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

A

ALT - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

C

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

CHROM - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

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

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

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

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

Creates a internal molgenis id from a vcf entity

D

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

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

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

E

EFFECT - Static variable in class org.molgenis.data.vcf.utils.VcfWriterUtils

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

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

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.model.VcfAttributes

FORMAT_GT - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

G

get() - Method in class org.molgenis.data.vcf.VcfReaderFactoryImpl

getAltAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getAtomicAttributesFromList(Iterable<Attribute>) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

getAttributesMapFromList(Iterable<Attribute>) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

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

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

getChromAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getEntityType() - Method in class org.molgenis.data.vcf.format.VcfToEntity

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

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

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

getFilterAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

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

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

getIdAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getIdFromInfoField(String) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

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(Scanner) - 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}));

getPosAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getQualAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getRefAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

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

getVCF() - Static method in enum org.molgenis.data.vcf.VcfFileExtensions

H

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

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

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

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

I

ID - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

INFO - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

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

INTERNAL_ID - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

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

Returns an iterator for this repository.

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

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

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

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

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

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

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

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

P

POS - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

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

Q

QUAL - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

R

REF - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

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.model.VcfAttributes

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

toEntity(String[]) - Method in class org.molgenis.data.vcf.format.VcfToEntity

toEntity(VcfRecord) - Method in class org.molgenis.data.vcf.format.VcfToEntity

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

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

toString() - Method in enum org.molgenis.data.vcf.VcfFileExtensions

toVcfDataType(AttributeType) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

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

tryCloseVcfReader(VcfReader) - Method in class org.molgenis.data.vcf.VcfReaderFactoryImpl

V

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

valueOf(String) - Static method in enum org.molgenis.data.vcf.VcfFileExtensions

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.data.vcf.VcfFileExtensions

Returns an array containing the constants of this enum type, in the order they are declared.

VARIANT - Static variable in class org.molgenis.data.vcf.utils.VcfWriterUtils

VcfAttributes - Class in org.molgenis.data.vcf.model

VcfAttributes(AttributeFactory) - Constructor for class org.molgenis.data.vcf.model.VcfAttributes

VcfDataConfig - Class in org.molgenis.data.vcf

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

VcfFileExtensions - Enum in org.molgenis.data.vcf

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

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

VcfReaderFactory - Interface in org.molgenis.data.vcf

VcfReaderFactoryImpl - Class in org.molgenis.data.vcf

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

VcfRepository - Class in org.molgenis.data.vcf

Repository implementation for vcf files.

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

VcfRepository(VcfReaderFactory, String, VcfAttributes, EntityTypeFactory, AttributeFactory) - 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

VcfToEntity - Class in org.molgenis.data.vcf.format

VcfToEntity(String, VcfMeta, VcfAttributes, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.vcf.format.VcfToEntity

vcfToEntitySupplier - Variable in class org.molgenis.data.vcf.VcfRepository

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

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

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

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

W

writeToVcf(Entity, BufferedWriter) - Static method in class org.molgenis.data.vcf.utils.VcfWriterUtils

Overload of writeToVcf to support a simpler call with only Entity and Writer.

writeToVcf(Entity, List<Attribute>, List<String>, BufferedWriter) - Static method in class org.molgenis.data.vcf.utils.VcfWriterUtils

Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty

writeVcfHeader(File, BufferedWriter, List<Attribute>) - Static method in class org.molgenis.data.vcf.utils.VcfWriterUtils

Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty

writeVcfHeader(File, BufferedWriter, List<Attribute>, List<String>) - Static method in class org.molgenis.data.vcf.utils.VcfWriterUtils

Checks for previous annotations

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