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ControlledVocabulary.h
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31 // $Maintainer: Andreas Bertsch $
32 // $Authors: Marc Sturm, Andreas Bertsch, Mathias Walzer $
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34 
35 #ifndef OPENMS_FORMAT_CONTROLLEDVOCABULARY_H
36 #define OPENMS_FORMAT_CONTROLLEDVOCABULARY_H
37 
41 
42 #include <set>
43 
44 namespace OpenMS
45 {
54  class OPENMS_DLLAPI ControlledVocabulary
55  {
56  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ControlledVocabulary& cv);
57 
58 public:
60  struct OPENMS_DLLAPI CVTerm
61  {
63  enum XRefType
64  {
65  XSD_STRING = 0, // xsd:string A string
66  XSD_INTEGER, // xsd:integer Any integer
67  XSD_DECIMAL, // xsd:decimal Any real number
68  XSD_NEGATIVE_INTEGER, // xsd:negativeInteger Any negative integer
69  XSD_POSITIVE_INTEGER, // xsd:positiveInteger Any integer > 0
70  XSD_NON_NEGATIVE_INTEGER, // xsd:nonNegativeInteger Any integer >= 0
71  XSD_NON_POSITIVE_INTEGER, // xsd:nonPositiveInteger Any integer < 0
72  XSD_BOOLEAN, // xsd:boolean True or false
73  XSD_DATE, // xsd:date An XML-Schema date
74  XSD_ANYURI, // xsd:anyURI uniform resource identifier
75  NONE
76  };
77 
78  static String getXRefTypeName(XRefType type);
79 
82  std::set<String> parents;
83  std::set<String> children;
84  bool obsolete;
90  std::set<String> units;
91 
93  CVTerm();
94 
95  CVTerm(const CVTerm& rhs);
96 
97  CVTerm& operator=(const CVTerm& rhs);
98 
100  String toXMLString(const String& ref, const String& value = String("")) const;
101 
103  String toXMLString(const String& ref, const DataValue& value) const;
104 
105  };
106 
109 
111  virtual ~ControlledVocabulary();
112 
114  const String& name() const;
115 
122  void loadFromOBO(const String& name, const String& filename);
123 
125  bool exists(const String& id) const;
126 
128  bool hasTermWithName(const String& name) const;
129 
135  const CVTerm& getTerm(const String& id) const;
136 
142  const CVTerm& getTermByName(const String& name, const String& desc = "") const;
143 
144 
146  const Map<String, CVTerm>& getTerms() const;
147 
155  void getAllChildTerms(std::set<String>& terms, const String& parent) const;
156 
162  bool isChildOf(const String& child, const String& parent) const;
163 
164 protected:
170  bool checkName_(const String& id, const String& name, bool ignore_case = true);
171 
178  };
179 
181  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ControlledVocabulary& cv);
182 
183 
184 } // namespace OpenMS
185 
186 #endif // OPENMS_FORMAT_CONTROLLEDVOCABULARY_H
Definition: ControlledVocabulary.h:67
Representation of a CV term.
Definition: ControlledVocabulary.h:60
A more convenient string class.
Definition: String.h:57
Map< String, CVTerm > terms_
Map from ID to CVTerm.
Definition: ControlledVocabulary.h:173
String id
Identifier.
Definition: ControlledVocabulary.h:81
Definition: ControlledVocabulary.h:74
StringList xref_binary
xref binary-data-type for the CV-term (list of all allowed data value types for the current binary da...
Definition: ControlledVocabulary.h:89
Definition: ControlledVocabulary.h:73
StringList unparsed
Unparsed lines from the definition file.
Definition: ControlledVocabulary.h:87
bool obsolete
Flag that indicates of the term is obsolete.
Definition: ControlledVocabulary.h:84
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:57
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
XRefType
define xsd types allowed in cv term to specify their value-type
Definition: ControlledVocabulary.h:63
Map< String, String > namesToIds_
Map from name to id.
Definition: ControlledVocabulary.h:175
std::set< String > units
unit accession ids, defined by relationship has units
Definition: ControlledVocabulary.h:90
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
XRefType xref_type
xref value-type for the CV-term
Definition: ControlledVocabulary.h:88
String name
Text name.
Definition: ControlledVocabulary.h:80
StringList synonyms
List of synonyms.
Definition: ControlledVocabulary.h:86
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:74
std::set< String > parents
The parent IDs.
Definition: ControlledVocabulary.h:82
std::set< String > children
The child IDs.
Definition: ControlledVocabulary.h:83
Definition: ControlledVocabulary.h:72
Definition: ControlledVocabulary.h:66
String name_
Name set in the load method.
Definition: ControlledVocabulary.h:177
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
String description
Term description.
Definition: ControlledVocabulary.h:85

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