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A

Allele - Class in com.dnastack.beacon.entity
 
Allele() - Constructor for class com.dnastack.beacon.entity.Allele
 
Allele(String, Double) - Constructor for class com.dnastack.beacon.entity.Allele
 

B

Beacon - Class in com.dnastack.beacon.entity
Beacon.
Beacon() - Constructor for class com.dnastack.beacon.entity.Beacon
 
Beacon(String, String, String, String, String, String, String, String, List<Dataset>, List<Query>) - Constructor for class com.dnastack.beacon.entity.Beacon
 
BeaconApplication - Class in com.dnastack.beacon.rest
REST beacon application.
BeaconApplication() - Constructor for class com.dnastack.beacon.rest.BeaconApplication
 
BeaconResource - Class in com.dnastack.beacon.rest
Beacon rest resource.
BeaconResource() - Constructor for class com.dnastack.beacon.rest.BeaconResource
 
BeaconResponse - Class in com.dnastack.beacon.entity
Beacon response.
BeaconResponse() - Constructor for class com.dnastack.beacon.entity.BeaconResponse
 
BeaconResponse(String, Query, Response) - Constructor for class com.dnastack.beacon.entity.BeaconResponse
 
BeaconService - Interface in com.dnastack.beacon.service
Beacon service.

C

Chromosome - Enum in com.dnastack.beacon.entity
Chromosome.
com.dnastack.beacon.entity - package com.dnastack.beacon.entity
 
com.dnastack.beacon.rest - package com.dnastack.beacon.rest
 
com.dnastack.beacon.service - package com.dnastack.beacon.service
 
com.dnastack.beacon.util - package com.dnastack.beacon.util
 

D

Dataset - Class in com.dnastack.beacon.entity
Data set.
Dataset() - Constructor for class com.dnastack.beacon.entity.Dataset
 
Dataset(String, String, String, DataSize, List<DataUse>) - Constructor for class com.dnastack.beacon.entity.Dataset
 
DataSize - Class in com.dnastack.beacon.entity
 
DataSize() - Constructor for class com.dnastack.beacon.entity.DataSize
 
DataSize(Integer, Integer) - Constructor for class com.dnastack.beacon.entity.DataSize
 
DataUse - Class in com.dnastack.beacon.entity
Data use limitations.
DataUse() - Constructor for class com.dnastack.beacon.entity.DataUse
 
DataUse(String, String, List<DataUseRequirement>) - Constructor for class com.dnastack.beacon.entity.DataUse
 
DataUseRequirement - Class in com.dnastack.beacon.entity
Data use requirement.
DataUseRequirement() - Constructor for class com.dnastack.beacon.entity.DataUseRequirement
 
DataUseRequirement(String, String) - Constructor for class com.dnastack.beacon.entity.DataUseRequirement
 

E

equals(Object) - Method in class com.dnastack.beacon.entity.Beacon
 
equals(Object) - Method in class com.dnastack.beacon.entity.BeaconResponse
 
Error - Class in com.dnastack.beacon.entity
Error.
Error() - Constructor for class com.dnastack.beacon.entity.Error
 
