A B C D E F G H I J K L M N O P R S T U V W X Y

S

save() - Static method in class pt.ua.bioinformatics.coeus.common.Builder

Saves new JS configuration file with updated information.

save() - Method in class pt.ua.bioinformatics.coeus.data.connect.CSVFactory

Updates the resource coeus:built property once the resource finished building.

save() - Method in class pt.ua.bioinformatics.coeus.data.connect.PluginFactory

Updates the resource coeus:built property once the resource finished building.

save() - Method in interface pt.ua.bioinformatics.coeus.data.connect.ResourceFactory

save() - Method in class pt.ua.bioinformatics.coeus.data.connect.SPARQLFactory

Updates the resource coeus:built property once the resource finished building.

save() - Method in class pt.ua.bioinformatics.coeus.data.connect.SQLFactory

Updates the resource coeus:built property once the resource finished building.

save() - Method in class pt.ua.bioinformatics.coeus.data.connect.XMLFactory

Updates the resource coeus:built property once the resource finished building.

schoolHomepage - Static variable in class de.fuberlin.wiwiss.pubby.vocab.FOAF

A homepage of a school attended by the person.

Seed - Class in pt.ua.bioinformatics.coeus.domain

Class handler for Seed information.

Seed() - Constructor for class pt.ua.bioinformatics.coeus.domain.Seed

select(String, String, boolean) - Method in class pt.ua.bioinformatics.coeus.api.API

Perform a SPARQL SELECT query to COEUS SDB with multiple output formats support.

selectRS(String, boolean) - Method in class pt.ua.bioinformatics.coeus.api.API

Perform a SPARQL SELECT query to COEUS SDB.

send404(HttpServletResponse, MappedResource) - Method in class de.fuberlin.wiwiss.pubby.servlets.BaseServlet

send404(HttpServletResponse, String, String) - Method in class de.fuberlin.wiwiss.pubby.servlets.BaseServlet

serve() - Method in class de.fuberlin.wiwiss.pubby.ModelResponse

setAPI(API) - Static method in class pt.ua.bioinformatics.coeus.common.Boot

setApi(API) - Method in class pt.ua.bioinformatics.coeus.data.Triplify

setBuilt(boolean) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setBuilt(boolean) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setConnected(boolean) - Static method in class pt.ua.bioinformatics.coeus.data.Storage

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.InfoActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.RedirectDocumentationActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.RedirectJavadocActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.RedirectOntologyActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.RedirectScienceActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.RedirectSPARQLerActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.RedirectTranslateActionBean

setContext(ActionBeanContext) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setCurrent(String, Object) - Method in class pt.ua.bioinformatics.coeus.ext.COEUSActionBeanContext

setData(JSONArray) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setDebug(boolean) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setDefaultAccept(String) - Method in class de.fuberlin.wiwiss.pubby.negotiation.ContentTypeNegotiator

Sets an Accept header to be used as the default if a client does not send an Accept header, or if the Accept header cannot be parsed.

setDescription(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setDescription(String) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setDescription(String) - Method in class pt.ua.bioinformatics.coeus.domain.Entity

setDescription(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setDescription(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setDisease(String, Object) - Method in class pt.ua.bioinformatics.coeus.ext.COEUSActionBeanContext

setDisease(Object) - Method in class pt.ua.bioinformatics.coeus.ext.COEUSActionBeanContext

setDiseases(HashMap<String, Disease>) - Method in class pt.ua.bioinformatics.coeus.api.plugins.OMIMPlugin

setEndpoint(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setEnvironment(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setExtendsConcept(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setExtension(String) - Method in class pt.ua.bioinformatics.coeus.data.Triplify

setExtension(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setFile(JSONObject) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setFormat(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setGenes(ArrayList<String>) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setGenotypes(HashMap<String, Disease>) - Method in class pt.ua.bioinformatics.coeus.api.plugins.OMIMPlugin

setGenotypes(ArrayList<Disease>) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setHasConcept(Concept) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setHasEntity(Entity) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setHasKey(InheritedResource) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setHasResource(Resource) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setId(String) - Method in class pt.ua.bioinformatics.coeus.actions.InfoActionBean

setId(String) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setId(int) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setInferredModel(InfModel) - Method in class pt.ua.bioinformatics.coeus.api.API

setInfmodel(InfModel) - Static method in class pt.ua.bioinformatics.coeus.data.Storage

setInternal(Internal) - Method in class pt.ua.bioinformatics.coeus.api.API

setIsEntityOf(ArrayList<Concept>) - Method in class pt.ua.bioinformatics.coeus.domain.Entity

setIsResourceOf(Concept) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setJs_full(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setJs_id(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setJs_type(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setJs_value(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setJsonparser(JSONParser) - Method in class pt.ua.bioinformatics.coeus.api.API

setKey(String) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setKeyPrefix(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setLabel(String) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setLabel(String) - Method in class pt.ua.bioinformatics.coeus.domain.Entity

setLabel(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setLabel(String) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setLabel(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setLoaded(boolean) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setLoaded(boolean) - Static method in class pt.ua.bioinformatics.coeus.data.Storage

