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

A

aa() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Authentication and Authorization.
aa() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
AASpecifications - Class in org.opentox.toxotis.core.component
Deprecated.  
AASpecifications(VRI) - Constructor for class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
AASpecifications() - Constructor for class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
AbstractClient - Class in org.opentox.toxotis.client
An abstract class providing necessary methods for the implementation of a HTTP client.
AbstractClient() - Constructor for class org.opentox.toxotis.client.AbstractClient
 
AbstractClient(VRI) - Constructor for class org.opentox.toxotis.client.AbstractClient
 
AbstractHttpClient - Class in org.opentox.toxotis.client.http
An abstract class providing necessary methods for the implementation of a HTTP client.
AbstractHttpClient() - Constructor for class org.opentox.toxotis.client.http.AbstractHttpClient
 
AbstractHttpsClient - Class in org.opentox.toxotis.client.https
 
AbstractHttpsClient() - Constructor for class org.opentox.toxotis.client.https.AbstractHttpsClient
 
AbstractHttpsClient(VRI) - Constructor for class org.opentox.toxotis.client.https.AbstractHttpsClient
 
ACCEPT - Static variable in class org.opentox.toxotis.client.RequestHeaders
Specifies which Internet media types are acceptable for the response and to assign preferences to them.
ACCEPT_CHARSET - Static variable in class org.opentox.toxotis.client.RequestHeaders
Specifies which character encodings (confusingly called "charsets") are acceptable for the response and to assign preferences to them.
ACCEPT_ENCODING - Static variable in class org.opentox.toxotis.client.RequestHeaders
Specifies which data format tranformations, confusingly called content (en)codings, such as compression mechanisms, are acceptable for the response and to assign preferences to them.
ACCEPT_LANGUAGE - Static variable in class org.opentox.toxotis.client.RequestHeaders
Specifies which natural languages are acceptable for the response and to assign preferences to them.
acceptValue() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
Datatype property used to link an ot:Nominal with its admissible values.
actor() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
The actor of an exceptional event.
acuteDermalToxicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Acute Dermal Toxicity.
acuteInhalationToxicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Acute Inhalation Toxicity.
acuteOralToxicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Acute toxicity when the substance is administered per os.
acutePhotoirritation() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Acute photo-irritation.
addAudience(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addAudience(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addAudience(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addAudience(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addAuthParameters(HttpParameter...) - Method in class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
addBibTeXReferences(VRI...) - Method in class org.opentox.toxotis.core.component.Model
 
addBibTeXReferences(VRI...) - Method in interface org.opentox.toxotis.core.IBibTexReferencable
 
addComment(String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addComment(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addComment(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addComment(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
Add comments to the current instance of MetaInfo
addComment(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
Add comments to the current instance of MetaInfo
addComponent(HTMLComponent) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addComponent(HTMLComponent) - Method in interface org.opentox.toxotis.core.html.HTMLExpandableComponent
Add an HTMLComponent object to the current expandable and modifiable HTML component.
addComponent(HTMLComponent) - Method in class org.opentox.toxotis.core.html.impl.HTMLExpandableComponentImpl
 
addComponent(HTMLComponent) - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
addContributor(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addContributor(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addContributor(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addContributor(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addCreator(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addCreator(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addCreator(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addCreator(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addDependentFeatures(Feature...) - Method in class org.opentox.toxotis.core.component.Model
Adds dependent features to the current list of features.
addDescription(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addDescription(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addDescription(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addDescription(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addDiv(String, HTMLComponent) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
addFeatureValue(int, FeatureValue) - Method in class org.opentox.toxotis.core.component.DataEntry
 
addFeatureValue(FeatureValue) - Method in class org.opentox.toxotis.core.component.DataEntry
 
addForm() - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addForm(String, String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addHasSource(ResourceValue) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addHasSource(ResourceValue) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addHeaderParameter(String, String) - Method in class org.opentox.toxotis.client.AbstractClient
Note: if the parameter name (paramName) is either 'Accept' or 'Content-type', this method will override setMediaType and setContentType respectively.
addHeaderParameter(String, String) - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
addHeaderParameter(String, String) - Method in interface org.opentox.toxotis.client.IClient
Note: if the parameter name (paramName) is either 'Accept' or 'Content-type', this method will override setMediaType and setContentType respectively.
addHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
addHttpParameters(HttpParameter...) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addHttpParameters(HttpParameter...) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addHttpStatusCodes(HttpStatus...) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addHttpStatusCodes(HttpStatus...) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addIdentifier(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addIdentifier(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addIdentifier(String) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addIdentifier(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addIdentifier(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addIndependentFeatures(Feature...) - Method in class org.opentox.toxotis.core.component.Model
Adds independent features to the current list of features.
addInputParamClass(OntologicalClass...) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
addMediaTypes(HttpMediatype...) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addMediaTypes(HttpMediatype...) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addOntologicalClasses(OntologicalClass...) - Method in interface org.opentox.toxotis.core.IOTComponent
Adds a list of ontological classes to the current ones.
addOntologicalClasses(OntologicalClass...) - Method in class org.opentox.toxotis.core.OTComponent
 
addParagraph(String, Alignment) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addParagraph(String) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
addParamContent(OntologicalClass...) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
addPolicies(Policy...) - Method in class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
addPostParameter(String, String) - Method in class org.opentox.toxotis.client.http.PostHttpClient
Add a parameter which will be posted to the target URI.
addPostParameter(String, String) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
Add a parameter which will be posted to the target URI.
addPostParameter(String, String) - Method in interface org.opentox.toxotis.client.IPostClient
Add a parameter which will be posted to the target URI.
addPredictedFeatures(Feature...) - Method in class org.opentox.toxotis.core.component.Model
Adds predicted features to the current list of features.
addPublisher(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addPublisher(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addPublisher(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addPublisher(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addRestClasses(OntologicalClass...) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addRestClasses(OntologicalClass...) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addRestOperations(IRestOperation...) - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
addRights(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addRights(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addRights(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addRights(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addRule(IPolicyRule) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
Add a rule to the current policy.
addRule(IPolicyRule) - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
addSameAs(ResourceValue) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addSameAs(ResourceValue) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addSeeAlso(ResourceValue) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addSeeAlso(ResourceValue) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addSimpleHeader(String, boolean, XSDDatatype) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addSimpleHeader(String, boolean, XSDDatatype, MetaInfo) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addSimpleHeader(String, boolean, XSDDatatype) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addSimpleHeader(String, boolean, XSDDatatype, MetaInfo) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addSimpleHeaderParameter(String, boolean, XSDDatatype) - Method in class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
addSubHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addSubHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
addSubject(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addSubject(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addSubject(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addSubject(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addSubject(PolicySubject) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
Add a new Policy Subject.
addSubject(PolicySubject) - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
addSubSubHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addSubSubHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
addSubSubSubHeading(String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addTable(int, int) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addTable(int) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
addTagAttribute(String, String) - Method in interface org.opentox.toxotis.core.html.HTMLTag
 
addTagAttribute(String, String) - Method in class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
addText(HTMLText) - Method in interface org.opentox.toxotis.core.html.HTMLParagraph
 
addText(HTMLText) - Method in class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
addTitle(String) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addTitle(LiteralValue...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addTitle(String...) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
addTitle(LiteralValue...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addTitle(String...) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
addUrlParameter(String, String) - Method in class org.opentox.toxotis.client.VRI
Add a URL parameter.
addUrlParameter(String, double) - Method in class org.opentox.toxotis.client.VRI
Add a double valued URL parameter.
addUrlParameter(String, int) - Method in class org.opentox.toxotis.client.VRI
Add an integer valued URL parameter.
addUrlParameter(String, boolean, XSDDatatype) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addUrlParameter(String, boolean, XSDDatatype, MetaInfo) - Method in class org.opentox.toxotis.core.component.RestOperation
 
addUrlParameter(String, boolean, XSDDatatype) - Method in interface org.opentox.toxotis.core.IRestOperation
 
addUrlParameter(String, boolean, XSDDatatype, MetaInfo) - Method in interface org.opentox.toxotis.core.IRestOperation
 
Admin1 - Static variable in class org.opentox.toxotis.util.aa.policy.SingleSubject
 
Admin2 - Static variable in class org.opentox.toxotis.util.aa.policy.SingleSubject
 
airWaterPartitionCoefficient() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Air- water partition coefficient (Henry's law constant, H).
Algorithm - Class in org.opentox.toxotis.core.component
Provides access to different types of algorithms.
Algorithm() - Constructor for class org.opentox.toxotis.core.component.Algorithm
Dummy constructor for an Algorithm object.
Algorithm(VRI) - Constructor for class org.opentox.toxotis.core.component.Algorithm
Create a new instance of Algorithm providing its identifier as a VRI.
Algorithm(String) - Constructor for class org.opentox.toxotis.core.component.Algorithm
Constructs a new instance of Algorithm with given URI.
algorithm() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
Ontological class that provides access to all OpenTox algorithms
algorithm() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
AlgorithmSpider - Class in org.opentox.toxotis.util.spiders
A downloader parser for data models of OpenTox algorithms.
AlgorithmSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.AlgorithmSpider
Create a new AlgorithmSpider providing the URI of the algorithm to be spidered, i.e.
AlgorithmSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.AlgorithmSpider
Constructor with an ontological resource and an ontological model.
AlgorithmSpider(VRI, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.spiders.AlgorithmSpider
Create a new AlgorithmSpider providing the URI of the algorithm to be spidered and an authentication token that will allow the client to access the content of the algorithm.
algorithmTemplate() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An OpenTox APIv1.2-compliant URI-template for algorithms.
algorithmType() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
Alignment - Enum in org.opentox.toxotis.core.html
Enumeration of available HTML component alignments.
ambitCactvsImage() - Static method in class org.opentox.toxotis.client.collection.Services.Depiction
AMBIT CACTVS-based depiction service.
ambitCdkImage() - Static method in class org.opentox.toxotis.client.collection.Services.Depiction
AMBIT CKD-based depiction.
ambitDaylightImage() - Static method in class org.opentox.toxotis.client.collection.Services.Depiction
AMBIT Daylight depiction service.
ambitUniPlovdiv() - Static method in class org.opentox.toxotis.client.collection.Services
Secure URI of resources with AMBIT at the University Plovdiv.
anonymous() - Static method in class org.opentox.toxotis.client.collection.Services
Anonymous URI for general use.
applicabilityDomain() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
ArffDownloader - Class in org.opentox.toxotis.util.arff
 
