org.molgenis.data.annotation.core

Interface RepositoryAnnotator

All Known Implementing Classes:

AbstractRepositoryAnnotator, AbstractRepositoryEntityAnnotator, EffectBasedAnnotator, RepositoryAnnotatorImpl, SnpEffRepositoryAnnotator

public interface RepositoryAnnotator

interface for annotators. annotators take an iterator and return an iterator with some information added or updated

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOTATOR_PREFIX

Method Summary

Modifier and Type	Method and Description
Iterator<Entity>	annotate(Iterable<Entity> source)
default Iterator<Entity>	annotate(Iterable<Entity> source, boolean updateMode)
Iterator<Entity>	annotate(Iterator<Entity> source)
boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
String	canAnnotate(EntityType inputMetaData) Returns null if the annotator will work for the given metadata, a reason if not so
List<Attribute>	createAnnotatorAttributes(AttributeFactory attributeFactory)
CmdLineAnnotatorSettingsConfigurer	getCmdLineAnnotatorSettingsConfigurer()
default String	getDescription()
String	getFullName()
AnnotatorInfo	getInfo()
List<Attribute>	getOutputAttributes() returns an EntityType containing the attributes the annotator will add
List<Attribute>	getRequiredAttributes() Returns a EntityType containing the attributes needed for the annotator to work
String	getSimpleName() Return the name of the annotator

Field Detail

ANNOTATOR_PREFIX

static final String ANNOTATOR_PREFIX

See Also:

Constant Field Values

Method Detail

getInfo

AnnotatorInfo getInfo()

annotate

default Iterator<Entity> annotate(Iterable<Entity> source,
                                  boolean updateMode)

annotate

Iterator<Entity> annotate(Iterable<Entity> source)

annotationDataExists

boolean annotationDataExists()

Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached

Returns:

boolean

annotate

Iterator<Entity> annotate(Iterator<Entity> source)

getOutputAttributes

List<Attribute> getOutputAttributes()

returns an EntityType containing the attributes the annotator will add

Returns:

ouputMetadata

getRequiredAttributes

List<Attribute> getRequiredAttributes()

Returns a EntityType containing the attributes needed for the annotator to work

Returns:

inputMetaData;

canAnnotate

String canAnnotate(EntityType inputMetaData)

Returns null if the annotator will work for the given metadata, a reason if not so

Returns:

canAnnotate

getSimpleName

String getSimpleName()

Return the name of the annotator

Returns:

name

getFullName

String getFullName()

getCmdLineAnnotatorSettingsConfigurer

CmdLineAnnotatorSettingsConfigurer getCmdLineAnnotatorSettingsConfigurer()

getDescription

default String getDescription()

createAnnotatorAttributes

List<Attribute> createAnnotatorAttributes(AttributeFactory attributeFactory)