Package ubic.gemma.core.ontology

Class FactorValueOntologyUtils

java.lang.Object

ubic.gemma.core.ontology.FactorValueOntologyUtils

public class FactorValueOntologyUtils
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	FactorValueOntologyUtils.Annotation
static class	FactorValueOntologyUtils.AnnotationIds
static interface	FactorValueOntologyUtils.StatementVisitor<U,E extends Throwable>

Constructor Summary

Constructors

Constructor	Description
FactorValueOntologyUtils()

Method Summary

Modifier and Type	Method	Description
static Map<String,FactorValueOntologyUtils.Annotation>	getAnnotationsById(FactorValue fv)	Create a mapping of annotation IDs to annotations for a FactorValue.
static String	getUri(Long factorValueId)	Obtain a suitable ontology ID for a given factor value ID.
static String	getUri(FactorValue factorValue)	Obtain a suitable ontology ID for a given factor value.
static boolean	isAnnotationUri(String uri)	Check if a URI refers to an annotation of a factor value.
static Long	parseUri(String uri)	Extract a factor value ID from a factor value URI.
static <E extends Throwable> void	visitCharacteristics(Long factorValueId, Collection<StatementValueObject> statements, FactorValueOntologyUtils.StatementVisitor<String,E> visitor)	Visit the characteristics of a FactorValue and generate their annotation IDs.
static <E extends Throwable> void	visitStatements(Long factorValueId, Collection<StatementValueObject> statements, FactorValueOntologyUtils.StatementVisitor<FactorValueOntologyUtils.AnnotationIds,E> visitor)	Visit the statements of a FactorValue and generate their annotation IDs.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

FactorValueOntologyUtils

public FactorValueOntologyUtils()

Method Details

getUri

public static String getUri(Long factorValueId)

Obtain a suitable ontology ID for a given factor value ID.

getUri

public static String getUri(FactorValue factorValue)

Obtain a suitable ontology ID for a given factor value.

parseUri

@Nullable
public static Long parseUri(String uri)

Extract a factor value ID from a factor value URI.

isAnnotationUri

public static boolean isAnnotationUri(String uri)

Check if a URI refers to an annotation of a factor value.

visitCharacteristics

public static <E extends Throwable> void visitCharacteristics(Long factorValueId,
 Collection<StatementValueObject> statements,
 FactorValueOntologyUtils.StatementVisitor<String,E> visitor)
                                                       throws E

Visit the characteristics of a FactorValue and generate their annotation IDs.

Characteristics also include subject-only statements.

Throws:

E

visitStatements

public static <E extends Throwable> void visitStatements(Long factorValueId,
 Collection<StatementValueObject> statements,
 FactorValueOntologyUtils.StatementVisitor<FactorValueOntologyUtils.AnnotationIds,E> visitor)
                                                  throws E

Visit the statements of a FactorValue and generate their annotation IDs.

Throws:

E

getAnnotationsById

public static Map<String,FactorValueOntologyUtils.Annotation> getAnnotationsById(FactorValue fv)

Create a mapping of annotation IDs to annotations for a FactorValue.