ArffDownloader(VRI) - Constructor for class org.opentox.toxotis.util.arff.ArffDownloader
 
arffSupport() - Method in class org.opentox.toxotis.util.arff.RemoteArffRertiever
 
article() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
An article in a journal.
asDatatypeProperty(OntModel) - Method in class org.opentox.toxotis.ontology.impl.OTDatatypePropertyImpl
 
asDatatypeProperty(OntModel) - Method in interface org.opentox.toxotis.ontology.OTDatatypeProperty
Cast this OTDatatypeProperty object as a Jena DatatypeProperty object.
asErrorReport() - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
asErrorReport() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Algorithm
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.BibTeX
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Bookmark
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Compound
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Conformer
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.DataEntry
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Dataset
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.DummyComponent
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Feature
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.FeatureValue
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.HttpMediatype
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.HttpMethod
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.HttpStatus
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Model
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.MultiParameter
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Parameter
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.ParameterValue
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.RestOperation
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.Task
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.User
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.VariableInfo
 
asIndividual(OntModel) - Method in class org.opentox.toxotis.core.component.VariableValue
 
asIndividual(OntModel) - Method in interface org.opentox.toxotis.core.IOTComponent
The OpenTox component as an individual.
asObjectProperty(OntModel) - Method in class org.opentox.toxotis.ontology.impl.OTObjectPropertyImpl
 
asObjectProperty(OntModel) - Method in interface org.opentox.toxotis.ontology.OTObjectProperty
Cast this OTObjectProperty object as a Jena ObjectProperty object.
asOntModel() - Method in interface org.opentox.toxotis.core.IOTComponent
Creates a new Ontological Model (uses an instance of SimpleOntModelImpl ) and assigns to it the Individual from the method asIndividual(OntModel).
asOntModel() - Method in class org.opentox.toxotis.core.OTComponent
Creates a new Ontological Model (uses an instance of SimpleOntModelImpl) and assigns to it the Individual from the method asIndividual(OntModel).
asProperty(OntModel) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
asProperty(OntModel) - Method in interface org.opentox.toxotis.ontology.OTProperty
The following note is copied here from the online OWL reference at http://www.w3.org/TR/owl-ref: Cast the OTProperty object as a Property object of Jena.
assessHttpStatus(int, VRI) - Method in class org.opentox.toxotis.util.spiders.Tarantula
 
attachTo(Resource, OntModel) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
attachTo(Resource, OntModel) - Method in interface org.opentox.toxotis.ontology.MetaInfo
Attaches the meta data to a given resource in an ontological model returning the updated resource.
augment(String...) - Method in class org.opentox.toxotis.client.VRI
Augments the URI with additional string blocks.
augment(Object...) - Method in class org.opentox.toxotis.client.VRI
An alternative to #augment(String[])
authenticate(AuthenticationToken) - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
AuthenticationToken - Class in org.opentox.toxotis.util.aa

OpenTox specific implementation regarding the token provided by the OpenSSO server.

AuthenticationToken() - Constructor for class org.opentox.toxotis.util.aa.AuthenticationToken
Initialize a new Authentication Token.
AuthenticationToken(String) - Constructor for class org.opentox.toxotis.util.aa.AuthenticationToken

Create a new token providing its String representation.

AuthenticationToken(String, String) - Constructor for class org.opentox.toxotis.util.aa.AuthenticationToken

Create a new Authentication token providing your credentials.

AuthenticationToken(AuthenticationToken) - Constructor for class org.opentox.toxotis.util.aa.AuthenticationToken
Construct an authentication token as a clone of an existing one.
AuthenticationToken(File) - Constructor for class org.opentox.toxotis.util.aa.AuthenticationToken
Cosntruct an authentication token using a password file.
AuthenticationToken.TokenStatus - Enum in org.opentox.toxotis.util.aa
Status of the token.
authFromFile(String) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Acquire an authentication token using the credentials in an encrypted file.
authFromFile(File) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Acquire an authentication token using the credentials in an encrypted file.
AUTHORIZATION - Static variable in class org.opentox.toxotis.client.RequestHeaders
Consists of credentials containing the authentication information of the client for the realm of the resource being requested
authorize(AuthenticationToken) - Method in class org.opentox.toxotis.client.AbstractClient
Provide an authentication token to the client.
authorize(AuthenticationToken) - Method in interface org.opentox.toxotis.client.IClient
Provide an authentication token to the client.
authorize(String, VRI) - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Ask the SSO server whether the user with the given token is allowed to perform an HTTP operation on a target URI.
authorize(String, String) - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Ask the SSO server whether the user with the given token is allowed to perform an HTTP operation on a target URI.

B

BadRequestException - Exception in org.opentox.toxotis.exceptions.impl
 
BadRequestException(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.BadRequestException
 
BadRequestException(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.BadRequestException
 
BadRequestException(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.BadRequestException
 
BadRequestException() - Constructor for exception org.opentox.toxotis.exceptions.impl.BadRequestException
 
BibTeX - Class in org.opentox.toxotis.core.component
Bibliographic reference designed according to the BibTeX specifications.
BibTeX() - Constructor for class org.opentox.toxotis.core.component.BibTeX
Empty constructor for BibTeX objects.
BibTeX(VRI) - Constructor for class org.opentox.toxotis.core.component.BibTeX
Create a new BibTeX object with specified URI.
bibTex() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
BibTeX.BibTYPE - Enum in org.opentox.toxotis.core.component
Enumeration for bibliographic types supported by the Knouf ontology.
BibTeXSprider - Class in org.opentox.toxotis.util.spiders
Downloads and parses data models of BibTeX resource represented in RDF according to the Knouf BibTeX ontology.
BibTeXSprider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.BibTeXSprider
 
BibTeXSprider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.BibTeXSprider
 
BibTeXSprider(VRI, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.spiders.BibTeXSprider
 
boilingPoint() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Boiling Point at atmospheric pressure.
book() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
 
booklet() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A booklet.
Bookmark - Class in org.opentox.toxotis.core.component
 
Bookmark() - Constructor for class org.opentox.toxotis.core.component.Bookmark
 
breakLine() - Method in interface org.opentox.toxotis.core.html.HTMLContainer
 
breakLine() - Method in class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
bufferSize - Static variable in class org.opentox.toxotis.client.AbstractClient
Size of a buffer used to download the data from the remote server

C

calculateDescriptors(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Dataset
 
calculateDescriptors(VRI, AuthenticationToken, String...) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
calculateDescriptors(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
calculateDescriptors(VRI, AuthenticationToken, String...) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
Calculates descriptors for this compound empoying a descriptor calculation web service at the specified location.
calculateDescriptors(VRI, AuthenticationToken) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
Calculates all available descriptors using a remote descriptor calculation service.
call() - Method in class org.opentox.toxotis.util.TaskRunner
Runs a remote task until it completes.
carcinogenicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Carcinogenicity.
CASRN() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
cdkPhysChem() - Static method in class org.opentox.toxotis.client.collection.Services.DescriptorCalculation
CDK physicochemical calculation service.
ChemicalName() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
classification() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Classification algorithm.
classificationStatistics() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
Classification statistics.
ClientFactory - Class in org.opentox.toxotis.client
Factory for creating clients.
ClientFactory() - Constructor for class org.opentox.toxotis.client.ClientFactory
 
close() - Method in class org.opentox.toxotis.client.AbstractClient
Closes this stream and releases any system resources associated with it.
close() - Method in interface org.opentox.toxotis.client.IClient
Closes this stream and releases any system resources associated with it.
close() - Method in class org.opentox.toxotis.util.arff.RemoteArffRertiever
 
close() - Method in class org.opentox.toxotis.util.spiders.Tarantula
Closes the ontological model used by the Spider (if any) and releases all resources it holds.
Compound - Class in org.opentox.toxotis.core.component
Provides different representations for chemical compounds with a unique and defined chemical structure up to its 2D characteristics.
Compound(VRI) - Constructor for class org.opentox.toxotis.core.component.Compound
Construct a new compound identified by its URI.
Compound() - Constructor for class org.opentox.toxotis.core.component.Compound
Create a new (empty) instance of Compound
compound() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
A compound.
compound() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
COMPOUND_URI - Static variable in class org.opentox.toxotis.core.component.Dataset
 
CompoundFactory - Class in org.opentox.toxotis.factory
CompoundFactory provides methods for creating new compounds and publishing them to remote compound services.
CompoundSpider - Class in org.opentox.toxotis.util.spiders
Downloader and parser for a compound resource available in RDF.
CompoundSpider(String, String) - Constructor for class org.opentox.toxotis.util.spiders.CompoundSpider
 
CompoundSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.CompoundSpider
 
CompoundSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.CompoundSpider
 
CompoundSpider(OntModel, String) - Constructor for class org.opentox.toxotis.util.spiders.CompoundSpider
 
conference() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A conference.
configureLog4j(URL) - Static method in class org.opentox.toxotis.util.LoggingConfiguration
Configure the apache log4j logger providing the name of the configuration resource.
configureLog4j(Class, String) - Static method in class org.opentox.toxotis.util.LoggingConfiguration
 
configureLog4j(String) - Static method in class org.opentox.toxotis.util.LoggingConfiguration
Configure the apache log4j logger providing the name of the configuration resource.
configureLog4jDefault() - Static method in class org.opentox.toxotis.util.LoggingConfiguration
Default configuration for LOG4J.
Conformer - Class in org.opentox.toxotis.core.component
Conformers are compounds with 3D characteristics.
Conformer() - Constructor for class org.opentox.toxotis.core.component.Conformer
 