Error(String, String) - Constructor for class com.dnastack.beacon.entity.Error
 

F

fromString(String) - Static method in enum com.dnastack.beacon.entity.Chromosome
 
fromString(String) - Static method in enum com.dnastack.beacon.entity.Reference
 

G

getAllele() - Method in class com.dnastack.beacon.entity.Allele
 
getAllele() - Method in class com.dnastack.beacon.entity.Query
 
getAlleles() - Method in class com.dnastack.beacon.entity.Response
 
getApi() - Method in class com.dnastack.beacon.entity.Beacon
 
getAuth() - Method in class com.dnastack.beacon.entity.Beacon
 
getBeacon_id() - Method in class com.dnastack.beacon.entity.BeaconResponse
 
getCategory() - Method in class com.dnastack.beacon.entity.DataUse
 
getChromosome() - Method in class com.dnastack.beacon.entity.Query
 
getClasses() - Method in class com.dnastack.beacon.rest.BeaconApplication
 
getData_uses() - Method in class com.dnastack.beacon.entity.Dataset
 
getDataset_id() - Method in class com.dnastack.beacon.entity.Query
 
getDatasets() - Method in class com.dnastack.beacon.entity.Beacon
 
getDescription() - Method in class com.dnastack.beacon.entity.Beacon
 
getDescription() - Method in class com.dnastack.beacon.entity.Dataset
 
getDescription() - Method in class com.dnastack.beacon.entity.DataUse
 
getDescription() - Method in class com.dnastack.beacon.entity.DataUseRequirement
 
getDescription() - Method in class com.dnastack.beacon.entity.Error
 
getEmail() - Method in class com.dnastack.beacon.entity.Beacon
 
getError() - Method in class com.dnastack.beacon.entity.Response
 
getExists() - Method in class com.dnastack.beacon.entity.Response
 
getFrequency() - Method in class com.dnastack.beacon.entity.Allele
 
getHomepage() - Method in class com.dnastack.beacon.entity.Beacon
 
getId() - Method in class com.dnastack.beacon.entity.Beacon
 
getId() - Method in class com.dnastack.beacon.entity.Dataset
 
getInfo() - Method in class com.dnastack.beacon.entity.Response
 
getName() - Method in class com.dnastack.beacon.entity.Beacon
 
getName() - Method in class com.dnastack.beacon.entity.DataUseRequirement
 
getName() - Method in class com.dnastack.beacon.entity.Error
 
getObserved() - Method in class com.dnastack.beacon.entity.Response
 
getOrganization() - Method in class com.dnastack.beacon.entity.Beacon
 
getPosition() - Method in class com.dnastack.beacon.entity.Query
 
getQueries() - Method in class com.dnastack.beacon.entity.Beacon
 
getQuery() - Method in class com.dnastack.beacon.entity.BeaconResponse
 
getQuery(String, Long, String, String, String) - Static method in class com.dnastack.beacon.util.QueryUtils
Obtains a canonical query object.
getReference() - Method in class com.dnastack.beacon.entity.Dataset
 
getReference() - Method in class com.dnastack.beacon.entity.Query
 
getRequirements() - Method in class com.dnastack.beacon.entity.DataUse
 
getResponse() - Method in class com.dnastack.beacon.entity.BeaconResponse
 
getSamples() - Method in class com.dnastack.beacon.entity.DataSize
 
getSize() - Method in class com.dnastack.beacon.entity.Dataset
 
getVariants() - Method in class com.dnastack.beacon.entity.DataSize
 

H

hashCode() - Method in class com.dnastack.beacon.entity.Beacon
 
hashCode() - Method in class com.dnastack.beacon.entity.BeaconResponse
 

I

info() - Method in interface com.dnastack.beacon.service.BeaconService
Obtains beacon information.
info() - Method in class com.dnastack.beacon.service.SampleBeaconService
 
InfoResource - Class in com.dnastack.beacon.rest
Beacon rest resource.
InfoResource() - Constructor for class com.dnastack.beacon.rest.InfoResource
 
init() - Method in class com.dnastack.beacon.service.SampleBeaconService
 

N

normalizeAllele(String) - Static method in class com.dnastack.beacon.util.QueryUtils
Generate a canonical allele string.
normalizeChromosome(String) - Static method in class com.dnastack.beacon.util.QueryUtils
Generates a canonical chrom ID.
normalizePosition(Long) - Static method in class com.dnastack.beacon.util.QueryUtils
Converts 0-based position to 1-based position.
normalizeReference(String) - Static method in class com.dnastack.beacon.util.QueryUtils
Generate a canonical genome representation (hg*).

