OpenMS  2.8.0
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 
46 namespace OpenMS
47 {
48  namespace Internal
49  {
50 
56  class OPENMS_DLLAPI TraMLHandler :
57  public XMLHandler
58  {
59 public:
60 
61  TraMLHandler() = delete;
62  TraMLHandler(const TraMLHandler & rhs) = delete;
63  TraMLHandler & operator=(const TraMLHandler & rhs) = delete;
64 
65  typedef std::vector<ReactionMonitoringTransition::Product> ProductListType;
66  typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType;
67 
71  TraMLHandler(const TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);
72 
74  TraMLHandler(TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);
75 
77  ~TraMLHandler() override;
79 
80 
81  // Docu in base class
82  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
83 
84  // Docu in base class
85  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
86 
87  // Docu in base class
88  void characters(const XMLCh * const chars, const XMLSize_t length) override;
89 
90  //Docu in base class
91  void writeTo(std::ostream & os) override;
92 
93 protected:
94 
97 
100 
102 
104 
106 
108 
110 
112 
114 
116 
118 
120 
122 
124 
126 
128 
130 
132 
133  std::vector<ReactionMonitoringTransition::Product> actual_intermediate_products_;
134 
136 
138 
140 
142  void handleCVParam_(const String & parent_parent_tag, const String & parent_tag, const CVTerm & cv_term);
143 
145  void handleUserParam_(const String & parent_parent_tag, const String & parent_tag, const String & name, const String & type, const String & value);
146 
148  void writeUserParam_(std::ostream & os, const MetaInfoInterface & meta, UInt indent) const;
149 
150  void writeUserParams_(std::ostream & os, const std::vector<MetaInfoInterface> & meta, UInt indent) const;
151 
152  void writeCVParams_(std::ostream & os, const CVTermList & cv_terms, UInt indent) const;
153  void writeCVParams_(std::ostream & os, const CVTermListInterface & cv_terms, UInt indent) const;
154 
155  void writeCVList_(std::ostream & os, const Map<String, std::vector<CVTerm>> & cv_terms, UInt indent) const;
156 
157  // subfunctions of write
158  void writeTarget_(std::ostream & os, const std::vector<IncludeExcludeTarget>::const_iterator & it) const;
159 
160  void writeRetentionTime_(std::ostream& os, const TargetedExperimentHelper::RetentionTime& rt) const;
161 
162  void writeProduct_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Product>::const_iterator & prod_it) const;
163 
164  void writeConfiguration_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Configuration>::const_iterator & cit) const;
165 
167  ControlledVocabulary::CVTerm getChildWithName_(const String & parent_accession, const String & name) const;
168 
170  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
171 
172  };
173  } // namespace Internal
174 } // namespace OpenMS
175 
176 
Interface to the controlled vocabulary term list.
Definition: CVTermListInterface.h:59
Representation of controlled vocabulary term list.
Definition: CVTermList.h:54
Representation of controlled vocabulary term.
Definition: CVTerm.h:53
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:55
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:54
XML handler for TraMLFile.
Definition: TraMLHandler.h:58
ControlledVocabulary::CVTerm getChildWithName_(const String &parent_accession, const String &name) const
Looks up a child CV term of parent_accession with the name name. If no such term is found,...
ReactionMonitoringTransition::Product actual_product_
Definition: TraMLHandler.h:135
std::vector< ReactionMonitoringTransition::Product > actual_intermediate_products_
Definition: TraMLHandler.h:133
std::vector< ReactionMonitoringTransition::Configuration > ConfigurationListType
Definition: TraMLHandler.h:66
TargetedExperiment::Peptide actual_peptide_
Definition: TraMLHandler.h:121
ReactionMonitoringTransition actual_transition_
Definition: TraMLHandler.h:125
TraMLHandler(const TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a write-only handler.
TargetedExperiment::RetentionTime actual_rt_
Definition: TraMLHandler.h:119
TargetedExperiment::Interpretation actual_interpretation_
Definition: TraMLHandler.h:131
void writeTo(std::ostream &os) override
Writes the contents to a stream.
const TargetedExperiment * cexp_
Definition: TraMLHandler.h:105
TraMLHandler(TargetedExperiment &exp, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a read-only handler.
const ProgressLogger & logger_
Progress logger.
Definition: TraMLHandler.h:96
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: TraMLHandler.h:99
String tag_
Definition: TraMLHandler.h:101
void writeUserParam_(std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
Writes user terms.
std::vector< ReactionMonitoringTransition::Product > ProductListType
Definition: TraMLHandler.h:65
CVTermList actual_validation_
Definition: TraMLHandler.h:129
TargetedExperiment::Contact actual_contact_
Definition: TraMLHandler.h:109
TargetedExperiment::Publication actual_publication_
Definition: TraMLHandler.h:107
SourceFile actual_sourcefile_
Definition: TraMLHandler.h:139
void writeUserParams_(std::ostream &os, const std::vector< MetaInfoInterface > &meta, UInt indent) const
ReactionMonitoringTransition::Configuration actual_configuration_
Definition: TraMLHandler.h:137
TargetedExperiment * exp_
Definition: TraMLHandler.h:103
void writeCVParams_(std::ostream &os, const CVTermList &cv_terms, UInt indent) const
~TraMLHandler() override
Destructor.
TargetedExperiment::Compound actual_compound_
Definition: TraMLHandler.h:123
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
void writeCVParams_(std::ostream &os, const CVTermListInterface &cv_terms, UInt indent) const
TargetedExperiment::Instrument actual_instrument_
Definition: TraMLHandler.h:111
void writeRetentionTime_(std::ostream &os, const TargetedExperimentHelper::RetentionTime &rt) const
TraMLHandler(const TraMLHandler &rhs)=delete
void writeConfiguration_(std::ostream &os, const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &cit) const
void writeTarget_(std::ostream &os, const std::vector< IncludeExcludeTarget >::const_iterator &it) const
void characters(const XMLCh *const chars, const XMLSize_t length) override
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void handleUserParam_(const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
Handles user terms.
void writeProduct_(std::ostream &os, const std::vector< ReactionMonitoringTransition::Product >::const_iterator &prod_it) const
void writeCVList_(std::ostream &os, const Map< String, std::vector< CVTerm >> &cv_terms, UInt indent) const
TargetedExperiment::Prediction actual_prediction_
Definition: TraMLHandler.h:113
void handleCVParam_(const String &parent_parent_tag, const String &parent_tag, const CVTerm &cv_term)
Handles CV terms.
TraMLHandler & operator=(const TraMLHandler &rhs)=delete
Software actual_software_
Definition: TraMLHandler.h:115
TargetedExperiment::Protein actual_protein_
Definition: TraMLHandler.h:117
IncludeExcludeTarget actual_target_
Definition: TraMLHandler.h:127
Base class for XML handlers.
Definition: XMLHandler.h:325
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:58
Description of the software used for processing.
Definition: Software.h:50
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:48
A more convenient string class.
Definition: String.h:60
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:323
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:360
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:126
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:65
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Representation of a CV term.
Definition: ControlledVocabulary.h:61
Definition: TargetedExperimentHelper.h:66
Definition: TargetedExperimentHelper.h:429
Definition: TargetedExperimentHelper.h:463
Product ion interpretation.
Definition: TargetedExperimentHelper.h:505
Definition: TargetedExperimentHelper.h:480
Definition: TargetedExperimentHelper.h:100
Definition: TargetedExperimentHelper.h:446
Represents a product ion.
Definition: TargetedExperimentHelper.h:573