Conformer(VRI) - Constructor for class org.opentox.toxotis.core.component.Conformer
 
conformer() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
A conformer.
conformer() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
ConformerSpider - Class in org.opentox.toxotis.util.spiders
 
ConformerSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.ConformerSpider
 
ConformerSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.ConformerSpider
 
ConformerSpider(OntModel, String) - Constructor for class org.opentox.toxotis.util.spiders.ConformerSpider
 
connect(URI) - Method in class org.opentox.toxotis.client.AbstractClient
 
ConnectionException - Exception in org.opentox.toxotis.exceptions.impl
 
ConnectionException(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ConnectionException
 
ConnectionException(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ConnectionException
 
ConnectionException(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.ConnectionException
 
ConnectionException() - Constructor for exception org.opentox.toxotis.exceptions.impl.ConnectionException
 
CONTENT_ENCODING - Static variable in class org.opentox.toxotis.client.RequestHeaders
Used as a modifier to the media-type, to indicate what additional data format transformations such as compression have been applied to the entity-body.
CONTENT_LENGTH - Static variable in class org.opentox.toxotis.client.RequestHeaders
Indicates the size (in octets) of the entity-body that is sent or that would have been sent if it has reen requested.
CONTENT_TYPE - Static variable in class org.opentox.toxotis.client.RequestHeaders
Specifies the Internet media type of the entity-body that is sent or would have been sent if requested.
countCompounds() - Method in class org.opentox.toxotis.core.component.Dataset
 
countFeatures() - Method in class org.opentox.toxotis.core.component.Dataset
 
createAndPublishFeature(String, String, ResourceValue, VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.factory.FeatureFactory
Created and publishes online a new Feature given its title and source (acting as a reason for its creation).
createAndPublishFeature(MetaInfo, String, VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.factory.FeatureFactory
Created and publishes online a new Feature given its title and source (acting as a reason for its creation).
createComponentList(Collection<? extends OTComponent>, String, String) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Returns a list of objects in an HTML container out of a given list of ToxOtis Components.
createDataEntry(Instance) - Method in class org.opentox.toxotis.factory.DatasetFactory
Create a data entry from a single instance.
createFromArff(Instances) - Method in class org.opentox.toxotis.factory.DatasetFactory
Create a dataset using a weka.core.Instances object (based on Weka, version 3.6.2).
createFromArff(File) - Method in class org.opentox.toxotis.factory.DatasetFactory
Create a dataset using an ARFF file at a given location.
createFromArff(InputStream) - Method in class org.opentox.toxotis.factory.DatasetFactory
 
createFromArff(Reader) - Method in class org.opentox.toxotis.factory.DatasetFactory
 
createGetClient(VRI) - Static method in class org.opentox.toxotis.client.ClientFactory
Create a Get-client as an instance of IGetClient providing it's URI.
createLiteralList(Collection<LiteralValue>, String, String, boolean) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Returns a list of elements in an HTML container out of a given list of Literals.
createMasterPasswordFile(String, String, int, boolean) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Create a master password file for managing you password files.
createObjectList(Collection, String, String) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Returns a list of objects in an HTML container out of a given list of objects.
createOntClassList(Collection<OntologicalClass>, String, String, boolean) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Returns a list of elements in an HTML container out of a given list of OntologicalClass instances.
createPasswordFile(String, String, String) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Create an encrypted file containing the credentials provided in this method.
createPostClient(VRI) - Static method in class org.opentox.toxotis.client.ClientFactory
Create a POST-client as an instance of IPostClient providing it's URI.
createResourceList(Collection<ResourceValue>, String, String, boolean) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Returns a list of elements in an HTML container out of a given list of Resources.
CRYPTO - Static variable in class org.opentox.toxotis.util.aa.PasswordFileManager
This class is a singleton and this is the access point for it.
currentRow() - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
currentRow() - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
Return the current row defined by the cursor on the HTML table.
cursorDown() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
cursorDown() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
cursorPosition() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
cursorPosition() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
cursorUp() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
cursorUp() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 

D

dataCleanup() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Data-cleanup preprocessing algorithm.
DataEntry - Class in org.opentox.toxotis.core.component
A DataEntry is a set a multiplicity consisting of a compounds and a set of feature-value pairs assigned to it.
DataEntry() - Constructor for class org.opentox.toxotis.core.component.DataEntry
 
DataEntry(Compound, List<FeatureValue>) - Constructor for class org.opentox.toxotis.core.component.DataEntry
 
dataEntry() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
dataEntry() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
DataEntrySpider - Class in org.opentox.toxotis.util.spiders
Parser for a DataEntry individual in an RDF graph.
DataEntrySpider() - Constructor for class org.opentox.toxotis.util.spiders.DataEntrySpider
Dummy empty constructor.
DataEntrySpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.DataEntrySpider
DataEntrySpider constructor with an ontological resource and an ontological model.
Dataset - Class in org.opentox.toxotis.core.component
A dataset provides access to chemical compounds and their features (e.g.
Dataset(VRI) - Constructor for class org.opentox.toxotis.core.component.Dataset
Constructor for a Dataset object providing its URI.
Dataset() - Constructor for class org.opentox.toxotis.core.component.Dataset
Dummy constructor for a dataset.
Dataset(List<DataEntry>) - Constructor for class org.opentox.toxotis.core.component.Dataset
Create a new Dataset object providing a list of data entries.
dataset() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
A Dataset Provides access to chemical compounds and their features (e.g.
DatasetFactory - Class in org.opentox.toxotis.factory
DatasetFactory provides methods for creating Datasets from various sources.
DatasetSpider - Class in org.opentox.toxotis.util.spiders
A parser for RDF representations of OpenTox datasets.
DatasetSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.DatasetSpider
 
DatasetSpider(VRI, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.spiders.DatasetSpider
 
DatasetSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.DatasetSpider
 
DatasetSpider(OntModel, String) - Constructor for class org.opentox.toxotis.util.spiders.DatasetSpider
 
dataType() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
decrypt(String) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
 
defaultSignleUserPolicy(String, VRI, String) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
Creates the default policy for a user.
defaultSignleUserPolicy(String, VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
 
DELETE - Static variable in class org.opentox.toxotis.ontology.collection.HttpMethods
 
deleteAllMyPolicies(VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
Delete all
deleteFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for and operation that deletes a feature.
DeleteHttpClient - Class in org.opentox.toxotis.client.http
 
DeleteHttpClient() - Constructor for class org.opentox.toxotis.client.http.DeleteHttpClient
 
DeleteHttpsClient - Class in org.opentox.toxotis.client.https
 
DeleteHttpsClient(VRI) - Constructor for class org.opentox.toxotis.client.https.DeleteHttpsClient
 
DeleteHttpsClient() - Constructor for class org.opentox.toxotis.client.https.DeleteHttpsClient
 
deleteModel() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for and operation that deletes a model.
deleteOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the DELETE REST operation.
deleteRemotePolicy(VRI, String, AuthenticationToken) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
 
deleteTask() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for and operation that deletes/cancels a task.
dependentVariables() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
DescriptorCaclulation<T extends OTPublishable> - Class in org.opentox.toxotis.core
Abstact class that implements the interface IDescriptorCalculation offering some facilities for easier calculation of descriptors using a remote DC algorithm.
DescriptorCaclulation() - Constructor for class org.opentox.toxotis.core.DescriptorCaclulation
 
DescriptorCaclulation(VRI) - Constructor for class org.opentox.toxotis.core.DescriptorCaclulation
 
details() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
A detailed message with debugging information returned to the client when an exceptional even occurs.
DEVELOPMENT - Static variable in class org.opentox.toxotis.util.aa.policy.GroupSubject
Group of all OpenTox developers.
dissociationConstantPKa() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Dissociation Constant pKa.
dnaBinding() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
DNA-binding
doDelete() - Method in class org.opentox.toxotis.client.https.DeleteHttpsClient
 
download(String, Media, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
Downloads a certain representation of the compound in a specified MIME type.
download(OutputStream, Media, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
Downloads a certain representation of the compound in a specified MIME type.
download(File, Media, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
Downloads a certain representation of the compound in a specified MIME type.
download(Writer, Media, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
Downloads a certain representation of the compound in a specified MIME type.
downloadImage(Media, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
 
DummyComponent - Class in org.opentox.toxotis.core.component
A minimal implementaiton of a component with just a URI and a set of ontological classes and not much functionality therein.
DummyComponent() - Constructor for class org.opentox.toxotis.core.component.DummyComponent
Dummy constructor for this component with no arguments.
DummyComponent(VRI) - Constructor for class org.opentox.toxotis.core.component.DummyComponent
 
duration() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
The duration of a task.

E

eagerLearning() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Eager Learning algorithm.
ecotoxicEffects() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Eco-toxicological effects.
EINECS() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
EmailValidator - Class in org.opentox.toxotis.util.aa

A Class for validating email addresses according to the RFC syntax rules (RFC 2822 specification) and other syntatical rules that can identify various fake email addresses like john@yahoo.wtf.

