Uses of Class
org.molgenis.omx.xgap.Variant

Packages that use Variant

Package	Description
org.molgenis.omx.das
org.molgenis.omx.patient
org.molgenis.omx.xgap
org.molgenis.omx.xgap.db
org.molgenis.service

Uses of Variant in org.molgenis.omx.das

Methods in org.molgenis.omx.das that return types with arguments of type Variant

Modifier and Type	Method and Description
protected List<Variant>	DasOmxDataSource.queryVariants(String segmentId, int start, int stop, Patient patientObject)

Methods in org.molgenis.omx.das with parameters of type Variant

Modifier and Type	Method and Description
protected uk.ac.ebi.mydas.model.DasFeature	DasOmxDataSource.createDasFeature(Variant variant)

Uses of Variant in org.molgenis.omx.patient

Methods in org.molgenis.omx.patient that return Variant

Modifier and Type	Method and Description
Variant	Patient.getAllele1() Get the Allele1.
Variant	Patient.getAllele1(Database db) Deprecated.
Variant	Patient.getAllele2() Get the Allele2.
Variant	Patient.getAllele2(Database db) Deprecated.

Methods in org.molgenis.omx.patient with parameters of type Variant

Modifier and Type	Method and Description
void	Patient.setAllele1(Variant allele1) Set the Allele1.
void	Patient.setAllele2(Variant allele2) Set the Allele2.

Uses of Variant in org.molgenis.omx.xgap

Methods in org.molgenis.omx.xgap that return Variant

Modifier and Type	Method and Description
Variant	Variant.create(Entity entity)
static Variant	Variant.findById(Database db, Integer id)
static Variant	Variant.findByIdentifier(Database db, String identifier)

Methods in org.molgenis.omx.xgap that return types with arguments of type Variant

Modifier and Type	Method and Description
static List<? extends Variant>	Variant.find(Database db, QueryRule... rules) Shorthand for db.find(Variant.class, org.molgenis.framework.db.QueryRule ...
static Query<? extends Variant>	Variant.query(Database db) Shorthand for db.query(Variant.class).

Constructors in org.molgenis.omx.xgap with parameters of type Variant

Constructor and Description
Variant(Variant copyMe) copy constructor

Uses of Variant in org.molgenis.omx.xgap.db

Classes in org.molgenis.omx.xgap.db with type parameters of type Variant

Modifier and Type	Class and Description
class	VariantSecurityDecorator<E extends Variant> TODO add column level security filters

Methods in org.molgenis.omx.xgap.db that return Variant

Modifier and Type	Method and Description
Variant	VariantJpaMapper.create()

Methods in org.molgenis.omx.xgap.db that return types with arguments of type Variant

Modifier and Type	Method and Description
List<Variant>	VariantJpaMapper.createList(int size) Return EMPTY list of given allocated size

Methods in org.molgenis.omx.xgap.db with parameters of type Variant

Modifier and Type	Method and Description
void	VariantJpaMapper.create(Variant entity) This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object
void	VariantJpaMapper.destroy(Variant variant)
void	VariantJpaMapper.edit(Variant variant)

Method parameters in org.molgenis.omx.xgap.db with type arguments of type Variant

Modifier and Type	Method and Description
int	VariantJpaMapper.executeAdd(List<? extends Variant> entities)
int	VariantJpaMapper.executeRemove(List<? extends Variant> entities)
int	VariantJpaMapper.executeUpdate(List<? extends Variant> entities)
void	VariantJpaMapper.prepareFileAttachements(List<Variant> entities, File baseDir)
void	VariantJpaMapper.resolveForeignKeys(List<Variant> entities)
boolean	VariantJpaMapper.saveFileAttachements(List<Variant> entities, File baseDir)

Uses of Variant in org.molgenis.service

Methods in org.molgenis.service that return Variant

Modifier and Type	Method and Description
Variant	VariantService.create(Variant variant)
Variant	VariantService.read(Integer id)

Methods in org.molgenis.service that return types with arguments of type Variant

Modifier and Type	Method and Description
Iterable<Variant>	VariantService.readAll()
EntityPager<Variant>	VariantService.readAll(int start, int num, List<QueryRule> queryRules)

Methods in org.molgenis.service with parameters of type Variant

Modifier and Type	Method and Description
Variant	VariantService.create(Variant variant)
void	VariantService.update(Variant variant)