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A B C D F G H O Q R S T U V 

A

addRelationship(Beacon, Beacon) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Creates parent-child association.

B

BasicEntity<I> - Interface in com.dnastack.bob.persistence.entity
Parent of all the entities.
Beacon - Class in com.dnastack.bob.persistence.entity
Beacon.
Beacon() - Constructor for class com.dnastack.bob.persistence.entity.Beacon
 
BeaconDao - Interface in com.dnastack.bob.persistence.api
Beacon DAO.
BeaconResponse - Class in com.dnastack.bob.persistence.entity
Representation of a query result provided by a beacon.
BeaconResponse() - Constructor for class com.dnastack.bob.persistence.entity.BeaconResponse
 
BeaconResponseDao - Interface in com.dnastack.bob.persistence.api
Beacon response DAO.

C

Chromosome - Enum in com.dnastack.bob.persistence.enumerated
Canonical chromosome representation.
com.dnastack.bob.persistence.api - package com.dnastack.bob.persistence.api
 
com.dnastack.bob.persistence.entity - package com.dnastack.bob.persistence.entity
 
com.dnastack.bob.persistence.enumerated - package com.dnastack.bob.persistence.enumerated
 
countAll() - Method in interface com.dnastack.bob.persistence.api.GenericDao
 

D

Dataset - Class in com.dnastack.bob.persistence.entity
Beacon's data set.
Dataset() - Constructor for class com.dnastack.bob.persistence.entity.Dataset
 
DatasetDao - Interface in com.dnastack.bob.persistence.api
Dataset DAO.
DataSize - Class in com.dnastack.bob.persistence.entity
Data size.
DataSize() - Constructor for class com.dnastack.bob.persistence.entity.DataSize
 
DataUse - Class in com.dnastack.bob.persistence.entity
Data use.
DataUse() - Constructor for class com.dnastack.bob.persistence.entity.DataUse
 
DataUseDao - Interface in com.dnastack.bob.persistence.api
DataUse DAO.
DataUseRequirement - Class in com.dnastack.bob.persistence.entity
 
DataUseRequirement() - Constructor for class com.dnastack.bob.persistence.entity.DataUseRequirement
 
DataUseRequirementDao - Interface in com.dnastack.bob.persistence.api
DataUseRequirement DAO.
delete(I) - Method in interface com.dnastack.bob.persistence.api.GenericDao
 

F

findAll() - Method in interface com.dnastack.bob.persistence.api.GenericDao
 
findByAggregation(boolean) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Retrieves beacons by aggregation flag.
findById(I) - Method in interface com.dnastack.bob.persistence.api.GenericDao
 
findByIdAndVisibility(String, boolean) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Retrieves a beacon by its ID and visibility.
findByIdAndVisibility(String, boolean) - Method in interface com.dnastack.bob.persistence.api.OrganizationDao
 
findByIds(Collection<String>) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Retrieves beacons by their IDs.
findByIds(Collection<String>) - Method in interface com.dnastack.bob.persistence.api.OrganizationDao
 
findByIdsAndVisibility(Collection<String>, boolean) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Retrieves beacons by visibility.
findByIdsAndVisibility(Collection<String>, boolean) - Method in interface com.dnastack.bob.persistence.api.OrganizationDao
 
findByIp(String) - Method in interface com.dnastack.bob.persistence.api.UserDao
 
findByName(String) - Method in interface com.dnastack.bob.persistence.api.OrganizationDao
 
findByUserName(String) - Method in interface com.dnastack.bob.persistence.api.UserDao
 
findByVisibility(boolean) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Retrieves beacons by visibility.
findByVisibility(boolean) - Method in interface com.dnastack.bob.persistence.api.OrganizationDao
 
findDescendants(Beacon, boolean, boolean, boolean, boolean) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Computes a set of nodes covered by a specific node transitively.
flush() - Method in interface com.dnastack.bob.persistence.api.GenericDao
 
fromString(String) - Static method in enum com.dnastack.bob.persistence.enumerated.Chromosome
 
fromString(String) - Static method in enum com.dnastack.bob.persistence.enumerated.Reference
 

G

GenericDao<T extends BasicEntity<I>,I> - Interface in com.dnastack.bob.persistence.api
DAO for generic entities.
getId() - Method in interface com.dnastack.bob.persistence.entity.BasicEntity
 
getReferenceById(I) - Method in interface com.dnastack.bob.persistence.api.GenericDao
 

H

haveRelationship(Beacon, Beacon) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Checks existence of a parent-child association.

O

Organization - Class in com.dnastack.bob.persistence.entity
Organization owning a beacon.
Organization() - Constructor for class com.dnastack.bob.persistence.entity.Organization
 
OrganizationDao - Interface in com.dnastack.bob.persistence.api
Organization DAO.

Q

Query - Class in com.dnastack.bob.persistence.entity
Generalized beacon query representation.
Query() - Constructor for class com.dnastack.bob.persistence.entity.Query
 
QueryDao - Interface in com.dnastack.bob.persistence.api
Query DAO.

R

Reference - Enum in com.dnastack.bob.persistence.enumerated
Canonical genome representation.
removeRelationship(Beacon, Beacon) - Method in interface com.dnastack.bob.persistence.api.BeaconDao
Removes parent-child association.

S

save(T) - Method in interface com.dnastack.bob.persistence.api.GenericDao
 

T

toString() - Method in enum com.dnastack.bob.persistence.enumerated.Chromosome
 
toString() - Method in enum com.dnastack.bob.persistence.enumerated.Reference
 

U

update(T) - Method in interface com.dnastack.bob.persistence.api.GenericDao
 
User - Class in com.dnastack.bob.persistence.entity
User.
User() - Constructor for class com.dnastack.bob.persistence.entity.User
 
UserDao - Interface in com.dnastack.bob.persistence.api
User DAO.

V

valueOf(String) - Static method in enum com.dnastack.bob.persistence.enumerated.Chromosome
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dnastack.bob.persistence.enumerated.Reference
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.dnastack.bob.persistence.enumerated.Chromosome
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dnastack.bob.persistence.enumerated.Reference
Returns an array containing the constants of this enum type, in the order they are declared.
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