OpenMS
ControlledVocabulary.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Marc Sturm, Andreas Bertsch, Mathias Walzer $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
14 
15 #include <set>
16 #include <map>
17 
18 namespace OpenMS
19 {
28  class OPENMS_DLLAPI ControlledVocabulary
29  {
30  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ControlledVocabulary& cv);
31 
32 public:
34  struct OPENMS_DLLAPI CVTerm
35  {
37  enum XRefType
38  {
39  XSD_STRING = 0, // xsd:string A string
40  XSD_INTEGER, // xsd:integer Any integer
41  XSD_DECIMAL, // xsd:decimal Any real number
42  XSD_NEGATIVE_INTEGER, // xsd:negativeInteger Any negative integer
43  XSD_POSITIVE_INTEGER, // xsd:positiveInteger Any integer > 0
44  XSD_NON_NEGATIVE_INTEGER, // xsd:nonNegativeInteger Any integer >= 0
45  XSD_NON_POSITIVE_INTEGER, // xsd:nonPositiveInteger Any integer < 0
46  XSD_BOOLEAN, // xsd:boolean True or false
47  XSD_DATE, // xsd:date An XML-Schema date
48  XSD_ANYURI, // xsd:anyURI uniform resource identifier
49  NONE
50  };
51 
53  //static bool isSearchEngineSpecificScore();
55 
58  std::set<String> parents;
59  std::set<String> children;
60  bool obsolete;
66  std::set<String> units;
67 
69  CVTerm();
70 
71  CVTerm(const CVTerm& rhs);
72 
73  CVTerm& operator=(const CVTerm& rhs);
74 
76  String toXMLString(const String& ref, const String& value = String("")) const;
77 
79  String toXMLString(const String& ref, const DataValue& value) const;
80 
81  };
82 
85 
88 
90  const String& name() const;
91 
93  const String& label() const;
94 
96  const String& version() const;
97 
99  const String& url() const;
100 
107  void loadFromOBO(const String& name, const String& filename);
108 
110  bool exists(const String& id) const;
111 
113  bool hasTermWithName(const String& name) const;
114 
120  const CVTerm& getTerm(const String& id) const;
121 
127  const CVTerm& getTermByName(const String& name, const String& desc = "") const;
128 
129 
131  const std::map<String, CVTerm>& getTerms() const;
132 
140  void getAllChildTerms(std::set<String>& terms, const String& parent_id) const;
141 
153  template <class LAMBDA>
154  bool iterateAllChildren(const String& parent_id, LAMBDA lbd) const
155  {
156  for (const auto& child_id : getTerm(parent_id).children)
157  {
158  if (lbd(child_id) || iterateAllChildren(child_id, lbd))
159  return true;
160  }
161  return false;
162  }
163 
170 
176  bool isChildOf(const String& child_id, const String& parent_id) const;
177 
178 
194 
195 protected:
201  bool checkName_(const String& id, const String& name, bool ignore_case = true) const;
202 
204  std::map<String, CVTerm> terms_;
206  std::map<String, String> namesToIds_;
215  };
216 
218  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ControlledVocabulary& cv);
219 
220 
221 } // namespace OpenMS
222 
Definition: ControlledVocabulary.h:29
ControlledVocabulary()
Constructor.
bool checkName_(const String &id, const String &name, bool ignore_case=true) const
checks if a name corresponds to an id
static const ControlledVocabulary & getPSIMSCV()
Returns a CV for parsing/storing PSI-MS related data, e.g. mzML, or handle accessions/ids in datastru...
bool hasTermWithName(const String &name) const
Returns true if a term with the given name is in the CV. Returns false otherwise.
const CVTerm & getTerm(const String &id) const
Returns a term specified by ID.
bool iterateAllChildren(const String &parent_id, LAMBDA lbd) const
Iterates over all children (incl. subchildren etc) of parent recursively, i.e. the whole subtree.
