OpenMS  3.0.0
MzQuantMLHandler.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer $
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34 
35 #pragma once
36 
40 
41 #include <map>
42 
43 namespace OpenMS
44 {
45  class ProgressLogger;
46 
47  namespace Internal
48  {
49 
55  class OPENMS_DLLAPI MzQuantMLHandler :
56  public XMLHandler
57  {
58 public:
61  MzQuantMLHandler(const MSQuantifications & msq, const String & filename, const String & version, const ProgressLogger & logger);
63 
65  MzQuantMLHandler(MSQuantifications & msq, const String & filename, const String & version, const ProgressLogger & logger);
66 
68  ~MzQuantMLHandler() override;
70 
71 
72  // Docu in base class
73  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
74 
75  // Docu in base class
76  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
77 
78  // Docu in base class
79  void characters(const XMLCh * const chars, const XMLSize_t length) override;
80 
81  //Docu in base class
82  void writeTo(std::ostream & os) override;
83 
84 protected:
85 
88 
91 
93 
95 
97 
99  void handleCVParam_(const String & parent_parent_tag, const String & parent_tag, const String & accession, const String & name, const String & value, const xercesc::Attributes & attributes, const String & cv_ref, const String & unit_accession = "");
100 
102  void handleUserParam_(const String & parent_parent_tag, const String & parent_tag, const String & name, const String & type, const String & value);
103 
105  //~ TODO rewirte writeCVParams_ in baseclass to be more convenient
106  //~ void MzQuantMLHandler::writeCVParams_(std::ostream& os, const Map< String, std::vector < CVTerm > > & , UInt indent);
107  void writeCVParams_(String & s, const std::map<String, std::vector<CVTerm> > &, UInt indent);
108 
110  void writeUserParams_(std::ostream & os, const MetaInfoInterface & meta, UInt indent);
111  void writeUserParams_(String & s, const MetaInfoInterface & meta, UInt indent);
112 
114  ControlledVocabulary::CVTerm getChildWithName_(const String & parent_accession, const String & name) const;
115 
116 
118  void writeFeature_(String & feature_xml, const std::vector<FeatureMap >& fm, UInt indentation_level);
119 
121  //void writeSourceFile_(std::ostream& os, const String& id, const SourceFile& software);
122 
123 
124 private:
126  MzQuantMLHandler(const MzQuantMLHandler & rhs);
127  MzQuantMLHandler & operator=(const MzQuantMLHandler & rhs);
128 
129  std::map<String, std::vector<ExperimentalSettings> > current_files_;
133 
134  std::vector<MetaInfo> up_stack_;
135  std::vector<CVTerm> cvp_stack_;
137 
138  std::multimap<String, String> cm_cf_ids_;
139  std::map<String, String> f_cf_ids_;
140  std::map<String, ConsensusFeature> cf_cf_obj_;
141  std::map<String, FeatureHandle> f_f_obj_;
142  std::map<String, ConsensusFeature::Ratio> r_rtemp_;
143  std::map<String, String> numden_r_ids_;
144  std::map<String, ConsensusFeature::Ratio> r_r_obj_;
145 
146  //~ Software current_sw_;
147  std::map<String, Software> current_sws_;
148  std::map<int, DataProcessing> current_orderedps_;
149  std::pair<int, DataProcessing> current_dp_;
150  std::set<DataProcessing::ProcessingAction> current_pas_;
151 
152  std::vector<String> current_col_types_;
153  std::vector<double> current_dm_values_;
154  std::vector<double> current_row_;
155 
156  };
157  } // namespace Internal
158 } // namespace OpenMS
159 
OpenMS::MSQuantifications::Assay
Definition: MSQuantifications.h:128
OpenMS::Internal::MzQuantMLHandler::logger_
const ProgressLogger & logger_
Progress logger.
Definition: MzQuantMLHandler.h:87
OpenMS::Internal::MzQuantMLHandler::current_pas_
std::set< DataProcessing::ProcessingAction > current_pas_
Definition: MzQuantMLHandler.h:150
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
OpenMS::Internal::MzQuantMLHandler::current_orderedps_
std::map< int, DataProcessing > current_orderedps_
Definition: MzQuantMLHandler.h:148
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
ControlledVocabulary.h
OpenMS::Internal::MzQuantMLHandler
XML handler for MzQuantMLFile.
