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ADD_INFERENCES
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
annotations
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
annotations
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
AuthorizationRequestFilter
- Class in
owltools.gaf.lego.server
AuthorizationRequestFilter()
- Constructor for class owltools.gaf.lego.server.
AuthorizationRequestFilter
B
BeforeSaveModelValidator
- Class in
owltools.gaf.lego.server.validation
BeforeSaveModelValidator()
- Constructor for class owltools.gaf.lego.server.validation.
BeforeSaveModelValidator
C
CachingExternalLookupService
- Class in
owltools.gaf.lego.server.external
CachingExternalLookupService(ExternalLookupService, int)
- Constructor for class owltools.gaf.lego.server.external.
CachingExternalLookupService
CachingExternalLookupService(Iterable<ExternalLookupService>, int)
- Constructor for class owltools.gaf.lego.server.external.
CachingExternalLookupService
CachingExternalLookupService(int, ExternalLookupService...)
- Constructor for class owltools.gaf.lego.server.external.
CachingExternalLookupService
CHECK_LITERAL_IDENTIFIERS
- Variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
checkPermissions(M3BatchHandler.Entity, M3BatchHandler.Operation, boolean)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
CombinedExternalLookupService
- Class in
owltools.gaf.lego.server.external
CombinedExternalLookupService(ExternalLookupService...)
- Constructor for class owltools.gaf.lego.server.external.
CombinedExternalLookupService
CombinedExternalLookupService(Iterable<ExternalLookupService>)
- Constructor for class owltools.gaf.lego.server.external.
CombinedExternalLookupService
D
dataProperties
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.MetaResponse
E
ENFORCE_EXTERNAL_VALIDATE
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
evidence
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.MetaResponse
exportModel
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
ExternalLookupService
- Interface in
owltools.gaf.lego.server.external
Interface for wrapping a service to lookup information for a given identifier.
ExternalLookupService.LookupEntry
- Class in
owltools.gaf.lego.server.external
Result of an id lookup.
ExternalLookupService.LookupEntry(String, String, String, String)
- Constructor for class owltools.gaf.lego.server.external.
ExternalLookupService.LookupEntry
F
facts
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
facts
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
filter(ContainerRequestContext)
- Method in class owltools.gaf.lego.server.
AuthorizationRequestFilter
filter(ContainerRequestContext)
- Method in class owltools.gaf.lego.server.
RequireJsonpFilter
fromProcessGet(String, String, M3SeedHandler.SeedRequest)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
fromProcessGet(String, String, M3SeedHandler.SeedRequest)
- Method in interface owltools.gaf.lego.server.handler.
M3SeedHandler
Jersey REST method for GET with three query parameters.
fromProcessGetPrivileged(String, String, String, M3SeedHandler.SeedRequest)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
fromProcessGetPrivileged(String, String, String, M3SeedHandler.SeedRequest)
- Method in interface owltools.gaf.lego.server.handler.
M3SeedHandler
Jersey REST method for GET with three query parameters with privileged rights.
fromProcessPost(String, String, M3SeedHandler.SeedRequest)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
fromProcessPost(String, String, M3SeedHandler.SeedRequest)
- Method in interface owltools.gaf.lego.server.handler.
M3SeedHandler
Jersey REST method for POST with three form parameters.
fromProcessPostPrivileged(String, String, String, M3SeedHandler.SeedRequest)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
fromProcessPostPrivileged(String, String, String, M3SeedHandler.SeedRequest)
- Method in interface owltools.gaf.lego.server.handler.
M3SeedHandler
Jersey REST method for POST with three form parameters with privileged rights.
G
generateId()
- Static method in class owltools.gaf.lego.server.handler.
PacketIdGenerator
GenerateProteinOntologies
- Class in
owltools.gaf.lego.server
Helper to generate the protein ontologies from the QfO xml files.
GenerateProteinOntologies()
- Constructor for class owltools.gaf.lego.server.
GenerateProteinOntologies
getAssertedSubProperties(OWLObjectProperty, OWLGraphWrapper)
- Static method in class owltools.gaf.lego.server.
StartUpTool
Find all asserted direct sub properties of the parent property.
getFunctions(Set<Bioentity>)
- Method in class owltools.annotation.lego.generate.
GolrSeedingDataProvider
getFunctions(Set<Bioentity>)
- Method in interface owltools.annotation.lego.generate.
