org.molgenis.data.annotation.impl

Class GoNLServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.VariantAnnotator

org.molgenis.data.annotation.impl.GoNLServiceAnnotator

All Implemented Interfaces:

EventListener, RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

@Component(value="gonlService")
public class GoNLServiceAnnotator
extends VariantAnnotator

GoNl annotator data: https://molgenis26.target.rug.nl/downloads/gonl_public/variants/release5_with_GTC/ release5_noContam_noChildren_with_AN_AC_GTC_stripped.tgz PLUS chrX from http://molgenis15.target.rug.nl/release4_noContam_noChildren_with_AN_AC_GTC_stripped.tgz GoNL example line: 1 126108 rs146756510 G A . PASS AC=37;AN=996;DB;GTC=461,37,0;set=SNP TODO: right now there are no multiple alternative alleles in GoNL, but will there be in the future??

Field Summary

Fields

Modifier and Type	Field and Description
static String	GONL_DIRECTORY_LOCATION_PROPERTY
static String	GONL_GTC
static String	GONL_MAF

Fields inherited from class org.molgenis.data.annotation.VariantAnnotator

ALTERNATIVE, REFERENCE

Fields inherited from class org.molgenis.data.annotation.LocusAnnotator

CHROMOSOME, POSITION

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

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
GoNLServiceAnnotator(File gonlR5directory, File inputVcfFile, File outputVCFFile)
GoNLServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotatorService)

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity)
boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Methods inherited from class org.molgenis.data.annotation.VariantAnnotator

getInputMetaData

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

annotate, canAnnotate, 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.RepositoryAnnotator

annotate, canAnnotate, getDescription, getFullName

Field Detail

GONL_MAF

public static final String GONL_MAF

See Also:

Constant Field Values

GONL_GTC

public static final String GONL_GTC

See Also:

Constant Field Values

GONL_DIRECTORY_LOCATION_PROPERTY

public static final String GONL_DIRECTORY_LOCATION_PROPERTY

See Also:

Constant Field Values

Constructor Detail

GoNLServiceAnnotator

@Autowired
public GoNLServiceAnnotator(MolgenisSettings molgenisSettings,
                                       AnnotationService annotatorService)
                                throws IOException

Throws:

IOException

GoNLServiceAnnotator

public GoNLServiceAnnotator(File gonlR5directory,
                            File inputVcfFile,
                            File outputVCFFile)
                     throws Exception

Throws:

Exception

Method Detail

onApplicationEvent

public void onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Specified by:

onApplicationEvent in interface org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

Overrides:

onApplicationEvent in class AbstractRepositoryAnnotator

annotationDataExists

public boolean annotationDataExists()

Description copied from class: AbstractRepositoryAnnotator

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 class AbstractRepositoryAnnotator

Returns:

boolean

getSimpleName

public String getSimpleName()

annotateEntity

public List<Entity> annotateEntity(Entity entity)
                            throws IOException,
                                   InterruptedException

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

InterruptedException

getOutputMetaData

public EntityMetaData getOutputMetaData()