| OpenMS 2.5.0

ControlledVocabulary.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Andreas Bertsch, Mathias Walzer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
38 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
39 #include <OpenMS/DATASTRUCTURES/Map.h>
40 #include <OpenMS/CONCEPT/Exception.h>
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 //static bool isSearchEngineSpecificScore();
80 static bool isHigherBetterScore(ControlledVocabulary::CVTerm term);
81
82 String name;
83 String id;
84 std::set<String> parents;
85 std::set<String> children;
86 bool obsolete;
87 String description;
88 StringList synonyms;
89 StringList unparsed;
90 XRefType xref_type;
91 StringList xref_binary;
92 std::set<String> units;
93
95 CVTerm();
96
97 CVTerm(const CVTerm& rhs);
98
99 CVTerm& operator=(const CVTerm& rhs);
100
102 String toXMLString(const String& ref, const String& value = String("")) const;
103
105 String toXMLString(const String& ref, const DataValue& value) const;
106
107 };
108
110 ControlledVocabulary();
111
113 virtual ~ControlledVocabulary();
114
116 const String& name() const;
117
124 void loadFromOBO(const String& name, const String& filename);
125
127 bool exists(const String& id) const;
128
130 bool hasTermWithName(const String& name) const;
131
137 const CVTerm& getTerm(const String& id) const;
138
144 const CVTerm& getTermByName(const String& name, const String& desc = "") const;
145
146
148 const Map<String, CVTerm>& getTerms() const;
149
157 void getAllChildTerms(std::set<String>& terms, const String& parent) const;
158
164 bool isChildOf(const String& child, const String& parent) const;
165
166 protected:
172 bool checkName_(const String& id, const String& name, bool ignore_case = true);
173
175 Map<String, CVTerm> terms_;
177 Map<String, String> namesToIds_;
179 String name_;
180 };
181
183 OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ControlledVocabulary& cv);
184
185
186 } // namespace OpenMS
187
OpenMS::ControlledVocabulary::CVTerm::XSD_NEGATIVE_INTEGER
Definition: ControlledVocabulary.h:68
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DataValue
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
OpenMS::ControlledVocabulary::CVTerm::XSD_DATE
Definition: ControlledVocabulary.h:73
OpenMS::ControlledVocabulary::CVTerm::xref_binary
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:91
OpenMS::ControlledVocabulary::CVTerm::XSD_INTEGER
Definition: ControlledVocabulary.h:66
OpenMS::ControlledVocabulary::CVTerm::id
String id
Identifier.
Definition: ControlledVocabulary.h:83
OpenMS::ControlledVocabulary::CVTerm::XSD_NON_NEGATIVE_INTEGER
Definition: ControlledVocabulary.h:70
Exception.h
OpenMS::ControlledVocabulary::CVTerm::XSD_NON_POSITIVE_INTEGER
Definition: ControlledVocabulary.h:71
OpenMS::ControlledVocabulary::CVTerm::XSD_POSITIVE_INTEGER
Definition: ControlledVocabulary.h:69
OpenMS::ControlledVocabulary::CVTerm::xref_type
XRefType xref_type
xref value-type for the CV-term
Definition: ControlledVocabulary.h:90
OpenMS::ControlledVocabulary::CVTerm::XSD_BOOLEAN
Definition: ControlledVocabulary.h:72
OpenMS::ControlledVocabulary::terms_
Map< String, CVTerm > terms_
Map from ID to CVTerm.
Definition: ControlledVocabulary.h:175
OpenMS::ControlledVocabulary::name_
String name_
Name set in the load method.
Definition: ControlledVocabulary.h:179
StringListUtils.h
OpenMS::ControlledVocabulary::CVTerm::unparsed
StringList unparsed
Unparsed lines from the definition file.
Definition: ControlledVocabulary.h:89
OpenMS::ControlledVocabulary::CVTerm::name
String name
if it is a score type, lookup has_order
Definition: ControlledVocabulary.h:82
OpenMS::ControlledVocabulary::CVTerm::synonyms
StringList synonyms
List of synonyms.
Definition: ControlledVocabulary.h:88
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ControlledVocabulary::CVTerm::XRefType
XRefType
define xsd types allowed in cv term to specify their value-type
Definition: ControlledVocabulary.h:63
OpenMS::ControlledVocabulary::CVTerm::XSD_DECIMAL
Definition: ControlledVocabulary.h:67
Map.h
OpenMS::ControlledVocabulary::CVTerm::units
std::set< String > units
unit accession ids, defined by relationship has units
Definition: ControlledVocabulary.h:92
OpenMS::ControlledVocabulary::CVTerm::XSD_ANYURI
Definition: ControlledVocabulary.h:74
OpenMS::ControlledVocabulary::CVTerm
Representation of a CV term.
Definition: ControlledVocabulary.h:60
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ControlledVocabulary::namesToIds_
Map< String, String > namesToIds_
Map from name to id.
Definition: ControlledVocabulary.h:177
OpenMS::ControlledVocabulary
Representation of a controlled vocabulary.
Definition: ControlledVocabulary.h:54
ListUtils.h
OpenMS::ControlledVocabulary::CVTerm::description
String description
Term description.
Definition: ControlledVocabulary.h:87
OpenMS::ControlledVocabulary::CVTerm::obsolete
bool obsolete
Flag that indicates of the term is obsolete.
Definition: ControlledVocabulary.h:86
OpenMS::ControlledVocabulary::CVTerm::children
std::set< String > children
The child IDs.
Definition: ControlledVocabulary.h:85
OpenMS::ControlledVocabulary::CVTerm::parents
std::set< String > parents
The parent IDs.
Definition: ControlledVocabulary.h:84