org.molgenis.data.annotation.impl

Class KeggServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.impl.KeggServiceAnnotator

All Implemented Interfaces:

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

@Component(value="KeggService")
public class KeggServiceAnnotator
extends LocusAnnotator

Author:

jvelde

Field Summary

Fields

Modifier and Type	Field and Description
static String	KEGG_GENE_ID
static String	KEGG_PATHWAYS_IDS
static String	KEGG_PATHWAYS_NAMES

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
KeggServiceAnnotator(AnnotationService annotatorService, HgncLocationsProvider hgncLocationsProvider, KeggDataProvider keggDataProvider)

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
static Map<String,ArrayList<String>>	getKeggGenePathways(Map<String,ArrayList<String>> pathwayGenes) Convert map of (pathway -> genes) to (gene -> pathways)
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

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

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

KEGG_GENE_ID

public static final String KEGG_GENE_ID

See Also:

Constant Field Values

KEGG_PATHWAYS_IDS

public static final String KEGG_PATHWAYS_IDS

See Also:

Constant Field Values

KEGG_PATHWAYS_NAMES

public static final String KEGG_PATHWAYS_NAMES

See Also:

Constant Field Values

Constructor Detail

KeggServiceAnnotator

@Autowired
public KeggServiceAnnotator(AnnotationService annotatorService,
                                       HgncLocationsProvider hgncLocationsProvider,
                                       KeggDataProvider keggDataProvider)
                                throws IOException

Throws:

IOException

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

getSimpleName

public String getSimpleName()

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

annotateEntity

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

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

getKeggGenePathways

public static Map<String,ArrayList<String>> getKeggGenePathways(Map<String,ArrayList<String>> pathwayGenes)

Convert map of (pathway -> genes) to (gene -> pathways)

Parameters:

pathwayGenes -

Returns:

getOutputMetaData

public EntityMetaData getOutputMetaData()