OpenMS  2.5.0
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 <ostream>
45 
46 namespace OpenMS
47 {
48  namespace Internal
49  {
50 
56  class OPENMS_DLLAPI TraMLHandler :
57  public XMLHandler
58  {
59 public:
60 
61  typedef std::vector<ReactionMonitoringTransition::Product> ProductListType;
62  typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType;
63 
66  TraMLHandler(const TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);
68 
70  TraMLHandler(TargetedExperiment & exp, const String & filename, const String & version, const ProgressLogger & logger);
71 
73  ~TraMLHandler() override;
75 
76 
77  // Docu in base class
78  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
79 
80  // Docu in base class
81  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
82 
83  // Docu in base class
84  void characters(const XMLCh * const chars, const XMLSize_t length) override;
85 
86  //Docu in base class
87  void writeTo(std::ostream & os) override;
88 
89 protected:
90 
93 
96 
98 
100 
102 
104 
106 
108 
110 
112 
114 
116 
118 
120 
122 
124 
126 
128 
129  std::vector<ReactionMonitoringTransition::Product> actual_intermediate_products_;
130 
132 
134 
136 
138  void handleCVParam_(const String & parent_parent_tag, const String & parent_tag, const CVTerm & cv_term);
139 
141  void handleUserParam_(const String & parent_parent_tag, const String & parent_tag, const String & name, const String & type, const String & value);
142 
144  void writeUserParam_(std::ostream & os, const MetaInfoInterface & meta, UInt indent) const;
145 
146  void writeUserParams_(std::ostream & os, const std::vector<MetaInfoInterface> & meta, UInt indent) const;
147 
148  template <typename CVTList>
149  void writeCVParams_(std::ostream & os, const CVTList & cv_terms, UInt indent) const
150  {
151  for (Map<String, std::vector<CVTerm> >::const_iterator it = cv_terms.getCVTerms().begin();
152  it != cv_terms.getCVTerms().end(); ++it)
153  {
154  for (std::vector<CVTerm>::const_iterator cit = it->second.begin(); cit != it->second.end(); ++cit)
155  {
156  os << String(2 * indent, ' ') << "<cvParam cvRef=\"" << cit->getCVIdentifierRef() << "\" accession=\"" << cit->getAccession() << "\" name=\"" << cit->getName() << "\"";
157  if (cit->hasValue() && !cit->getValue().isEmpty() && !cit->getValue().toString().empty())
158  {
159  os << " value=\"" << cit->getValue().toString() << "\"";
160  }
161 
162  if (cit->hasUnit())
163  {
164  os << " unitCvRef=\"" << cit->getUnit().cv_ref << "\" unitAccession=\"" << cit->getUnit().accession << "\" unitName=\"" << cit->getUnit().name << "\"";
165  }
166  os << "/>" << "\n";
167  }
168  }
169  }
170 
171  // subfunctions of write
172  void writeTarget_(std::ostream & os, const std::vector<IncludeExcludeTarget>::const_iterator & it) const;
173 
174  void writeRetentionTime_(std::ostream& os, const TargetedExperimentHelper::RetentionTime& rt) const;
175 
176  void writeProduct_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Product>::const_iterator & prod_it) const;
177 
178  void writeConfiguration_(std::ostream & os, const std::vector<ReactionMonitoringTransition::Configuration>::const_iterator & cit) const;
179 
181  ControlledVocabulary::CVTerm getChildWithName_(const String & parent_accession, const String & name) const;
182 
184  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
185 
186 private:
187 
188  TraMLHandler();
189  TraMLHandler(const TraMLHandler & rhs);
190  TraMLHandler & operator=(const TraMLHandler & rhs);
191  };
192  } // namespace Internal
193 } // namespace OpenMS
194 
195 
OpenMS::Software
Description of the software used for processing.
Definition: Software.h:48
OpenMS::TargetedExperimentHelper::Instrument
Definition: TargetedExperimentHelper.h:478
TargetedExperiment.h
OpenMS::Internal::TraMLHandler::exp_
TargetedExperiment * exp_
Definition: TraMLHandler.h:99
OpenMS::Internal::TraMLHandler::actual_software_
Software actual_software_
Definition: TraMLHandler.h:111
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
ControlledVocabulary.h
OpenMS::Internal::TraMLHandler::cexp_
const TargetedExperiment * cexp_
Definition: TraMLHandler.h:101
OpenMS::Internal::TraMLHandler::actual_peptide_
TargetedExperiment::Peptide actual_peptide_
Definition: TraMLHandler.h:117
OpenMS::TargetedExperimentHelper::Contact
Definition: TargetedExperimentHelper.h:444
OpenMS::Internal::TraMLHandler::actual_contact_
TargetedExperiment::Contact actual_contact_
Definition: TraMLHandler.h:105
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::TraMLHandler::ProductListType
std::vector< ReactionMonitoringTransition::Product > ProductListType
Definition: TraMLHandler.h:61
OpenMS::Internal::TraMLHandler::actual_validation_
CVTermList actual_validation_
Definition: TraMLHandler.h:125
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:133
XMLHandler.h
OpenMS::Internal::TraMLHandler::ConfigurationListType
std::vector< ReactionMonitoringTransition::Configuration > ConfigurationListType
Definition: TraMLHandler.h:62
OpenMS::Internal::TraMLHandler::actual_product_
ReactionMonitoringTransition::Product actual_product_
Definition: TraMLHandler.h:131
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Internal::TraMLHandler::actual_prediction_
TargetedExperiment::Prediction actual_prediction_
Definition: TraMLHandler.h:109
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
OpenMS::Internal::TraMLHandler::actual_sourcefile_
SourceFile actual_sourcefile_
Definition: TraMLHandler.h:135
OpenMS::Internal::TraMLHandler::actual_publication_
TargetedExperiment::Publication actual_publication_
Definition: TraMLHandler.h:103
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:92
OpenMS::Internal::TraMLHandler::actual_intermediate_products_
std::vector< ReactionMonitoringTransition::Product > actual_intermediate_products_
Definition: TraMLHandler.h:129
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:495
OpenMS::Internal::TraMLHandler::actual_interpretation_
TargetedExperiment::Interpretation actual_interpretation_
Definition: TraMLHandler.h:127
OpenMS::Internal::TraMLHandler::writeCVParams_
void writeCVParams_(std::ostream &os, const CVTList &cv_terms, UInt indent) const
Definition: TraMLHandler.h:149
OpenMS::TargetedExperimentHelper::TraMLProduct
Represents a product ion.
Definition: TargetedExperimentHelper.h:588
OpenMS::TargetedExperimentHelper::Compound
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
OpenMS::Internal::TraMLHandler::cv_
ControlledVocabulary cv_
Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)
Definition: TraMLHandler.h:95
OpenMS::Internal::TraMLHandler::tag_
String tag_
Definition: TraMLHandler.h:97
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::TraMLHandler::actual_protein_
TargetedExperiment::Protein actual_protein_
Definition: TraMLHandler.h:113
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:119
OpenMS::Internal::TraMLHandler
XML handler for TraMLFile.
Definition: TraMLHandler.h:56
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
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:121
OpenMS::TargetedExperimentHelper::Publication
Definition: TargetedExperimentHelper.h:461
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
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:107
OpenMS::Internal::TraMLHandler::actual_target_
IncludeExcludeTarget actual_target_
Definition: TraMLHandler.h:123
OpenMS::TargetedExperimentHelper::Interpretation
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
OpenMS::Internal::TraMLHandler::actual_rt_
TargetedExperiment::RetentionTime actual_rt_
Definition: TraMLHandler.h:115