EmailValidator() - Constructor for class org.opentox.toxotis.util.aa.EmailValidator
 
encrypt(String) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
 
endocrineActivity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Endocrine Activity.
endowUri(VRI) - Method in class org.opentox.toxotis.core.component.Parameter
 
endpoints() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Toxicological ECHA Endpoints.
endRdfWriter(XMLStreamWriter) - Method in class org.opentox.toxotis.core.OTComponent
 
entry() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
Any BibTeX entry.
environmentalFateParameters() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Generally environmental parameters.
equals(Object) - Method in class org.opentox.toxotis.client.VRI
 
equals(Object) - Method in class org.opentox.toxotis.core.component.DataEntry
 
equals(Object) - Method in class org.opentox.toxotis.core.component.Dataset
 
equals(Object) - Method in class org.opentox.toxotis.core.component.Feature
 
equals(Object) - Method in class org.opentox.toxotis.core.component.FeatureValue
 
equals(Object) - Method in class org.opentox.toxotis.core.component.HttpStatus
 
equals(Object) - Method in class org.opentox.toxotis.core.component.Model
 
equals(Object) - Method in class org.opentox.toxotis.core.component.Parameter
 
equals(Object) - Method in class org.opentox.toxotis.core.component.RestOperation
 
equals(Object) - Method in class org.opentox.toxotis.core.OTComponent
 
equals(Object) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
equals(Object) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
equals(Object) - Method in class org.opentox.toxotis.ontology.LiteralValue
 
equals(Object) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
equals(Object) - Method in class org.opentox.toxotis.ontology.ResourceValue
 
equals(Object) - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Two Authentication tokens are equal to each other if and only if, none of them is null and they have the same string representation when non encoded.
equals(Object) - Method in class org.opentox.toxotis.util.aa.policy.PolicySubject
 
errorCode() - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
errorCode() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
errorCode() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
An error code.
ErrorReport - Class in org.opentox.toxotis.core.component
Error Reports are part of the OpenTox API since version 1.1.
ErrorReport() - Constructor for class org.opentox.toxotis.core.component.ErrorReport
 
ErrorReport(VRI) - Constructor for class org.opentox.toxotis.core.component.ErrorReport
 
ErrorReport(int, String, String, String, String) - Constructor for class org.opentox.toxotis.core.component.ErrorReport
 
errorReport() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
Instances of the class ErrorReport appear in ontological models to report some exceptional event that happened during the transaction of data from one server to another, request errors or internal server errors.
errorReport() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
errorReportProperty() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
This is a generic property.
ErrorReportSpider - Class in org.opentox.toxotis.util.spiders
Parser for an ErrorReport RDF representation.
ErrorReportSpider() - Constructor for class org.opentox.toxotis.util.spiders.ErrorReportSpider
Create an empty error report.
ErrorReportSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.ErrorReportSpider
Create an ErrorReportSpider entity using a given ontological resource and ontological model.
ErrorReportSpider(OntModel) - Constructor for class org.opentox.toxotis.util.spiders.ErrorReportSpider
Create an ErrorReportSpider over a given ontological model.
EXPECT - Static variable in class org.opentox.toxotis.client.RequestHeaders
Indicates that particular server behaviors are required by the client.
eyeIrritationCorrosion() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Ocular irritation and/or corrosion.

F

Feature - Class in org.opentox.toxotis.core.component
A Feature is an object,representing any kind of property, assigned to a Compound.
Feature() - Constructor for class org.opentox.toxotis.core.component.Feature
 
Feature(VRI) - Constructor for class org.opentox.toxotis.core.component.Feature
 
feature() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
feature() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
FeatureFactory - Class in org.opentox.toxotis.factory
A factory-like class that provides methods for looking up features in remote databases through the OpenTox REST API.
FeatureFactory() - Constructor for class org.opentox.toxotis.factory.FeatureFactory
 
featureSelection() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Feature selection algorithm.
FeatureSpider - Class in org.opentox.toxotis.util.spiders
Downloader and parser for a Feature resource available in RDF.s
FeatureSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.FeatureSpider
 
FeatureSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.FeatureSpider
 
FeatureSpider(OntModel, String) - Constructor for class org.opentox.toxotis.util.spiders.FeatureSpider
 
FeatureValue - Class in org.opentox.toxotis.core.component
A pair of a feature and a Literal value.
FeatureValue() - Constructor for class org.opentox.toxotis.core.component.FeatureValue
 
FeatureValue(Feature, LiteralValue) - Constructor for class org.opentox.toxotis.core.component.FeatureValue
 
featureValue() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
featureValueNominal() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
featureValueNumeric() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
featureValuePair() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
FeatureValueSpider - Class in org.opentox.toxotis.util.spiders
Parser for a FeatureValue resource in a given RDF graph.
FeatureValueSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.FeatureValueSpider
Default constructor.
featureValuesSize() - Method in class org.opentox.toxotis.core.component.DataEntry
 
featureValueString() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
filter() - Static method in class org.opentox.toxotis.client.collection.Services.NtuaAlgorithms
Generic Dataset Filter.
ForbiddenRequest - Exception in org.opentox.toxotis.exceptions.impl
 
ForbiddenRequest(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ForbiddenRequest
 
ForbiddenRequest(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ForbiddenRequest
 
ForbiddenRequest(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.ForbiddenRequest
 
ForbiddenRequest() - Constructor for exception org.opentox.toxotis.exceptions.impl.ForbiddenRequest
 
formatBold(boolean) - Method in interface org.opentox.toxotis.core.html.HTMLText
Format the text as bold using the HTML tag <b>
formatBold(boolean) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
formatItalics(boolean) - Method in interface org.opentox.toxotis.core.html.HTMLText
Format the text as italics using the HTML tag <em>
formatItalics(boolean) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
formatPRE(boolean) - Method in interface org.opentox.toxotis.core.html.HTMLText
Encapsulates the formatted text in a pre block using the tag <pre;gt;
formatPRE(boolean) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
formatTrueType(boolean) - Method in interface org.opentox.toxotis.core.html.HTMLText
Format the text as true-type using the HTML tag <tt>
formatTrueType(boolean) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
formatUnderlined(boolean) - Method in interface org.opentox.toxotis.core.html.HTMLText
Undeline the text using the HTML tag <u>
formatUnderlined(boolean) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
forName(String) - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
Case-insensitive search for a Knouf ontological class.
forName(String) - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
forName(String) - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
forName(String) - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
forName(String) - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
Return a datatype property given its name.
forName(String) - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
FROM - Static variable in class org.opentox.toxotis.client.RequestHeaders
The Internet e-mail address for the human user who controls the requesting browser or other client.
futureCDKPhysChemDescriptors(AuthenticationToken, VRI) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
futureCDKPhysChemDescriptors(AuthenticationToken, VRI) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
 
futureDescriptors(VRI, AuthenticationToken, String...) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
futureDescriptors(VRI, AuthenticationToken, ExecutorService, String...) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
futureDescriptors(VRI, AuthenticationToken, VRI) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
futureDescriptors(VRI, AuthenticationToken, ExecutorService, String...) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
Use a remote Service to calculate (some or all available) descriptors for a chemical compound.
futureDescriptors(VRI, AuthenticationToken, VRI) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
Calculate descriptors for a chemical compound or a dataset providing the URI of the descriptor calculation algorithm, the URI of a dataset service where the result should be stored and an authentication token for accessing the various services.
futureDescriptors(VRI, AuthenticationToken, String...) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
 
futureJoeLibDescriptors(AuthenticationToken, VRI) - Method in class org.opentox.toxotis.core.DescriptorCaclulation
 
futureJoeLibDescriptors(AuthenticationToken, VRI) - Method in interface org.opentox.toxotis.core.IDescriptorCalculation
 

G

gastrointestinalAbsorption() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Gastrointestinal absorption
get(int) - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
get(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
GET - Static variable in class org.opentox.toxotis.ontology.collection.HttpMethods
 
getAbstract() - Method in class org.opentox.toxotis.core.component.BibTeX
The abstract of the BibTeX object.
getActionUrl() - Method in interface org.opentox.toxotis.core.html.HTMLForm
 
getActionUrl() - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
getActor() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getActor() - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
getActor() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
getActualModel() - Method in class org.opentox.toxotis.core.component.Model
The actual model, serializable object, that encapsulates all necessary information for the calculated model that was trained by some algorithm.
getAddress() - Method in class org.opentox.toxotis.core.component.BibTeX
Usually the address of the publisher or other type of institution.
getAddress() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getAdmissibleValues() - Method in class org.opentox.toxotis.core.component.Feature
 
getAffiliation() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getAlgorithm() - Method in class org.opentox.toxotis.core.component.Model
The algorithm with which the model was built/trained.
getAlgorithm() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for and operation that retrieves meta-data about an algorithm.
getAlgorithm() - Method in class org.opentox.toxotis.training.Trainer
 
getAlgorithms() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for and operation that retrieves a list of algorithms.
getAlignment() - Method in interface org.opentox.toxotis.core.html.HTMLParagraph
 
getAlignment() - Method in class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
getAll() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
getAll() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
getAnnotation() - Method in class org.opentox.toxotis.core.component.BibTeX
An annotation.
getApplicabilityDomainResult() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
GetArff - Class in org.opentox.toxotis.util.arff
Downloads ARFF from a remote location.
GetArff(VRI) - Constructor for class org.opentox.toxotis.util.arff.GetArff
 
getAssayProperty(OntologicalClass, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
 
getAudiences() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getAudiences() - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
getAuthor() - Method in class org.opentox.toxotis.core.component.BibTeX
The name(s) of the author(s), in the format described in the LaTeX book.
getAuthor() - Method in interface org.opentox.toxotis.core.html.HTMLHead
Getter method for the authtor(s) of the current HTML document
getAuthor() - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
getAuthors() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getAuthParameters() - Method in class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
getBibTeXReferences() - Method in class org.opentox.toxotis.core.component.Model
 
getBibTeXReferences() - Method in interface org.opentox.toxotis.core.IBibTexReferencable
 
getBibTexService() - Method in class org.opentox.toxotis.core.component.BibTeX
The bibtex service.
getBibType() - Method in class org.opentox.toxotis.core.component.BibTeX
The bibliographic type.
getBlob() - Method in class org.opentox.toxotis.core.component.Model
 
getBlob() - Method in class org.opentox.toxotis.ontology.MetaInfoDeblobber
 
getBookTitle() - Method in class org.opentox.toxotis.core.component.BibTeX
Title of a book, part of which is being cited.
getCasrn() - Method in class org.opentox.toxotis.core.component.Compound
 
getChapter() - Method in class org.opentox.toxotis.core.component.BibTeX
A chapter (or section or whatever) number.
getCols() - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
getCols() - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
getComments() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getComments() - Method in interface org.opentox.toxotis.ontology.MetaInfo
The property rdfs:comment is used to provide a human-readable description of a resource.
getComponent() - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
getComponents() - Method in interface org.opentox.toxotis.core.html.HTMLExpandableComponent
A list of all
getComponents() - Method in class org.opentox.toxotis.core.html.impl.HTMLExpandableComponentImpl
 
