- get(String) - Method in class org.phenotips.vocabulary.script.OntologyScriptService
-
- get(String) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
-
Retrieve a vocabulary given its identifier.
- get(String) - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Generic property access.
- getAliases() - Method in interface org.phenotips.vocabulary.Vocabulary
-
A vocabulary has an official name, but it can also have other aliases, for example the Human Phenotype Ontology
is known both as HP
, which is the official prefix for its terms, HPO
, which is its acronym, or
the lowercase hpo
.
- getAncestors() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Returns the ancestors (both direct and indirect ancestors) of this term.
- getAncestorsAndSelf() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Returns the ancestors (both direct and indirect ancestors) of this term and the term itself.
- getAnnotationSource() - Method in interface org.phenotips.vocabulary.VocabularyExtension
-
Specifies the annotation source URL.
- getAvailableCategories() - Method in interface org.phenotips.vocabulary.VocabularyManager
-
- getAvailableVocabularies() - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
-
- getAvailableVocabularies() - Method in interface org.phenotips.vocabulary.VocabularyManager
-
- getCitation() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the citation for the vocabulary.
- getContainer() - Method in interface org.phenotips.vocabulary.SolrCoreContainerHandler
-
Gets the Solr core container.
- getDefaultSourceLocation() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the default location where the sources for this vocabulary can be fetched from.
- getDescription() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
The human-readable term description, usually a longer phrase or paragraph that describes the term.
- getDistance(String, String) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Find the distance between two terms identified by their
term identifiers
, if this
is a structured ontology that supports computing such a distance.
- getDistance(VocabularyTerm, VocabularyTerm) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Find the distance between two terms, if this is a structured ontology that supports computing such a distance.
- getDistanceTo(VocabularyTerm) - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Find the distance to another term in the same vocabulary, if the owner vocabulary is a structured ontology that
supports computing such a distance.
- getExtensions() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the list of
VocabularyExtension
s that extend a base vocabulary with additional annotations.
- getId() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
The (mandatory) term identifier, in the format <vocabulary prefix>:<term id>
, for example
HP:0002066
or MIM:260540
.
- getIdentifier() - Method in interface org.phenotips.vocabulary.Vocabulary
-
The identifier of the vocabulary, used internally to differentiate between different vocabularies and different
implementations of the same vocabulary.
- getName() - Method in interface org.phenotips.vocabulary.Vocabulary
-
The official name of the vocabulary.
- getName() - Method in interface org.phenotips.vocabulary.VocabularyExtension
-
The official name of the vocabulary extension.
- getName() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
The short human-readable term name, for example Gait ataxia
.
- getOntologiesVersions() - Method in class org.phenotips.vocabulary.listeners.PatientVocabularyVersionRecorder
-
Modify this function to add more version types.
- getOntology(String) - Method in class org.phenotips.vocabulary.script.OntologyScriptService
-
- getParents() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Returns the parents (direct ancestors) of this term.
- getRelocation(String) - Method in interface org.phenotips.vocabulary.VocabularySourceRelocationService
-
get the XObject of type PhenoTips.VocabularySourceRelocationClass with the value for the original
property equal to the value of the original
argument, and if not null
, return the value of the
relocation property.
- getReplacementSolrConnection(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
-
Get the temporary Solr core used for a vocabulary during reindexing.
- getRowItem(CSVRecord, int) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
-
Helper method that gets the cell on the specified column, as string, if it exists, without throwing exceptions.
- getSolrConnection(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
-
Get the Solr core used for a vocabulary.
- getSourceLocation() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the location where the sources for this vocabulary can be fetched from.
- getSupportedCategories() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Reports the categories of terms supported by this vocabulary.
- getTargetVocabularyIds() - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
-
Specifies the vocabularies targeted by this extension.
- getTerm(String) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Access an individual term from the vocabulary, identified by its
term identifier
.
- getTermCache(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
-
Get the cache instance created for handling vocabulary terms.
- getTerms(Collection<String>) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Access a list of terms from the vocabulary, identified by their
term identifiers
.
- getTranslatedDescription() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
The human-readable term description, translated in the current locale if a translation is available, usually a
longer phrase or paragraph that describes the term.
- getTranslatedName() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
The short human-readable term name, translated in the current locale if a translation is available, for example
Marcha atáxica
if the current user is browsing in Spanish.
- getTranslatedValues(String) - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Generic translated property access.
- getVersion() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the available version of the vocabulary.
- getVocabularies(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
-
Retrieve a set of
Vocabulary
objects that fall under the provided vocabulary
category
.
- getVocabulary(String) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
-
Retrieve a vocabulary given its identifier.
- getVocabulary(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
-
Retrieve a vocabulary given its identifier.
- getVocabulary() - Method in interface org.phenotips.vocabulary.VocabularyTerm
-
Returns the vocabulary where this term is defined.
- getWebsite() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the website url for the vocabulary.
- search(String, String, int) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
-
- search(Map<String, ?>) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Generic search method, which looks for terms that match the specified term properties.
- search(Map<String, ?>, Map<String, String>) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Generic search method, which looks for terms that match the specified meta-properties.
- search(String) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Suggest the terms that best match the user's input.
- search(String, int, String, String) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Suggest the terms that best match the user's input.
- search(String, String, int, String, String) - Method in interface org.phenotips.vocabulary.Vocabulary
-
Suggest the terms that best match the user's input, in a specific sub-category of this vocabulary.
- search(String, String, int) - Method in interface org.phenotips.vocabulary.VocabularyManager
-
- set(String, Object) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
-
Generic property setter.
- setDescription(String) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
-
Sets the human-readable term description, usually a longer phrase or paragraph that describes the term.
- setId(String) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
-
Sets the (mandatory) term identifier.
- setName(String) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
-
Sets the short human-readable term name.
- setParents(Set<VocabularyTerm>) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
-
Sets the parents (direct ancestors) of this term.
- setupCSVParser(Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
-
Sets up a CSV parser so that it accepts the format of the input file, and has names for each column of interest.
- size() - Method in interface org.phenotips.vocabulary.Vocabulary
-
Get the size (i.e.
- SolrCoreContainerHandler - Interface in org.phenotips.vocabulary
-
Provides access to the configured Solr instance.
- SolrVocabularyResourceManager - Interface in org.phenotips.vocabulary
-
Provides methods for initializing the resources needed by vocabularies stored in a Solr index.