A C D E F G H I N O P Q R S T V

A

addEntityMeta(EntityMetaData) - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

ALT - Static variable in class org.molgenis.data.vcf.VcfRepository

ALT_META - Static variable in class org.molgenis.data.vcf.VcfRepository

C

canImport(File, RepositoryCollection) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

checkPreviouslyAnnotatedAndAddMetadata(File, PrintWriter, List<AttributeMetaData>, String) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

Checks for previous annotations

CHROM - Static variable in class org.molgenis.data.vcf.VcfRepository

CHROM_META - Static variable in class org.molgenis.data.vcf.VcfRepository

close() - Method in class org.molgenis.data.vcf.VcfRepository

convertToVCF(Entity) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

Convert an vcfEntity to a VCF line

count() - Method in class org.molgenis.data.vcf.VcfRepository

createVcfReader() - Method in class org.molgenis.data.vcf.VcfRepository

D

doImport(RepositoryCollection, DatabaseAction, String) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

E

equals(Object) - Method in class org.molgenis.data.vcf.datastructures.Sample

equalsSampleOrString(Object) - Method in class org.molgenis.data.vcf.datastructures.Sample

Allows compare with String or Sample object

F

FILTER - Static variable in class org.molgenis.data.vcf.VcfRepository

FILTER_META - Static variable in class org.molgenis.data.vcf.VcfRepository

G

getCapabilities() - Method in class org.molgenis.data.vcf.VcfRepository

getChild() - Method in class org.molgenis.data.vcf.datastructures.Trio

getEntityMetaData() - Method in class org.molgenis.data.vcf.VcfRepository

getEntityNames() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

getFather() - Method in class org.molgenis.data.vcf.datastructures.Trio

getGenotype() - Method in class org.molgenis.data.vcf.datastructures.Sample

getId() - Method in class org.molgenis.data.vcf.datastructures.Sample

getInfoPrefix() - Static method in class org.molgenis.data.vcf.VcfRepository

Prefix to make INFO column names safe-ish.

getMother() - Method in class org.molgenis.data.vcf.datastructures.Trio

getMustChangeEntityName() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getName() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

getOrder() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getPedigree(File) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

Get pedigree data from VCF Now only support child, father, mother No fancy data structure either Output: result.put(childID, Arrays.asList(new String[]{motherID, fatherID}));

getRepository(String) - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

getSupportedDatabaseActions() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getSupportedFileExtensions() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

H

hashCode() - Method in class org.molgenis.data.vcf.datastructures.Sample

hasRepository(String) - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

I

ID - Static variable in class org.molgenis.data.vcf.VcfRepository

ID_META - Static variable in class org.molgenis.data.vcf.VcfRepository

importVcf(File) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

INFO - Static variable in class org.molgenis.data.vcf.VcfRepository

INTERNAL_ID - Static variable in class org.molgenis.data.vcf.VcfRepository

iterator() - Method in class org.molgenis.data.vcf.VcfRepository

iterator() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

N

NAME - Static variable in class org.molgenis.data.vcf.VcfRepository

NAME - Static variable in class org.molgenis.data.vcf.VcfRepositoryCollection

O

onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.data.vcf.importer.VcfImporterServiceRegistrator

org.molgenis.data.vcf - package org.molgenis.data.vcf

org.molgenis.data.vcf.datastructures - package org.molgenis.data.vcf.datastructures

org.molgenis.data.vcf.importer - package org.molgenis.data.vcf.importer

org.molgenis.data.vcf.utils - package org.molgenis.data.vcf.utils

P

POS - Static variable in class org.molgenis.data.vcf.VcfRepository

POS_META - Static variable in class org.molgenis.data.vcf.VcfRepository

PREFIX - Static variable in class org.molgenis.data.vcf.VcfRepository

Q

QUAL - Static variable in class org.molgenis.data.vcf.VcfRepository

QUAL_META - Static variable in class org.molgenis.data.vcf.VcfRepository

R

REF - Static variable in class org.molgenis.data.vcf.VcfRepository

REF_META - Static variable in class org.molgenis.data.vcf.VcfRepository

registerVcfRepositorySource() - Method in class org.molgenis.data.vcf.VcfDataConfig

Registers the VcfRepositorySource factory so it can be used by DataService.createFileRepositorySource(File file);

S

Sample - Class in org.molgenis.data.vcf.datastructures

Sample() - Constructor for class org.molgenis.data.vcf.datastructures.Sample

Sample(String) - Constructor for class org.molgenis.data.vcf.datastructures.Sample

Sample(String, Entity) - Constructor for class org.molgenis.data.vcf.datastructures.Sample

SAMPLES - Static variable in class org.molgenis.data.vcf.VcfRepository

setChild(Sample) - Method in class org.molgenis.data.vcf.datastructures.Trio

setFather(Sample) - Method in class org.molgenis.data.vcf.datastructures.Trio

setGenotype(Entity) - Method in class org.molgenis.data.vcf.datastructures.Sample

setId(String) - Method in class org.molgenis.data.vcf.datastructures.Sample

setMother(Sample) - Method in class org.molgenis.data.vcf.datastructures.Trio

T

TAB - Static variable in class org.molgenis.data.vcf.utils.VcfUtils

toEntity(EntityMetaData, VcfRecord, VcfMeta) - Method in class org.molgenis.data.vcf.VcfRepository

toString() - Method in class org.molgenis.data.vcf.datastructures.Sample

toString() - Method in class org.molgenis.data.vcf.datastructures.Trio

Trio - Class in org.molgenis.data.vcf.datastructures

Trio() - Constructor for class org.molgenis.data.vcf.datastructures.Trio

Trio(Sample, Sample, Sample) - Constructor for class org.molgenis.data.vcf.datastructures.Trio

V

validateImport(File, RepositoryCollection) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

VcfDataConfig - Class in org.molgenis.data.vcf

VcfDataConfig() - Constructor for class org.molgenis.data.vcf.VcfDataConfig

VcfImporterService - Class in org.molgenis.data.vcf.importer

VcfImporterService(FileRepositoryCollectionFactory, DataService, PermissionSystemService) - Constructor for class org.molgenis.data.vcf.importer.VcfImporterService

VcfImporterServiceRegistrator - Class in org.molgenis.data.vcf.importer

VcfImporterServiceRegistrator(VcfImporterService, ImportServiceFactory) - Constructor for class org.molgenis.data.vcf.importer.VcfImporterServiceRegistrator

VcfRepository - Class in org.molgenis.data.vcf

Repository implementation for vcf files.

VcfRepository(File, String) - Constructor for class org.molgenis.data.vcf.VcfRepository

VcfRepositoryCollection - Class in org.molgenis.data.vcf

VcfRepositoryCollection(File) - Constructor for class org.molgenis.data.vcf.VcfRepositoryCollection

VcfUtils - Class in org.molgenis.data.vcf.utils

VcfUtils() - Constructor for class org.molgenis.data.vcf.utils.VcfUtils

A C D E F G H I N O P Q R S T V