getComponents() - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
getCompound() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getCompoundId() - Method in class org.opentox.toxotis.core.component.Compound
Return the (local) identifier of the compound as it is extracted from its URI.
getCompoundUri() - Method in class org.opentox.toxotis.core.component.Conformer
 
getConformer() - Method in class org.opentox.toxotis.core.component.DataEntry
 
getConformerId() - Method in class org.opentox.toxotis.core.component.Conformer
 
getConformers() - Method in class org.opentox.toxotis.core.component.Compound
 
getConnection() - Method in class org.opentox.toxotis.client.AbstractClient
 
getConnectionInputStream() - Method in class org.opentox.toxotis.client.AbstractClient
 
getConnectionLock() - Method in class org.opentox.toxotis.client.AbstractClient
 
getConnectionLock() - Method in interface org.opentox.toxotis.client.IClient
Returns the connection lock.
getContactInfo() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getContainedFeatures() - Method in class org.opentox.toxotis.core.component.Dataset
All features in the dataset.
getContainedFeatureUris() - Method in class org.opentox.toxotis.core.component.Dataset
The set of all feature URIs in the dataset.
getContentType() - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
getContentType() - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
getContentType() - Method in interface org.opentox.toxotis.client.IPostClient
 
getContributors() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getContributors() - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
getCopyright() - Method in class org.opentox.toxotis.core.component.BibTeX
 
getCreatedBy() - Method in class org.opentox.toxotis.core.component.BibTeX
The user that created the BibTeX object.
getCreatedBy() - Method in class org.opentox.toxotis.core.component.Model
The user that created the model.
getCreatedBy() - Method in class org.opentox.toxotis.core.component.Task
Retrieve the user which created the task.
getCreators() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getCreators() - Method in interface org.opentox.toxotis.ontology.MetaInfo
The creator is an entity primarily responsible for making the content of the resource.
getCrossref() - Method in class org.opentox.toxotis.core.component.BibTeX
The database key of the entry being cross referenced.
getCryptoIterations() - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Number of salting iterations that is used by this encryption/decryption algorithm.
getCssUrl() - Method in interface org.opentox.toxotis.core.html.HTMLHead
Returns the URL of the CSS document related to the current HTML document.
getCssUrl() - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
getCurrent() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
getCurrent() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
getDataEntries() - Method in class org.opentox.toxotis.core.component.Dataset
 
getDataset() - Method in class org.opentox.toxotis.core.component.Model
Get the URI of the dataset that was used to train the model.
getDataset() - Method in class org.opentox.toxotis.training.Trainer
The dataset used to train the model.
getDate() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getDate() - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
getDependentFeatures() - Method in class org.opentox.toxotis.core.component.Model
A list of the dependent features of the model, i.e.
getDepiction(String) - Method in class org.opentox.toxotis.core.component.Compound
 
getDepictionFromRemote(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
Deprecated. 
getDepictionService() - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
getDescriptions() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getDescriptions() - Method in interface org.opentox.toxotis.ontology.MetaInfo
An account of the content of the resource.
getDescriptorDomain() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getDetails() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getDetails() - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
getDetails() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
getDisjointWith() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
getDisjointWith() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
getDiv() - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
getDoAName() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getDoaUri() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getDocument() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyWrapper
 
getDocument() - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
getDocument() - Method in class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
getDocumentation() - Method in enum org.opentox.toxotis.client.HttpStatusCodes
Get some short documentation about the status code.
getDomain() - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getDomain() - Method in interface org.opentox.toxotis.ontology.OTProperty
We quote an excperpt of the documentation about the property rdfs:domain found at W3C online reference:
A domain of a property limits the individuals to which the property can be applied.
getDuration() - Method in class org.opentox.toxotis.core.component.Task
The duration of the task, that is the overall time since its execution started, not including the time it was queued.
getEdition() - Method in class org.opentox.toxotis.core.component.BibTeX
The edition of a book—for example, "Second".
getEditor() - Method in class org.opentox.toxotis.core.component.BibTeX
Name(s) of editor(s), typed as indicated in the LaTeX book.
getEinecs() - Method in class org.opentox.toxotis.core.component.Compound
 
getEmail() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getEncoding() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Retrieve the encoding used to encode tokens.
getErrorCause() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getErrorCode() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getErrorReport() - Method in class org.opentox.toxotis.core.component.Task
 
getErrorReport() - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
getErrorReport() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
Returns the error report related to the current exception that is received by some other remote service.
getExperimentalResult() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getExperimentalValues() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getExpResultUnits() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getFeature() - Method in class org.opentox.toxotis.core.component.FeatureValue
 
getFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for any operation that retrieves meta-data about a feature.
getFeatures() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for any operation that retrieves a list of features.
getFeatureValue(int) - Method in class org.opentox.toxotis.core.component.DataEntry
 
getFeatureValues() - Method in class org.opentox.toxotis.core.component.DataEntry
 
getFeatureValues() - Method in class org.opentox.toxotis.core.component.Dataset
 
getFirstName() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getGAaccount() - Static method in class org.opentox.toxotis.core.html.GoogleAnalytics
 
getGAjs() - Static method in class org.opentox.toxotis.core.html.GoogleAnalytics
 
getHash() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getHash() - Method in class org.opentox.toxotis.ontology.LiteralValue
Getter fot the hash code of the current LiteralValue object.
getHash() - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
getHash() - Method in class org.opentox.toxotis.ontology.ResourceValue
 
getHashedPass() - Method in class org.opentox.toxotis.core.component.User
 
getHasSources() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getHasSources() - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
getHeaderValues() - Method in class org.opentox.toxotis.client.AbstractClient
 
getHost() - Method in class org.opentox.toxotis.client.VRI
Returns the host of the URI.
getHtmlBody() - Method in interface org.opentox.toxotis.core.html.HTMLPage
Get the HTML body from the page.
getHtmlBody() - Method in class org.opentox.toxotis.core.html.impl.HTMLPageImpl
 
getHTMLHead() - Method in interface org.opentox.toxotis.core.html.HTMLPage
Getter method for the HTML Head of the HTML page.
getHTMLHead() - Method in class org.opentox.toxotis.core.html.impl.HTMLPageImpl
 
GetHttpClient - Class in org.opentox.toxotis.client.http
A client that performs GET requests.
GetHttpClient() - Constructor for class org.opentox.toxotis.client.http.GetHttpClient
Create a new instance of GetHttpClient
GetHttpClient(VRI) - Constructor for class org.opentox.toxotis.client.http.GetHttpClient
Instantiates a GET client with a given target URI.
getHttpParameters() - Method in class org.opentox.toxotis.core.component.RestOperation
Set of input parameters which are expected by the client on POST.
getHttpParameters() - Method in interface org.opentox.toxotis.core.IRestOperation
Set of input parameters which are expected by the client on POST.
GetHttpsClient - Class in org.opentox.toxotis.client.https
 
GetHttpsClient(VRI) - Constructor for class org.opentox.toxotis.client.https.GetHttpsClient
 
GetHttpsClient() - Constructor for class org.opentox.toxotis.client.https.GetHttpsClient
 
getHttpStatus() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getHttpStatus() - Method in class org.opentox.toxotis.core.component.Task
 
getHttpStatus() - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
getHttpStatus() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
getHttpStatusClass() - Method in class org.opentox.toxotis.core.component.HttpStatus
 
getHttpStatusCodes() - Method in class org.opentox.toxotis.core.component.RestOperation
A set of the status codes that might occur when invoking the service, including all redirection, error and success status codes.
getHttpStatusCodes() - Method in interface org.opentox.toxotis.core.IRestOperation
A set of the status codes that might occur when invoking the service, including all redirection, error and success status codes.
getId() - Method in class org.opentox.toxotis.client.VRI
 
getIdentifiers() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getIdentifiers() - Method in interface org.opentox.toxotis.ontology.MetaInfo
Get the identifier (ID) of the described entity.
getInchi() - Method in class org.opentox.toxotis.core.component.Compound
 
getInchiKey() - Method in class org.opentox.toxotis.core.component.Compound
 
getIndependentFeatures() - Method in class org.opentox.toxotis.core.component.Model
A list of the independent features of the model, i.e.
getIndex() - Method in class org.opentox.toxotis.core.component.ParameterValue
 
getInputParamClass() - Method in class org.opentox.toxotis.core.component.HttpParameter
 
getInstance() - Static method in class org.opentox.toxotis.factory.CompoundFactory
Returns the CompoundFactory object associated with the current Java application.
getInstance() - Static method in class org.opentox.toxotis.factory.DatasetFactory
Returns the DatasetFactory object associated with the current Java application.
getInstance() - Static method in class org.opentox.toxotis.util.aa.TokenPool
 
getInstances() - Method in class org.opentox.toxotis.core.component.Dataset

Creates and returns a weka.core.Instances object from the data contained in this Dataset.