Q

Query - Class in com.dnastack.beacon.entity
Query.
Query(String, Chromosome, Long, Reference, String) - Constructor for class com.dnastack.beacon.entity.Query
 
Query() - Constructor for class com.dnastack.beacon.entity.Query
 
query(String, Long, String, String, String) - Method in class com.dnastack.beacon.rest.BeaconResource
 
query(String, Long, String, String, String) - Method in interface com.dnastack.beacon.service.BeaconService
Executes a query.
query(String, Long, String, String, String) - Method in class com.dnastack.beacon.service.SampleBeaconService
 
QueryUtils - Class in com.dnastack.beacon.util
Utils for query manipulation.
QueryUtils() - Constructor for class com.dnastack.beacon.util.QueryUtils
 

R

Reference - Enum in com.dnastack.beacon.entity
Genome.
Response - Class in com.dnastack.beacon.entity
Response.
Response(Boolean, Integer, List<Allele>, String, Error) - Constructor for class com.dnastack.beacon.entity.Response
 
Response() - Constructor for class com.dnastack.beacon.entity.Response
 

S

SampleBeaconService - Class in com.dnastack.beacon.service
Sample implementation of a beacon service.
SampleBeaconService() - Constructor for class com.dnastack.beacon.service.SampleBeaconService
 
setAllele(String) - Method in class com.dnastack.beacon.entity.Allele
 
setAllele(String) - Method in class com.dnastack.beacon.entity.Query
 
setAlleles(List<Allele>) - Method in class com.dnastack.beacon.entity.Response
 
setApi(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setAuth(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setBeacon_id(String) - Method in class com.dnastack.beacon.entity.BeaconResponse
 
setCategory(String) - Method in class com.dnastack.beacon.entity.DataUse
 
setChromosome(Chromosome) - Method in class com.dnastack.beacon.entity.Query
 
setData_uses(List<DataUse>) - Method in class com.dnastack.beacon.entity.Dataset
 
setDataset_id(String) - Method in class com.dnastack.beacon.entity.Query
 
setDatasets(List<Dataset>) - Method in class com.dnastack.beacon.entity.Beacon
 
setDescription(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setDescription(String) - Method in class com.dnastack.beacon.entity.Dataset
 
setDescription(String) - Method in class com.dnastack.beacon.entity.DataUse
 
setDescription(String) - Method in class com.dnastack.beacon.entity.DataUseRequirement
 
setDescription(String) - Method in class com.dnastack.beacon.entity.Error
 
setEmail(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setError(Error) - Method in class com.dnastack.beacon.entity.Response
 
setExists(Boolean) - Method in class com.dnastack.beacon.entity.Response
 
setFrequency(Double) - Method in class com.dnastack.beacon.entity.Allele
 
setHomepage(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setId(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setId(String) - Method in class com.dnastack.beacon.entity.Dataset
 
setInfo(String) - Method in class com.dnastack.beacon.entity.Response
 
setName(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setName(String) - Method in class com.dnastack.beacon.entity.DataUseRequirement
 
setName(String) - Method in class com.dnastack.beacon.entity.Error
 
setObserved(Integer) - Method in class com.dnastack.beacon.entity.Response
 
setOrganization(String) - Method in class com.dnastack.beacon.entity.Beacon
 
setPosition(Long) - Method in class com.dnastack.beacon.entity.Query
 
setQueries(List<Query>) - Method in class com.dnastack.beacon.entity.Beacon
 
setQuery(Query) - Method in class com.dnastack.beacon.entity.BeaconResponse
 
setReference(String) - Method in class com.dnastack.beacon.entity.Dataset
 
setReference(Reference) - Method in class com.dnastack.beacon.entity.Query
 
setRequirements(List<DataUseRequirement>) - Method in class com.dnastack.beacon.entity.DataUse
 
setResponse(Response) - Method in class com.dnastack.beacon.entity.BeaconResponse
 
setSamples(Integer) - Method in class com.dnastack.beacon.entity.DataSize
 
setSize(DataSize) - Method in class com.dnastack.beacon.entity.Dataset
 
setVariants(Integer) - Method in class com.dnastack.beacon.entity.DataSize
 
show() - Method in class com.dnastack.beacon.rest.InfoResource
 

T

toString() - Method in class com.dnastack.beacon.entity.Beacon
 
toString() - Method in class com.dnastack.beacon.entity.BeaconResponse
 
toString() - Method in enum com.dnastack.beacon.entity.Chromosome
 
toString() - Method in enum com.dnastack.beacon.entity.Reference
 

V

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