org.molgenis.data.annotation.core.resources.impl.tabix

Class TabixRepository

java.lang.Object

org.molgenis.data.support.AbstractRepository

org.molgenis.data.annotation.core.resources.impl.tabix.TabixRepository

All Implemented Interfaces:

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

public class TabixRepository
extends AbstractRepository

Constructor Summary

Constructors

Constructor and Description
TabixRepository(File file, EntityType entityType) Creates a new TabixRepository
TabixRepository(File file, EntityType entityType, String chromosomeAttributeName, String positionAttributeName)

Method Summary

Modifier and Type	Method and Description
Stream<Entity>	findAll(Query<Entity> q)
Set<RepositoryCapability>	getCapabilities()
static au.com.bytecode.opencsv.CSVParser	getCsvParser()
EntityType	getEntityType()
Iterator<Entity>	iterator()
protected Entity	toEntity(String line)

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

add, add, aggregate, close, count, count, delete, delete, deleteAll, deleteAll, deleteById, 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

Constructor Detail

TabixRepository

public TabixRepository(File file,
                       EntityType entityType)
                throws IOException

Creates a new TabixRepository

Parameters:

file - the Tabix file

entityType - EntityType for the tabix file. Attributes should be in the order of the file's columns

Throws:

IOException - if something goes wrong creating the TabixReader for the file

TabixRepository

public TabixRepository(File file,
                       EntityType entityType,
                       String chromosomeAttributeName,
                       String positionAttributeName)
                throws IOException

Throws:

IOException

Method Detail

getCsvParser

public static au.com.bytecode.opencsv.CSVParser getCsvParser()

getCapabilities

public Set<RepositoryCapability> getCapabilities()

getEntityType

public EntityType getEntityType()

findAll

public Stream<Entity> findAll(Query<Entity> q)

Specified by:

findAll in interface Repository<Entity>

Overrides:

findAll in class AbstractRepository

toEntity

protected Entity toEntity(String line)
                   throws IOException

Throws:

IOException

iterator

public Iterator<Entity> iterator()