setLoadsFrom(ArrayList<Object>) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setLocation(String) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setMap(ArrayList<String>) - Method in class pt.ua.bioinformatics.coeus.data.Triplify

setMethod(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setModel(Model) - Method in class pt.ua.bioinformatics.coeus.api.API

setModel(Model) - Static method in class pt.ua.bioinformatics.coeus.data.Storage

setName(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setName(String) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setNames(ArrayList<String>) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setObj(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setOmimId(String) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setOntology(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setPath(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setPhenotypes(ArrayList<Disease>) - Method in class pt.ua.bioinformatics.diseasecard.domain.Disease

setPred(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setPredicates(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setPredicates(HashMap<String, Property>) - Static method in class pt.ua.bioinformatics.coeus.data.Predicate

setPrefixes(HashMap<String, String>) - Static method in class pt.ua.bioinformatics.coeus.api.PrefixFactory

setProperties(HashMap<String, String>) - Method in class pt.ua.bioinformatics.coeus.data.Triplify

setProperties(HashMap<String, String>) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setProperties(HashMap<String, String>) - Method in class pt.ua.bioinformatics.coeus.domain.Entity

setProperties(HashMap<String, String>) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setProperty(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setPublisher(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setQuery(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setQuery(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setReader(CSVReader) - Static method in class pt.ua.bioinformatics.coeus.data.connect.CSVFactory

setReasoner(Reasoner) - Static method in class pt.ua.bioinformatics.coeus.data.Storage

setRegex(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setRes(Resource) - Method in class pt.ua.bioinformatics.coeus.api.plugins.OMIMPlugin

setRes(Resource) - Method in class pt.ua.bioinformatics.coeus.data.connect.CSVFactory

setRes(Resource) - Method in class pt.ua.bioinformatics.coeus.data.connect.PluginFactory

setRes(Resource) - Method in class pt.ua.bioinformatics.coeus.data.connect.SPARQLFactory

setRes(Resource) - Method in class pt.ua.bioinformatics.coeus.data.connect.SQLFactory

setRes(Resource) - Method in class pt.ua.bioinformatics.coeus.data.connect.XMLFactory

setResource(Resource) - Method in class pt.ua.bioinformatics.coeus.data.Triplify

setResources(ArrayList<Resource>) - Static method in class pt.ua.bioinformatics.coeus.common.Builder

setSdb(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setSearchResults(String, ArrayList<Disease>) - Method in class pt.ua.bioinformatics.coeus.ext.COEUSActionBeanContext

setSetup(String) - Static method in class pt.ua.bioinformatics.coeus.common.Config

setSource(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setStarted(boolean) - Static method in class pt.ua.bioinformatics.coeus.common.Boot

setStore(Store) - Static method in class pt.ua.bioinformatics.coeus.data.Storage

setSub(String) - Method in class pt.ua.bioinformatics.coeus.actions.TripleActionBean

setSubject(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setTitle(String) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setTitle(String) - Method in class pt.ua.bioinformatics.coeus.domain.Entity

setTitle(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setTitle(String) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setTitle(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

setUri(String) - Method in class pt.ua.bioinformatics.coeus.domain.Concept

setUri(String) - Method in class pt.ua.bioinformatics.coeus.domain.Entity

setUri(String) - Method in class pt.ua.bioinformatics.coeus.domain.InheritedResource

setUri(String) - Method in class pt.ua.bioinformatics.coeus.domain.Item

setUri(String) - Method in class pt.ua.bioinformatics.coeus.domain.Resource

sha1 - Static variable in class de.fuberlin.wiwiss.pubby.vocab.FOAF

A sha1sum hash, in hex.

SingleImport - Class in pt.ua.bioinformatics.coeus.api.plugins

Single thread handler for importing single resources.

SingleImport(String) - Constructor for class pt.ua.bioinformatics.coeus.api.plugins.SingleImport

singleImport(String) - Static method in class pt.ua.bioinformatics.coeus.common.Boot

Starts Seed for importing data from a single Resource.

sparqlDefaultGraph - Static variable in class de.fuberlin.wiwiss.pubby.vocab.CONF

sparqlEndpoint - Static variable in class de.fuberlin.wiwiss.pubby.vocab.CONF

SPARQLFactory - Class in pt.ua.bioinformatics.coeus.data.connect

Data factory for transforming SPARQL data into RDF items using generic Triplify.

SPARQLFactory(Resource) - Constructor for class pt.ua.bioinformatics.coeus.data.connect.SPARQLFactory

SQLFactory - Class in pt.ua.bioinformatics.coeus.data.connect

Data factory for transforming SQL data into RDF items using generic Triplify.

SQLFactory(Resource) - Constructor for class pt.ua.bioinformatics.coeus.data.connect.SQLFactory

start() - Static method in class pt.ua.bioinformatics.coeus.common.Boot

Starts the configured COEUS instance.

Storage - Class in pt.ua.bioinformatics.coeus.data

COEUS Data Storage key class.

Storage() - Constructor for class pt.ua.bioinformatics.coeus.data.Storage

surname - Static variable in class de.fuberlin.wiwiss.pubby.vocab.FOAF

The surname of some person.