLHandler.h:66
OpenMS::Internal::TraMLHandler::actual_validation_
CVTermList actual_validation_
Definition: TraMLHandler.h:130
OpenMS::IncludeExcludeTarget
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:52
OpenMS::Internal::TraMLHandler::actual_configuration_
ReactionMonitoringTransition::Configuration actual_configuration_
Definition: TraMLHandler.h:138
XMLHandler.h
OpenMS::Internal::TraMLHandler::ConfigurationListType
std::vector< ReactionMonitoringTransition::Configuration > ConfigurationListType
Definition: TraMLHandler.h:67
OpenMS::Internal::TraMLHandler::actual_product_
ReactionMonitoringTransition::Product actual_product_
Definition: TraMLHandler.h:136
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::TraMLHandler::actual_prediction_
TargetedExperiment::Prediction actual_prediction_
Definition: TraMLHandler.h:114
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::Internal::TraMLHandler::actual_sourcefile_
SourceFile actual_sourcefile_
Definition: TraMLHandler.h:140
OpenMS::Internal::TraMLHandler::actual_publication_
TargetedExperiment::Publication actual_publication_
Definition: TraMLHandler.h:108
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Internal::TraMLHandler::logger_
const ProgressLogger & logger_
Progress logger.
Definition: TraMLHandler.h:97
OpenMS::Internal::TraMLHandler::actual_intermediate_products_
std::vector< ReactionMonitoringTransition::Product > actual_intermediate_products_
Definition: TraMLHandler.h:134
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
OpenMS::TargetedExperimentHelper::Protein
Definition: TargetedExperimentHelper.h:98
OpenMS::TargetedExperimentHelper::Prediction
Definition: TargetedExperimentHelper.h:478
OpenMS::CVTermListInterface
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:57
OpenMS::Internal::TraMLHandler::actual_interpretation_
TargetedExperiment::Interpretation actual_interpretation_
Definition: TraMLHandler.h:132
OpenMS::TargetedExperimentHelper::TraMLProduct
Represents a product ion.
Definition: TargetedExperimentHelper.h:571
OpenMS::TargetedExperimentHelper::Compound
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:321
OpenMS::Internal::TraMLHandler::cv_
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: TraMLHandler.h:100
OpenMS::Internal::TraMLHandler::tag_
String tag_
Definition: TraMLHandler.h:102
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::TraMLHandler::actual_protein_
TargetedExperiment::Protein actual_protein_
Definition: TraMLHandler.h:118
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
CVTermList.h
OpenMS::ControlledVocabulary::CVTerm
Representation of a CV term.
Definition: ControlledVocabulary.h:60
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
OpenMS::TargetedExperimentHelper::Configuration
Definition: TargetedExperimentHelper.h:64
OpenMS::Internal::TraMLHandler::actual_compound_
TargetedExperiment::Compound actual_compound_
Definition: TraMLHandler.h:124
OpenMS::Internal::TraMLHandler
XML handler for TraMLFile.
Definition: TraMLHandler.h:57
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:124
OpenMS::SourceFile
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
OpenMS::Internal::TraMLHandler::actual_transition_
ReactionMonitoringTransition actual_transition_
Definition: TraMLHandler.h:126
OpenMS::TargetedExperimentHelper::Publication
Definition: TargetedExperimentHelper.h:444
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
SourceFile.h
OpenMS::Internal::TraMLHandler::actual_instrument_
TargetedExperiment::Instrument actual_instrument_
Definition: TraMLHandler.h:112
OpenMS::Internal::TraMLHandler::actual_target_
IncludeExcludeTarget actual_target_
Definition: TraMLHandler.h:128
OpenMS::TargetedExperimentHelper::Interpretation
Product ion interpretation.
Definition: TargetedExperimentHelper.h:503
OpenMS::Internal::TraMLHandler::actual_rt_
TargetedExperiment::RetentionTime actual_rt_
Definition: TraMLHandler.h:120