getInstances() - Method in class org.opentox.toxotis.util.arff.ArffDownloader
 
getInstances() - Method in class org.opentox.toxotis.util.arff.GetArff
 
getIsbn() - Method in class org.opentox.toxotis.core.component.BibTeX
The ISBN of the resource.
getIssn() - Method in class org.opentox.toxotis.core.component.BibTeX
The ISSN of the resource.
getIupacName() - Method in class org.opentox.toxotis.core.component.Compound
 
getJournal() - Method in class org.opentox.toxotis.core.component.BibTeX
A journal name.
getKey() - Method in class org.opentox.toxotis.client.Pair
Returns the key corresponding to this entry.
getKey() - Method in class org.opentox.toxotis.core.component.BibTeX
Used for alphabetizing, cross referencing, and creating a label when the "author" information (described in Section 4) is missing.
getKeyword() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getKeywords() - Method in class org.opentox.toxotis.core.component.BibTeX
A list of keywords separated by any custom delimiter.
getLastName() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getLastUpdated() - Static method in enum org.opentox.toxotis.client.collection.OpenToxAlgorithms
 
getLocalCode() - Method in class org.opentox.toxotis.core.component.Model
If the actual model is stored as a file on the file system, this method returns the pathname for it.
getLoggedIn() - Method in class org.opentox.toxotis.util.aa.TokenPool
 
getLowLevelOntologies() - Method in class org.opentox.toxotis.core.component.Feature
The lower-level ontological classes that are necessary to characterize the features.
getMail() - Method in class org.opentox.toxotis.core.component.User
Retrieve the email of the user
getMaxBibTeX() - Method in class org.opentox.toxotis.core.component.User
 
getMaxModels() - Method in class org.opentox.toxotis.core.component.User
 
getMaxParallelTasks() - Method in class org.opentox.toxotis.core.component.User
 
getMechanismDomain() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getMediaType() - Method in class org.opentox.toxotis.client.AbstractClient
Retrieve the specified media type which is the value for the Accept HTTP Header.
getMediaType() - Method in interface org.opentox.toxotis.client.IClient
Retrieve the specified media type which is the value for the Accept HTTP Header.
getMediaTypes() - Method in class org.opentox.toxotis.core.component.RestOperation
 
getMediaTypes() - Method in interface org.opentox.toxotis.core.IRestOperation
 
getMessage() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getMessage() - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
getMeta() - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
getMeta() - Method in interface org.opentox.toxotis.core.IOTComponent
Obtain meta information about the underlying OpenTox resource/component.
getMeta() - Method in class org.opentox.toxotis.core.OTComponent
Obtain meta information about the underlying OpenTox resource/component.
getMeta() - Method in class org.opentox.toxotis.ontology.MetaInfoBlobber
 
getMetabolicDomain() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getMetaInfo() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
getMetaInfo() - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getMetaInfo() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
getMetaInfo() - Method in interface org.opentox.toxotis.ontology.OTProperty
Get the meta information available abou the property.
getMethod() - Method in class org.opentox.toxotis.core.component.RestOperation
The HTTP method which are supported by the web service.
getMethod() - Method in interface org.opentox.toxotis.core.html.HTMLForm
 
getMethod() - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
getMethod() - Method in interface org.opentox.toxotis.core.IRestOperation
The HTTP method which are supported by the web service.
getMime() - Method in enum org.opentox.toxotis.client.collection.Media
 
getModel() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getModel() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Any GET operation on a model.
getModelDate() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getModelInfo() - Method in class org.opentox.toxotis.ontology.ListModelRequest
 
getModels() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for any operation that retrieves a list of models.
getModelVersion() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getMolecularStructure() - Method in class org.opentox.toxotis.core.component.Compound
The molecular structure or a compound (MOL file, SDF etc).
getMultiParameters() - Method in class org.opentox.toxotis.core.component.Algorithm
 
getMultiParameters() - Method in class org.opentox.toxotis.core.component.Model
 
getName() - Method in class org.opentox.toxotis.core.component.Parameter
Is a proxy method for getting the dc:title of the Parameter (if any).
getName() - Method in class org.opentox.toxotis.core.component.User
 
getName() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
getName() - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getName() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
getName() - Method in interface org.opentox.toxotis.ontology.OTProperty
Returns the local name of the ontological property omiiting the namespace string.
getName() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Name of the rule.
getName() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
getNameSpace() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
getNameSpace() - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getNameSpace() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
getNameSpace() - Method in interface org.opentox.toxotis.ontology.OTProperty
Returns the namespace of the ontological property or null if not defined.
getNumber() - Method in class org.opentox.toxotis.core.component.BibTeX
The number of a journal, magazine, technical report, or of a work in a series.
getNumColumns() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
getNumColumns() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
getOntModel() - Method in class org.opentox.toxotis.util.spiders.Tarantula
Returns the ontological model held by this parser.
getOntologicalClass() - Method in class org.opentox.toxotis.client.VRI
The Ontological Class of the URI.
getOntologicalClass() - Method in class org.opentox.toxotis.ontology.ResourceValue
 
getOntologicalClasses() - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
getOntologicalClasses() - Method in interface org.opentox.toxotis.core.IOTComponent
The list of ontological classes for the current entity.
getOntologicalClasses() - Method in class org.opentox.toxotis.core.OTComponent
 
getOntologicalTypes(Resource) - Method in class org.opentox.toxotis.util.spiders.Tarantula
 
getOntologies() - Method in class org.opentox.toxotis.core.component.Algorithm
Get the ontological classes of the algorithm
getOpenToxType() - Method in class org.opentox.toxotis.client.VRI
Returns a Java class that best fits the pattern matched by this URI.
getOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the GET REST operation.
getOTATypes(Resource) - Method in class org.opentox.toxotis.util.spiders.Tarantula
 
getPage() - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
getPages() - Method in class org.opentox.toxotis.core.component.BibTeX
One or more page numbers or range of numbers, such as 42--111 or 7,41,73--97 or 43+ (the ‘+’ in this last example indicates pages following that don’t form a simple range).
getParamContent() - Method in class org.opentox.toxotis.core.component.HttpParameter
 
getParameters() - Method in class org.opentox.toxotis.core.component.Algorithm
Retrieve the set of parameters for this algorithm.
getParameters() - Method in class org.opentox.toxotis.core.component.Model
The parameters of the model.
getParameterValues() - Method in class org.opentox.toxotis.core.component.MultiParameter
 
getParamName() - Method in class org.opentox.toxotis.core.component.HttpParameter
 
getParseTime() - Method in class org.opentox.toxotis.util.spiders.Tarantula
Get the time needed to parse the Ontological Model into an in-house component of ToxOtis.
getPasswordGenerationProgress() - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Returns a double between 0 and 100 that monitors the progress of the password file creation.
getPercentageCompleted() - Method in class org.opentox.toxotis.core.component.Task
Get the percentage of completion of a running task.
getPlainText() - Method in class org.opentox.toxotis.core.component.BibTeX
Deprecated.  
getPolicies() - Method in class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
getPolicyName() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
The name of the policy.
getPolicyName() - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
getPolicyOwner(VRI, VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
Obtain the username of the owner of a policy for a given URI.
getPort() - Method in class org.opentox.toxotis.client.VRI
Delegates the method java.net.URI#getPort()::int
getPostLock() - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
getPostLock() - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
getPostLock() - Method in interface org.opentox.toxotis.client.IPostClient
 
getPredictedFeatures() - Method in class org.opentox.toxotis.core.component.Model
A list of the predicted features of the model, i.e.
getPredictionFeature() - Method in class org.opentox.toxotis.training.Trainer
 
getPredictionResult() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getPredResultUnits() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getProperties(AuthenticationToken, VRI...) - Method in class org.opentox.toxotis.core.component.Compound
Creates a dataset with the current compound and the features prescribed in the list of input arguments.
getPropertiesByOnt(OntologicalClass, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
Returns the sub-dataset that has properties of a given ontological type.
getProperty(Feature, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
Retrieves a property as a typed value, for a given feature, from the remote server that hosts the underlying compound.
getProperty(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
 
getProperty(OntModel) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getProperty(OntModel) - Method in interface org.opentox.toxotis.ontology.OTProperty
Extract the corresponding property (if any) from the given ontological model.
getProtocol() - Method in class org.opentox.toxotis.client.VRI
Returns the protocol of the URI (HTTP, HTTPS, etc)
getPublishers() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getPublishers() - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
getQMRFreference() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getQMRFReportDiscussion() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getQMRFReportReference() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getQueryAsString() - Method in class org.opentox.toxotis.client.VRI
Returns the query part of the URI as a String without the question mark.
getRange() - Method in class org.opentox.toxotis.ontology.impl.OTDatatypePropertyImpl
 
getRange() - Method in class org.opentox.toxotis.ontology.impl.OTObjectPropertyImpl
 
getRange() - Method in interface org.opentox.toxotis.ontology.OTDatatypeProperty

For a property one can define (multiple) rdfs:range axioms.

getRange() - Method in interface org.opentox.toxotis.ontology.OTObjectProperty
For a property one can define (multiple) rdfs:range axioms.
getReadLock() - Method in class org.opentox.toxotis.client.AbstractClient
 
getReadLock() - Method in interface org.opentox.toxotis.client.IClient
Returns the read-lock of the client.
getReadRemoteTime() - Method in class org.opentox.toxotis.util.spiders.Tarantula
Get the time needed to download the Ontological Model and cast it as an Ontological model (instance of com.hp.hpl.jena.ontology.OntModel).
getRegistrationDate() - Method in class org.opentox.toxotis.core.component.Compound
 
getRemoteStream() - Method in class org.opentox.toxotis.client.AbstractClient
Get the body of the HTTP response as InputStream.
getRemoteStream() - Method in interface org.opentox.toxotis.client.IClient
Get the body of the HTTP response as InputStream.
getReportDate() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getReportMeta() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getResourceValue() - Method in enum org.opentox.toxotis.ontology.collection.HttpMethods.MethodsEnum
 
getResponseCode() - Method in class org.opentox.toxotis.client.AbstractClient
Get the HTTP status of the response
getResponseCode() - Method in interface org.opentox.toxotis.client.IClient
Get the HTTP status of the response
getResponseContentType() - Method in class org.opentox.toxotis.client.AbstractClient
 
getResponseContentType() - Method in interface org.opentox.toxotis.client.IClient
Returns the content-type of the response.
getResponseHeader(String) - Method in class org.opentox.toxotis.client.AbstractClient
 