SeedingDataProvider
getGeneProducts(String)
- Method in class owltools.annotation.lego.generate.
GolrSeedingDataProvider
getGeneProducts(String)
- Method in interface owltools.annotation.lego.generate.
SeedingDataProvider
getLocations(Set<Bioentity>)
- Method in class owltools.annotation.lego.generate.
GolrSeedingDataProvider
getLocations(Set<Bioentity>)
- Method in interface owltools.annotation.lego.generate.
SeedingDataProvider
getOntologyIRIs()
- Method in class owltools.gaf.lego.server.external.
ProteinToolService
getRelation(String, OWLGraphWrapper)
- Static method in class owltools.gaf.lego.server.
StartUpTool
Try to resolve the given string into an
OWLObjectProperty
.
getSize(Object, Class<?>, Type, Annotation[], MediaType)
- Method in class owltools.gaf.lego.server.
GsonMessageBodyHandler
GolrExternalLookupService
- Class in
owltools.gaf.lego.server.external
GolrExternalLookupService(String)
- Constructor for class owltools.gaf.lego.server.external.
GolrExternalLookupService
GolrExternalLookupService(RetrieveGolrBioentities)
- Constructor for class owltools.gaf.lego.server.external.
GolrExternalLookupService
GolrSeedingDataProvider
- Class in
owltools.annotation.lego.generate
GolrSeedingDataProvider(String, OWLGraphWrapper, OWLReasoner, Set<OWLClass>, Set<String>, Set<String>, Set<String>)
- Constructor for class owltools.annotation.lego.generate.
GolrSeedingDataProvider
GsonMessageBodyHandler
- Class in
owltools.gaf.lego.server
GsonMessageBodyHandler()
- Constructor for class owltools.gaf.lego.server.
GsonMessageBodyHandler
I
id
- Variable in class owltools.gaf.lego.server.external.
ExternalLookupService.LookupEntry
id
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
id
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
inconsistentFlag
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
inconsistentFlag
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
individuals
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
individuals
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
individualsInferred
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
individualsInferred
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
initResponseData(JsonModel, M3BatchHandler.M3BatchResponse.ResponseData)
- Static method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
isReadable(Class<?>, Type, Annotation[], MediaType)
- Method in class owltools.gaf.lego.server.
GsonMessageBodyHandler
isWriteable(Class<?>, Type, Annotation[], MediaType)
- Method in class owltools.gaf.lego.server.
GsonMessageBodyHandler
J
JsonOrJsonpBatchHandler
- Class in
owltools.gaf.lego.server.handler
JsonOrJsonpBatchHandler(UndoAwareMolecularModelManager, Set<OWLObjectProperty>, ExternalLookupService)
- Constructor for class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
JsonOrJsonpSeedHandler
- Class in
owltools.gaf.lego.server.handler
JsonOrJsonpSeedHandler(UndoAwareMolecularModelManager, String, ExternalLookupService)
- Constructor for class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
JSONP_DEFAULT_CALLBACK
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
JSONP_DEFAULT_CALLBACK
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
JSONP_DEFAULT_OVERWRITE
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
JSONP_DEFAULT_OVERWRITE
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpSeedHandler
L
label
- Variable in class owltools.gaf.lego.server.external.
ExternalLookupService.LookupEntry
logRequest(URI)
- Method in class owltools.annotation.lego.generate.
GolrSeedingDataProvider
lookup(String)
- Method in class owltools.gaf.lego.server.external.
CachingExternalLookupService
lookup(String, String)
- Method in class owltools.gaf.lego.server.external.
CachingExternalLookupService
lookup(String)
- Method in class owltools.gaf.lego.server.external.
CombinedExternalLookupService
lookup(String, String)
- Method in class owltools.gaf.lego.server.external.
CombinedExternalLookupService
lookup(String)
- Method in interface owltools.gaf.lego.server.external.
ExternalLookupService
Lookup the information for the given identifier.
lookup(String, String)
- Method in interface owltools.gaf.lego.server.external.
ExternalLookupService
Lookup the information for the given identifier and taxon.
lookup(String)
- Method in class owltools.gaf.lego.server.external.
GolrExternalLookupService
lookup(String, String)
- Method in class owltools.gaf.lego.server.external.
GolrExternalLookupService
lookup(String)
- Method in class owltools.gaf.lego.server.external.
