A B C D E F G I J L M O P R S T U V W 

A

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
 
A B C D E F G I J L M O P R S T U V W 

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