Definition: MzQuantMLHandler.h:55
OpenMS::Internal::MzQuantMLHandler::current_assay_
MSQuantifications::Assay current_assay_
Definition: MzQuantMLHandler.h:136
OpenMS::Internal::MzQuantMLHandler::cmsq_
const MSQuantifications * cmsq_
Definition: MzQuantMLHandler.h:96
OpenMS::Internal::MzQuantMLHandler::current_id_
String current_id_
Definition: MzQuantMLHandler.h:130
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::MzQuantMLHandler::tag_
String tag_
Definition: MzQuantMLHandler.h:92
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Internal::MzQuantMLHandler::current_col_types_
std::vector< String > current_col_types_
Definition: MzQuantMLHandler.h:152
XMLHandler.h
OpenMS::Internal::MzQuantMLHandler::cf_cf_obj_
std::map< String, ConsensusFeature > cf_cf_obj_
Definition: MzQuantMLHandler.h:140
OpenMS::Internal::MzQuantMLHandler::up_stack_
std::vector< MetaInfo > up_stack_
Definition: MzQuantMLHandler.h:134
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::MzQuantMLHandler::current_dm_values_
std::vector< double > current_dm_values_
Definition: MzQuantMLHandler.h:153
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::Internal::MzQuantMLHandler::numden_r_ids_
std::map< String, String > numden_r_ids_
Definition: MzQuantMLHandler.h:143
OpenMS::Internal::MzQuantMLHandler::r_r_obj_
std::map< String, ConsensusFeature::Ratio > r_r_obj_
Definition: MzQuantMLHandler.h:144
MSQuantifications.h
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Internal::MzQuantMLHandler::f_cf_ids_
std::map< String, String > f_cf_ids_
Definition: MzQuantMLHandler.h:139
OpenMS::Internal::MzQuantMLHandler::current_row_
std::vector< double > current_row_
Definition: MzQuantMLHandler.h:154
OpenMS::Internal::MzQuantMLHandler::cv_
ControlledVocabulary cv_
Controlled vocabulary (hopefully the psi-pi from OpenMS/share/OpenMS/CV/psi-pi.obo)
Definition: MzQuantMLHandler.h:90
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::MzQuantMLHandler::current_sws_
std::map< String, Software > current_sws_
Definition: MzQuantMLHandler.h:147
OpenMS::Internal::MzQuantMLHandler::r_rtemp_
std::map< String, ConsensusFeature::Ratio > r_rtemp_
Definition: MzQuantMLHandler.h:142
OpenMS::ControlledVocabulary::CVTerm
Representation of a CV term.
Definition: ControlledVocabulary.h:60
OpenMS::Internal::MzQuantMLHandler::f_f_obj_
std::map< String, FeatureHandle > f_f_obj_
Definition: MzQuantMLHandler.h:141
OpenMS::Internal::MzQuantMLHandler::current_cf_id_
String current_cf_id_
Definition: MzQuantMLHandler.h:131
OpenMS::Internal::MzQuantMLHandler::current_dp_
std::pair< int, DataProcessing > current_dp_
Definition: MzQuantMLHandler.h:149
OpenMS::Internal::MzQuantMLHandler::cm_cf_ids_
std::multimap< String, String > cm_cf_ids_
Definition: MzQuantMLHandler.h:138
OpenMS::MSQuantifications
Definition: MSQuantifications.h:52
OpenMS::Internal::MzQuantMLHandler::cvp_stack_
std::vector< CVTerm > cvp_stack_
Definition: MzQuantMLHandler.h:135
OpenMS::Internal::MzQuantMLHandler::msq_
MSQuantifications * msq_
Definition: MzQuantMLHandler.h:94
OpenMS::Internal::MzQuantMLHandler::current_files_
std::map< String, std::vector< ExperimentalSettings > > current_files_
1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings
Definition: MzQuantMLHandler.h:129
OpenMS::Internal::MzQuantMLHandler::current_count_
Size current_count_
Definition: MzQuantMLHandler.h:132