ProteinToolService
lookup(String, String)
- Method in class owltools.gaf.lego.server.external.
ProteinToolService
lookup(String)
- Method in class owltools.gaf.lego.server.external.
TableLookupService
lookup(String, String)
- Method in class owltools.gaf.lego.server.external.
TableLookupService
M
m3Batch(String, String, String, M3BatchHandler.M3Request[], boolean)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
m3Batch(String, String, String, M3BatchHandler.M3Request[], boolean)
- Method in interface owltools.gaf.lego.server.handler.
M3BatchHandler
Process a batch request.
m3BatchGet(String, String, String)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
m3BatchGet(String, String, String)
- Method in interface owltools.gaf.lego.server.handler.
M3BatchHandler
Jersey REST method for GET with three query parameters.
m3BatchGetPrivileged(String, String, String, String)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
m3BatchGetPrivileged(String, String, String, String)
- Method in interface owltools.gaf.lego.server.handler.
M3BatchHandler
Jersey REST method for GET with three query parameters with privileged rights.
M3BatchHandler
- Interface in
owltools.gaf.lego.server.handler
M3BatchHandler.Entity
- Enum in
owltools.gaf.lego.server.handler
M3BatchHandler.M3Argument
- Class in
owltools.gaf.lego.server.handler
M3BatchHandler.M3Argument()
- Constructor for class owltools.gaf.lego.server.handler.
M3BatchHandler.M3Argument
M3BatchHandler.M3BatchResponse
- Class in
owltools.gaf.lego.server.handler
M3BatchHandler.M3BatchResponse(String, String, String)
- Constructor for class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse
M3BatchHandler.M3BatchResponse.MetaResponse
- Class in
owltools.gaf.lego.server.handler
M3BatchHandler.M3BatchResponse.MetaResponse()
- Constructor for class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.MetaResponse
M3BatchHandler.M3BatchResponse.ResponseData
- Class in
owltools.gaf.lego.server.handler
M3BatchHandler.M3BatchResponse.ResponseData()
- Constructor for class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
M3BatchHandler.M3Request
- Class in
owltools.gaf.lego.server.handler
M3BatchHandler.M3Request()
- Constructor for class owltools.gaf.lego.server.handler.
M3BatchHandler.M3Request
M3BatchHandler.Operation
- Enum in
owltools.gaf.lego.server.handler
m3BatchPost(String, String, String)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
m3BatchPost(String, String, String)
- Method in interface owltools.gaf.lego.server.handler.
M3BatchHandler
Jersey REST method for POST with three form parameters.
m3BatchPostPrivileged(String, String, String, String)
- Method in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
m3BatchPostPrivileged(String, String, String, String)
- Method in interface owltools.gaf.lego.server.handler.
M3BatchHandler
Jersey REST method for POST with three form parameters with privileged rights.
M3ExpressionParser
- Class in
owltools.gaf.lego.server.handler
M3SeedHandler
- Interface in
owltools.gaf.lego.server.handler
Alpha version interface for seeding a model.
M3SeedHandler.SeedRequest
- Class in
owltools.gaf.lego.server.handler
M3SeedHandler.SeedRequest()
- Constructor for class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedRequest
M3SeedHandler.SeedResponse
- Class in
owltools.gaf.lego.server.handler
M3SeedHandler.SeedResponse(String, String, String)
- Constructor for class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse
M3SeedHandler.SeedResponse.SeedResponseData
- Class in
owltools.gaf.lego.server.handler
M3SeedHandler.SeedResponse.SeedResponseData()
- Constructor for class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
main(String[])
- Static method in class owltools.gaf.lego.server.
GenerateProteinOntologies
main(String[])
- Static method in class owltools.gaf.lego.server.
StartUpTool
MESSAGE_TYPE_ERROR
- Static variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse
MESSAGE_TYPE_ERROR
- Static variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse
MESSAGE_TYPE_SUCCESS
- Static variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse
MESSAGE_TYPE_SUCCESS
- Static variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse
meta
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
modelIds
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.MetaResponse
ModelSeeding
<
METADATA
> - Class in
owltools.annotation.lego.generate
ModelSeeding(ExpressionMaterializingReasoner, SeedingDataProvider)
- Constructor for class owltools.annotation.lego.generate.
