org.molgenis.data.vcf

Class VcfRepository

java.lang.Object

org.molgenis.data.support.AbstractRepository

org.molgenis.data.vcf.VcfRepository

All Implemented Interfaces:

Closeable, AutoCloseable, Iterable<Entity>, Repository<Entity>

public class VcfRepository
extends AbstractRepository

Repository implementation for vcf files.

The filename without the extension is considered to be the entityname

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_ATTRIBUTE_DESCRIPTION
static String	NAME
static String	ORIGINAL_NAME
static String	PREFIX
protected com.google.common.base.Supplier<VcfToEntity>	vcfToEntitySupplier

Constructor Summary

Constructors

Modifier	Constructor and Description
	VcfRepository(File file, String entityTypeId, VcfAttributes vcfAttributes, EntityTypeFactory entityTypeFactory, AttributeFactory attrMetaFactory)
protected	VcfRepository(VcfReaderFactory vcfReaderFactory, String entityTypeId, VcfAttributes vcfAttributes, EntityTypeFactory entityTypeFactory, AttributeFactory attrMetaFactory)

Method Summary

Modifier and Type	Method and Description
void	close()
long	count()
Set<RepositoryCapability>	getCapabilities()
EntityType	getEntityType()
Iterator<Entity>	iterator() Returns an iterator for this repository.

Methods inherited from class org.molgenis.data.support.AbstractRepository

add, add, aggregate, count, delete, delete, deleteAll, deleteAll, deleteById, findAll, findAll, findAll, findOne, findOneById, findOneById, forEachBatched, getName, getQueryOperators, query, update, update

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.Repository

forEachBatched, getExistingIDs, upsertBatch

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

DEFAULT_ATTRIBUTE_DESCRIPTION

public static final String DEFAULT_ATTRIBUTE_DESCRIPTION

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

ORIGINAL_NAME

public static final String ORIGINAL_NAME

See Also:

Constant Field Values

PREFIX

public static final String PREFIX

See Also:

Constant Field Values

vcfToEntitySupplier

protected final com.google.common.base.Supplier<VcfToEntity> vcfToEntitySupplier

Constructor Detail

VcfRepository

public VcfRepository(File file,
                     String entityTypeId,
                     VcfAttributes vcfAttributes,
                     EntityTypeFactory entityTypeFactory,
                     AttributeFactory attrMetaFactory)
              throws IOException

Throws:

IOException

VcfRepository

protected VcfRepository(VcfReaderFactory vcfReaderFactory,
                        String entityTypeId,
                        VcfAttributes vcfAttributes,
                        EntityTypeFactory entityTypeFactory,
                        AttributeFactory attrMetaFactory)

Method Detail

iterator

public Iterator<Entity> iterator()

Returns an iterator for this repository.

Use with caution! Multiple iterators will all point to the same line in the VCF file, leading to unpredictable behaviour. If you want to get the EntityType of this repository and you can't access getEntityType(), convert the iterator to a PeekingIterator and peek the first Entity.

getEntityType

public EntityType getEntityType()

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class AbstractRepository

Throws:

IOException

getCapabilities

public Set<RepositoryCapability> getCapabilities()

count

public long count()

Specified by:

count in interface Repository<Entity>

Overrides:

count in class AbstractRepository