getResponseHeader(String) - Method in interface org.opentox.toxotis.client.IClient
The header of the response.
getResponseOntModel() - Method in class org.opentox.toxotis.client.AbstractClient
If possible, get the ontological model provided in the response.
getResponseOntModel(String) - Method in class org.opentox.toxotis.client.AbstractClient
If possible, get the ontological model provided in the response.
getResponseOntModel() - Method in interface org.opentox.toxotis.client.IClient
If possible, get the ontological model provided in the response.
getResponseOntModel(String) - Method in interface org.opentox.toxotis.client.IClient
If possible, get the ontological model provided in the response.
getResponseText() - Method in class org.opentox.toxotis.client.AbstractClient
Get the response body as a String in the format specified in the Accept header of the request.
getResponseText() - Method in interface org.opentox.toxotis.client.IClient
Get the response body as a String in the format specified in the Accept header of the request.
getResponseUriList() - Method in class org.opentox.toxotis.client.AbstractClient
Get the response of the remote service as a Set of URIs.
getResponseUriList() - Method in interface org.opentox.toxotis.client.IClient
Get the response of the remote service as a Set of URIs.
getRestClasses() - Method in class org.opentox.toxotis.core.component.RestOperation
Return the set of ontological classes that describe the underlying resource and define its REST interface available operations choosing from the collection OTRestClasses.
getRestClasses() - Method in interface org.opentox.toxotis.core.IRestOperation
Return the set of ontological classes that describe the underlying resource and define its REST interface available operations choosing from the collection OTRestClasses .
getRestOperations() - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
getResultUri() - Method in class org.opentox.toxotis.core.component.Task
 
getRights() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getRights() - Method in interface org.opentox.toxotis.ontology.MetaInfo
Copyright notes for the underlying resource.
getRows() - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
getRows() - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
getSameAs() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getSameAs() - Method in interface org.opentox.toxotis.ontology.MetaInfo
The built-in OWL property owl:sameAs links an individual to an individual (i.e.
getScope() - Method in class org.opentox.toxotis.core.component.MultiParameter
 
getScope() - Method in class org.opentox.toxotis.core.component.Parameter
 
getScope() - Method in class org.opentox.toxotis.core.component.VariableInfo
 
getSec32e() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec33c() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec34() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec35() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec41() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec42() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec43() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSec44() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSeeAlso() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getSeeAlso() - Method in interface org.opentox.toxotis.ontology.MetaInfo
Related to the datatype ontological property rdfs:seeAlso.
getSeries() - Method in class org.opentox.toxotis.core.component.BibTeX
The name of a series or set of books.
getServiceBaseUri() - Method in class org.opentox.toxotis.client.VRI
Returns the base URI of the service.
getServiceName() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Name of the service.
getServiceName() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
getServiceUri() - Method in enum org.opentox.toxotis.client.collection.OpenToxAlgorithms
 
getServiceVri() - Method in enum org.opentox.toxotis.client.collection.OpenToxAlgorithms
 
getSimilar(double, VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
Method for performing similarity search for this compound given a similarity measure which is usually a number between 0 and 1.
getSimilar(double, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
Get a set of URIs for similar compounds using the default similarity search service at http://apps.ideaconsut.net:8080/ambit2/query/similarity which is based on the Tanimoto Distance between compounds.
getSimilarityLevel() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getSmiles() - Method in class org.opentox.toxotis.core.component.Compound
 
getStatus() - Method in enum org.opentox.toxotis.client.HttpStatusCodes
Return the status code as an integer.
getStatus() - Method in class org.opentox.toxotis.core.component.Task
The status of the task as an element of the enumeration Task.Status.
getStatus() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Get the status of the token.
getStereoFeatures() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getStringNoQuery() - Method in class org.opentox.toxotis.client.VRI
Returns the URI without the query part.
getStructuralAnalogues() - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
getStructuralDomain() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
getSubjectName() - Method in class org.opentox.toxotis.util.aa.policy.PolicySubject
 
getSubjects() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getSubjects() - Method in interface org.opentox.toxotis.ontology.MetaInfo
Get the topic of the content of the resource.
getSubjectsCollectionName() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
The name of the collection of subjects.
getSubjectsCollectionName() - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
getSubjectsDescription() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
Description of the subject.
getSubjectsDescription() - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
getSuperClasses() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
getSuperClasses() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
getSuperProperties() - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getSuperProperties() - Method in interface org.opentox.toxotis.ontology.OTProperty
Get a collection of the super-properties of this ontological property declared using rdfs:subPropertyOf.
getSuperServiceUri() - Method in class org.opentox.toxotis.util.SuperPredictor
 
getSynonyms() - Method in class org.opentox.toxotis.core.component.Compound
 
getTag() - Method in interface org.opentox.toxotis.core.html.HTMLTag
 
getTag() - Method in class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
getTargetUri() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
URI of the resource for which the rule is written.
getTargetUri() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
getTask() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for any operation that retrieves meta-data for an asynchronous task.
getTask() - Method in class org.opentox.toxotis.util.TaskRunner
 
getTasks() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for any operation that retrieves a list of tasks.
getText() - Method in interface org.opentox.toxotis.core.html.HTMLText
Returns the text that was set to the current HTMLText object.
getText() - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
getText() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyWrapper
 
getText() - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
getText() - Method in class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
getTimeDownload() - Method in class org.opentox.toxotis.core.component.Dataset
 
getTimeInstancesConversion() - Method in class org.opentox.toxotis.core.component.Dataset
 
getTimeParse() - Method in class org.opentox.toxotis.core.component.Dataset
 
getTitle() - Method in class org.opentox.toxotis.core.component.BibTeX
The work’s title, typed as explained in the LaTeX book.
getTitle() - Method in interface org.opentox.toxotis.core.html.HTMLHead
Getter method for the title of the HTML document.
getTitle() - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
getTitles() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
getTitles() - Method in interface org.opentox.toxotis.ontology.MetaInfo
Get the name given to the resource.
getToken(String) - Method in class org.opentox.toxotis.util.aa.TokenPool
Returns the token for a certain user by searching in the pool.
getToken() - Method in class org.opentox.toxotis.util.TaskRunner
 
getTokenCreationDate() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
 
getTokenCreationTimestamp() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Retrieve the timestamp of the token creation.
getTokenUrlEncoded() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Returns the token as a URL encoded String.
getType() - Method in class org.opentox.toxotis.core.component.Parameter
 
getType() - Method in class org.opentox.toxotis.ontology.LiteralValue
Retrieve the datatype
getTypedValue() - Method in class org.opentox.toxotis.core.component.Parameter
 
getUid() - Method in class org.opentox.toxotis.core.component.User
 
getUnits() - Method in class org.opentox.toxotis.core.component.Feature
Returns the units of the feature as a string.
getUri() - Method in class org.opentox.toxotis.client.AbstractClient
Get the target URI.
getUri() - Method in interface org.opentox.toxotis.client.IClient
Get the targetted URI
getUri() - Method in class org.opentox.toxotis.client.VRI
Equivalent method to VRI.toString().
getUri() - Method in class org.opentox.toxotis.core.component.DataEntry
 
getUri() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
getUri() - Method in class org.opentox.toxotis.core.component.FeatureValue
 
getUri() - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
getUri() - Method in interface org.opentox.toxotis.core.IOTComponent
Get the URI of the resource (as an instance of VRI.
getUri() - Method in class org.opentox.toxotis.core.OTComponent
Get the URI of the resource (as an instance of VRI.
getUri() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
getUri() - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
getUri() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
getUri() - Method in interface org.opentox.toxotis.ontology.OTResource
The URI of the ontological resource that uniquely identifies it.
getUri() - Method in class org.opentox.toxotis.ontology.ResourceValue
 
getUrl() - Method in class org.opentox.toxotis.core.component.BibTeX
A URL where more information about the work described by this BibTeX can be found.
getURL() - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
getUrlParams() - Method in class org.opentox.toxotis.client.VRI
Returns a set of name-value pairs that constitute the set of URL parameters of the VRI.
getUser() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Information about the user that holds the token (for which the token was created).
getUser(String) - Method in class org.opentox.toxotis.util.aa.TokenPool
 
getValue() - Method in class org.opentox.toxotis.client.Pair
Returns the value corresponding to this entry.
getValue() - Method in class org.opentox.toxotis.core.component.FeatureValue
 
getValue() - Method in class org.opentox.toxotis.core.component.Parameter
 
getValue() - Method in class org.opentox.toxotis.core.component.VariableValue
 
getValue() - Method in class org.opentox.toxotis.ontology.LiteralValue
Retrieve the value
getValue() - Method in class org.opentox.toxotis.util.aa.policy.GroupSubject
 
getValue() - Method in class org.opentox.toxotis.util.aa.policy.PolicySubject
 
getValue() - Method in class org.opentox.toxotis.util.aa.policy.SingleSubject
 
getValueAsString() - Method in class org.opentox.toxotis.ontology.LiteralValue
Returns a String representation of the underlying value.
getValues() - Method in class org.opentox.toxotis.core.component.ParameterValue
 
getVariableInfo() - Method in class org.opentox.toxotis.core.component.VariableValue
 
getVolume() - Method in class org.opentox.toxotis.core.component.BibTeX
The volume of a journal or multivolume book.
getYear() - Method in class org.opentox.toxotis.core.component.BibTeX
The year of publication or, for an unpublished work, the year it was written.
GOOGLE_ANALYTICS - Static variable in class org.opentox.toxotis.core.html.GoogleAnalytics
 
GoogleAnalytics - Class in org.opentox.toxotis.core.html
 
GoogleAnalytics() - Constructor for class org.opentox.toxotis.core.html.GoogleAnalytics
 
GroupSubject - Class in org.opentox.toxotis.util.aa.policy
A collection of standard groups of Users used to identify certain access levels.
GroupSubject() - Constructor for class org.opentox.toxotis.util.aa.policy.GroupSubject
 