ModelSeeding
modelsMeta
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.MetaResponse
O
owltools.annotation.lego.generate
- package owltools.annotation.lego.generate
owltools.gaf.lego.server
- package owltools.gaf.lego.server
owltools.gaf.lego.server.external
- package owltools.gaf.lego.server.external
owltools.gaf.lego.server.handler
- package owltools.gaf.lego.server.handler
owltools.gaf.lego.server.validation
- package owltools.gaf.lego.server.validation
P
PacketIdGenerator
- Class in
owltools.gaf.lego.server.handler
PacketIdGenerator()
- Constructor for class owltools.gaf.lego.server.handler.
PacketIdGenerator
properties
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
properties
- Variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse.SeedResponseData
ProteinToolService
- Class in
owltools.gaf.lego.server.external
Load a folder of Protein ontologies for lookup as generated by
ProteinTools
.
ProteinToolService(String)
- Constructor for class owltools.gaf.lego.server.external.
ProteinToolService
R
readFrom(Class<Object>, Type, Annotation[], MediaType, MultivaluedMap<String, String>, InputStream)
- Method in class owltools.gaf.lego.server.
GsonMessageBodyHandler
redo
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
relations
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.MetaResponse
RequireJsonpFilter
- Class in
owltools.gaf.lego.server
Replace the accepted request type, if there is a 'json.wrf' query parameter.
This filter will be called before, the Jersey framework does the request matching.
RequireJsonpFilter()
- Constructor for class owltools.gaf.lego.server.
RequireJsonpFilter
S
SeedingDataProvider
- Interface in
owltools.annotation.lego.generate
seedModel(MolecularModelManager<METADATA>, String, METADATA)
- Method in class owltools.annotation.lego.generate.
ModelSeeding
seedModel(String, ModelContainer, MolecularModelManager<METADATA>, String, METADATA)
- Method in class owltools.annotation.lego.generate.
ModelSeeding
SIGNAL_MERGE
- Static variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse
SIGNAL_META
- Static variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse
SIGNAL_REBUILD
- Static variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse
SIGNAL_REBUILD
- Static variable in class owltools.gaf.lego.server.handler.
M3SeedHandler.SeedResponse
startUp(String, String, String, String, String, int, String, List<String>, String, ExternalLookupService, boolean)
- Static method in class owltools.gaf.lego.server.
StartUpTool
startUp(UndoAwareMolecularModelManager, int, String, Set<OWLObjectProperty>, ExternalLookupService, boolean)
- Static method in class owltools.gaf.lego.server.
StartUpTool
StartUpTool
- Class in
owltools.gaf.lego.server
StartUpTool()
- Constructor for class owltools.gaf.lego.server.
StartUpTool
T
TableLookupService
- Class in
owltools.gaf.lego.server.external
TableLookupService(Iterable<ExternalLookupService.LookupEntry>)
- Constructor for class owltools.gaf.lego.server.external.
TableLookupService
taxon
- Variable in class owltools.gaf.lego.server.external.
ExternalLookupService.LookupEntry
type
- Variable in class owltools.gaf.lego.server.external.
ExternalLookupService.LookupEntry
U
undo
- Variable in class owltools.gaf.lego.server.handler.
M3BatchHandler.M3BatchResponse.ResponseData
USE_USER_ID
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
V
VALIDATE_BEFORE_SAVE
- Static variable in class owltools.gaf.lego.server.handler.
JsonOrJsonpBatchHandler
validateBeforeSave(String, MolecularModelManager<?>)
- Method in class owltools.gaf.lego.server.validation.
BeforeSaveModelValidator
valueOf(String)
- Static method in enum owltools.gaf.lego.server.handler.
M3BatchHandler.Entity
Returns the enum constant of this type with the specified name.
valueOf(String)
- Static method in enum owltools.gaf.lego.server.handler.
M3BatchHandler.Operation
Returns the enum constant of this type with the specified name.
values()
- Static method in enum owltools.gaf.lego.server.handler.
M3BatchHandler.Entity
Returns an array containing the constants of this enum type, in the order they are declared.
values()
- Static method in enum owltools.gaf.lego.server.handler.
M3BatchHandler.Operation
Returns an array containing the constants of this enum type, in the order they are declared.
W
writeTo(Object, Class<?>, Type, Annotation[], MediaType, MultivaluedMap<String, Object>, OutputStream)
- Method in class owltools.gaf.lego.server.
GsonMessageBodyHandler
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