org.molgenis.data.annotation.core.entity.impl.snpeff

Class SnpEffRepositoryAnnotator

java.lang.Object

org.molgenis.data.annotation.core.AbstractRepositoryAnnotator

org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRepositoryAnnotator

All Implemented Interfaces:

EffectCreatingAnnotator, RepositoryAnnotator

public class SnpEffRepositoryAnnotator
extends AbstractRepositoryAnnotator
implements EffectCreatingAnnotator

Field Summary

Fields inherited from interface org.molgenis.data.annotation.core.RepositoryAnnotator

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
SnpEffRepositoryAnnotator(String name)

Method Summary

Modifier and Type	Method and Description
Iterator<Entity>	annotate(Iterable<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 repoMetaData) Returns null if the annotator will work for the given metadata, a reason if not so
List<Attribute>	createAnnotatorAttributes(AttributeFactory attributeFactory)
CmdLineAnnotatorSettingsConfigurer	getCmdLineAnnotatorSettingsConfigurer()
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
EntityType	getTargetEntityType(EntityType sourceEntityType) Annotators that add a new repository need the source meta data to construct the new repository's meta data.
void	init(SnpEffRunner snpEffRunner, Entity snpEffAnnotatorSettings, VcfAttributes vcfAttributes, EffectsMetaData effectsMetaData, DataService dataService)

Methods inherited from class org.molgenis.data.annotation.core.AbstractRepositoryAnnotator

annotate, getDescription, getFullName

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.molgenis.data.annotation.core.RepositoryAnnotator

annotate

Constructor Detail

SnpEffRepositoryAnnotator

public SnpEffRepositoryAnnotator(String name)

Method Detail

init

public void init(SnpEffRunner snpEffRunner,
                 Entity snpEffAnnotatorSettings,
                 VcfAttributes vcfAttributes,
                 EffectsMetaData effectsMetaData,
                 DataService dataService)

getInfo

public AnnotatorInfo getInfo()

Specified by:

getInfo in interface RepositoryAnnotator

annotate

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

Specified by:

annotate in interface RepositoryAnnotator

canAnnotate

public String canAnnotate(EntityType repoMetaData)

Description copied from interface: RepositoryAnnotator

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

Specified by:

canAnnotate in interface RepositoryAnnotator

Overrides:

canAnnotate in class AbstractRepositoryAnnotator

Returns:

canAnnotate

getRequiredAttributes

public List<Attribute> getRequiredAttributes()

Description copied from interface: RepositoryAnnotator

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

Specified by:

getRequiredAttributes in interface RepositoryAnnotator

Returns:

inputMetaData;

getSimpleName

public String getSimpleName()

Description copied from interface: RepositoryAnnotator

Return the name of the annotator

Specified by:

getSimpleName in interface RepositoryAnnotator

Returns:

name

annotationDataExists

public boolean annotationDataExists()

Description copied from interface: RepositoryAnnotator

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

Specified by:

annotationDataExists in interface RepositoryAnnotator

Returns:

boolean

getCmdLineAnnotatorSettingsConfigurer

public CmdLineAnnotatorSettingsConfigurer getCmdLineAnnotatorSettingsConfigurer()

Specified by:

getCmdLineAnnotatorSettingsConfigurer in interface RepositoryAnnotator

getTargetEntityType

public EntityType getTargetEntityType(EntityType sourceEntityType)

Description copied from interface: EffectCreatingAnnotator

Annotators that add a new repository need the source meta data to construct the new repository's meta data.

Specified by:

getTargetEntityType in interface EffectCreatingAnnotator

Parameters:

sourceEntityType - the meta data of the source repository

Returns:

the meta data of the new repository

getOutputAttributes

public List<Attribute> getOutputAttributes()

Description copied from interface: RepositoryAnnotator

returns an EntityType containing the attributes the annotator will add

Specified by:

getOutputAttributes in interface RepositoryAnnotator

Returns:

ouputMetadata

createAnnotatorAttributes

public List<Attribute> createAnnotatorAttributes(AttributeFactory attributeFactory)

Specified by:

createAnnotatorAttributes in interface RepositoryAnnotator