Definition: ControlledVocabulary.h:154
const String & label() const
Returns the CV label (set in the load method)
void loadFromOBO(const String &name, const String &filename)
Loads the CV from an OBO file.
String name_
Name set in the load method.
Definition: ControlledVocabulary.h:208
std::map< String, String > namesToIds_
Map from name to id.
Definition: ControlledVocabulary.h:206
String version_
CV version.
Definition: ControlledVocabulary.h:212
const CVTerm & getTermByName(const String &name, const String &desc="") const
Returns a term specified by name.
bool isChildOf(const String &child_id, const String &parent_id) const
Returns if child is a child of parent.
const String & url() const
Returns the CV url (set in the load method)
virtual ~ControlledVocabulary()
Destructor.
std::map< String, CVTerm > terms_
Map from ID to CVTerm.
Definition: ControlledVocabulary.h:204
void getAllChildTerms(std::set< String > &terms, const String &parent_id) const
Writes all child terms recursively into terms.
String label_
CV label.
Definition: ControlledVocabulary.h:210
const ControlledVocabulary::CVTerm * checkAndGetTermByName(const OpenMS::String &name) const
Searches the existing terms for the given name.
const String & name() const
Returns the CV name (set in the load method)
const String & version() const
Returns the CV version (set in the load method)
const std::map< String, CVTerm > & getTerms() const
returns all the terms stored in the CV
bool exists(const String &id) const
Returns true if the term is in the CV. Returns false otherwise.
String url_
CV URL.
Definition: ControlledVocabulary.h:214
friend std::ostream & operator<<(std::ostream &os, const ControlledVocabulary &cv)
Print the contents to a stream.
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:33
A more convenient string class.
Definition: String.h:34
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Representation of a CV term.
Definition: ControlledVocabulary.h:35
std::set< String > parents
The parent IDs.
Definition: ControlledVocabulary.h:58
String toXMLString(const String &ref, const DataValue &value) const
get mzidentml formatted string. i.e. a cvparam xml element, ref should be the name of the ControlledV...
StringList unparsed
Unparsed lines from the definition file.
Definition: ControlledVocabulary.h:63
std::set< String > children
The child IDs.
Definition: ControlledVocabulary.h:59
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:65
String id
Identifier.
Definition: ControlledVocabulary.h:57
String description
Term description.
Definition: ControlledVocabulary.h:61
bool obsolete
Flag that indicates of the term is obsolete.
Definition: ControlledVocabulary.h:60
static String getXRefTypeName(XRefType type)
String name
if it is a score type, lookup has_order
Definition: ControlledVocabulary.h:56
StringList synonyms
List of synonyms.
Definition: ControlledVocabulary.h:62
XRefType xref_type
xref value-type for the CV-term
Definition: ControlledVocabulary.h:64
std::set< String > units
unit accession ids, defined by relationship has units
Definition: ControlledVocabulary.h:66
String toXMLString(const String &ref, const String &value=String("")) const
get mzidentml formatted string. i.e. a cvparam xml element, ref should be the name of the ControlledV...
XRefType
define xsd types allowed in cv term to specify their value-type
Definition: ControlledVocabulary.h:38
@ XSD_BOOLEAN
Definition: ControlledVocabulary.h:46
@ XSD_DATE
Definition: ControlledVocabulary.h:47
@ XSD_NEGATIVE_INTEGER
Definition: ControlledVocabulary.h:42
@ XSD_POSITIVE_INTEGER
Definition: ControlledVocabulary.h:43
@ XSD_NON_POSITIVE_INTEGER
Definition: ControlledVocabulary.h:45
@ XSD_DECIMAL
Definition: ControlledVocabulary.h:41
@ XSD_NON_NEGATIVE_INTEGER
Definition: ControlledVocabulary.h:44
@ XSD_ANYURI
Definition: ControlledVocabulary.h:48
@ XSD_INTEGER
Definition: ControlledVocabulary.h:40
CVTerm & operator=(const CVTerm &rhs)
static bool isHigherBetterScore(ControlledVocabulary::CVTerm term)