GUEST - Static variable in class org.opentox.toxotis.core.component.User
 

H

hasAbstract() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasAddress() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasAffiliation() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasAnnotation() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasAttribute() - Static method in class org.opentox.toxotis.ontology.collection.OTRestDatatypeProperties
 
hasAuthor() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasBookTitle() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasChapter() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasCopyright() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasCrossRef() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasEdition() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasEditor() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasFeatureValues() - Method in class org.opentox.toxotis.core.component.DataEntry
 
hashCode() - Method in class org.opentox.toxotis.client.VRI
 
hashCode() - Method in class org.opentox.toxotis.core.component.DataEntry
 
hashCode() - Method in class org.opentox.toxotis.core.component.Dataset
 
hashCode() - Method in class org.opentox.toxotis.core.component.Feature
 
hashCode() - Method in class org.opentox.toxotis.core.component.FeatureValue
 
hashCode() - Method in class org.opentox.toxotis.core.component.HttpStatus
 
hashCode() - Method in class org.opentox.toxotis.core.component.Model
 
hashCode() - Method in class org.opentox.toxotis.core.component.Parameter
 
hashCode() - Method in class org.opentox.toxotis.core.component.RestOperation
 
hashCode() - Method in class org.opentox.toxotis.core.OTComponent
 
hashCode() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
hashCode() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
hashCode() - Method in class org.opentox.toxotis.ontology.LiteralValue
 
hashCode() - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
hashCode() - Method in class org.opentox.toxotis.ontology.ResourceValue
 
hashCode() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
 
hashCode() - Method in class org.opentox.toxotis.util.aa.policy.PolicySubject
 
hasHTTPMethod() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
hasHTTPStatus() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
hasISBN() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasISSN() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasJournal() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasKey() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasKeywords() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasMedia() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
hasMonth() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasNumber() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasOrganization() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasPages() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasRESTOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
hasSchool() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasSeries() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasSource() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
hasStatus() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
The property ot:hasStatus assigns status values to Tasks.
hasTitle() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasURI() - Static method in class org.opentox.toxotis.ontology.collection.OTRestDatatypeProperties
 
hasURL() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasVolume() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
hasYear() - Static method in class org.opentox.toxotis.ontology.collection.KnoufDatatypeProperties
 
HEAD - Static variable in class org.opentox.toxotis.ontology.collection.HttpMethods
 
header() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for HTTP Headers.
horizontalSeparator() - Method in interface org.opentox.toxotis.core.html.HTMLContainer
 
horizontalSeparator() - Method in class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
HOST - Static variable in class org.opentox.toxotis.client.RequestHeaders
Specifies the Internet host and port number of the resource being requested.
HTMLAppendableTableImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLAppendableTableImpl(int) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
HTMLAppendableTableImpl(int, int) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
HTMLBody - Interface in org.opentox.toxotis.core.html
Body of an HTML document.
HTMLBodyImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLBodyImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLBodyImpl
 
HTMLComponent - Interface in org.opentox.toxotis.core.html
Generic interface with no abstract methods that encapsulates all HTML-related classes.
HTMLContainer - Interface in org.opentox.toxotis.core.html
A div container for HTML content.
HTMLContainerImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLContainerImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
HTMLDivBuilder - Class in org.opentox.toxotis.core.html
 
HTMLDivBuilder() - Constructor for class org.opentox.toxotis.core.html.HTMLDivBuilder
 
HTMLDivBuilder(String) - Constructor for class org.opentox.toxotis.core.html.HTMLDivBuilder
 
HTMLExpandableComponent - Interface in org.opentox.toxotis.core.html
A component that can include other HTML components in it like an HTML table.
HTMLExpandableComponentImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLExpandableComponentImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLExpandableComponentImpl
 
HTMLForm - Interface in org.opentox.toxotis.core.html
An HTML form used to accept input by end-users.
HTMLFormImpl - Class in org.opentox.toxotis.core.html.impl
An HTML Form is a container of the form:
HTMLFormImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
HTMLHead - Interface in org.opentox.toxotis.core.html
Header of an HTML document.
HTMLHeadImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLHeadImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
HTMLInput - Interface in org.opentox.toxotis.core.html
 
HTMLInput.HTMLInputType - Enum in org.opentox.toxotis.core.html
 
HTMLInputImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLInputImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
HTMLLabel - Interface in org.opentox.toxotis.core.html
A label in an HTML document.
HTMLPage - Interface in org.opentox.toxotis.core.html
A page in an HTML document.
HTMLPageBuilder - Class in org.opentox.toxotis.core.html
 
HTMLPageBuilder() - Constructor for class org.opentox.toxotis.core.html.HTMLPageBuilder
 
HTMLPageImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLPageImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLPageImpl
 
HTMLParagraph - Interface in org.opentox.toxotis.core.html
A paragraph of formatted HTML text.
HTMLParagraphImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLParagraphImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
HTMLParagraphImpl(String) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
HTMLParagraphImpl(HTMLText) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
HTMLTable - Interface in org.opentox.toxotis.core.html
A table in an HTML document.
HTMLTableRow - Interface in org.opentox.toxotis.core.html
A row of an HTML table.
HTMLTableRowFixedLength - Class in org.opentox.toxotis.core.html.impl
 
HTMLTableRowFixedLength(int) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
HTMLTag - Interface in org.opentox.toxotis.core.html
Arbitrary user-defined HTML tag.
HTMLTagImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLTagImpl(String) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
HTMLTagImpl(String, String) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
HTMLTagImpl(String, HTMLComponent) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
HTMLText - Interface in org.opentox.toxotis.core.html
Formatted text in an HTML document.
HTMLTextImpl - Class in org.opentox.toxotis.core.html.impl
 
HTMLTextImpl() - Constructor for class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
HTMLTextImpl(String) - Constructor for class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
HTMLUtils - Class in org.opentox.toxotis.core.html
Utilities for automatically creating HTML code.
HTMLUtils() - Constructor for class org.opentox.toxotis.core.html.HTMLUtils
 
HttpMediatype - Class in org.opentox.toxotis.core.component
 
HttpMediatype() - Constructor for class org.opentox.toxotis.core.component.HttpMediatype
 
HttpMediatype(VRI) - Constructor for class org.opentox.toxotis.core.component.HttpMediatype
 
HttpMethod - Class in org.opentox.toxotis.core.component
 
HttpMethod(HttpMethods.MethodsEnum) - Constructor for class org.opentox.toxotis.core.component.HttpMethod
 
httpMethod() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for an HTTP Method.
HttpMethods - Class in org.opentox.toxotis.ontology.collection
Collection of HTTP methods as ontological individuals, instances of OTRestClasses#HTTPMethod() used to describe the available methods by a web service.
HttpMethods() - Constructor for class org.opentox.toxotis.ontology.collection.HttpMethods
 
HttpMethods.MethodsEnum - Enum in org.opentox.toxotis.ontology.collection
 
HttpParameter - Class in org.opentox.toxotis.core.component
An HTTP parameter is a component that defines the parameters expected from the client on a POST request.
HttpParameter() - Constructor for class org.opentox.toxotis.core.component.HttpParameter
 
HttpParameter(VRI) - Constructor for class org.opentox.toxotis.core.component.HttpParameter
 
httpProtocol - Static variable in interface org.opentox.toxotis.client.IClient
 
httpSecureProtocol - Static variable in interface org.opentox.toxotis.client.IClient
 
HttpStatus - Class in org.opentox.toxotis.core.component
 
HttpStatus(VRI) - Constructor for class org.opentox.toxotis.core.component.HttpStatus
 
HttpStatus() - Constructor for class org.opentox.toxotis.core.component.HttpStatus
 
HttpStatus(OntologicalClass) - Constructor for class org.opentox.toxotis.core.component.HttpStatus
 
httpStatus() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
The HTTP status.
httpStatus() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for an HTTP Status.
HttpStatusCodes - Enum in org.opentox.toxotis.client
Standard HTTP status codes.
humanHealthEffects() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Effects to Human Health.

I

IBadRequest - Interface in org.opentox.toxotis.exceptions
 
IBibTexReferencable - Interface in org.opentox.toxotis.core
 
IClient - Interface in org.opentox.toxotis.client
Generic interface for a client in ToxOtis.
IClientException - Interface in org.opentox.toxotis.exceptions
 
IConnectionException - Interface in org.opentox.toxotis.exceptions
 
ideaCactvsImage() - Static method in class org.opentox.toxotis.client.collection.Services.Depiction
IDEAconsult CACTVS-based depiction service.
ideaCdkImage() - Static method in class org.opentox.toxotis.client.collection.Services.Depiction
IDEAconsult CDK-based depiction service.
ideaconsult() - Static method in class org.opentox.toxotis.client.collection.Services
URI of services by IDEAconsult ltd.
ideaDaylightImage() - Static method in class org.opentox.toxotis.client.collection.Services.Depiction
IDEAconsult DAYLIGHT-based depiction service.
IDescriptorCalculation - Interface in org.opentox.toxotis.core
An interface implemented by OpenTox components on which descriptor calculation can be applied such as Datasets and Compounds.
IF_MATCH - Static variable in class org.opentox.toxotis.client.RequestHeaders
Used with a method to make it conditional: a client that has previously obtained entities can verify that one of those entities is current by including a list of their associated entity tags in the If-Match header field.
IForbidden - Interface in org.opentox.toxotis.exceptions
 
IGetClient - Interface in org.opentox.toxotis.client
Interface for clients that perform GET requests.
IHTMLSupport - Interface in org.opentox.toxotis.core
HTML support for online resources.
IMethodNotAllowed - Interface in org.opentox.toxotis.exceptions
 
inbook() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A chapter or section in a book.
InChI_std() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
InChIKey_std() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
incollection() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
Part of a collection.
independentVariables() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
index() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
An index for a parameter value.
inHtml() - Method in class org.opentox.toxotis.core.component.Algorithm
 
inHtml() - Method in class org.opentox.toxotis.core.component.BibTeX
 
inHtml() - Method in class org.opentox.toxotis.core.component.Bookmark
 
inHtml() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
inHtml() - Method in class org.opentox.toxotis.core.component.Model
 
inHtml() - Method in class org.opentox.toxotis.core.component.Parameter
 
inHtml() - Method in class org.opentox.toxotis.core.component.Task
 
inHtml() - Method in class org.opentox.toxotis.core.component.User
 
inHtml() - Method in interface org.opentox.toxotis.core.IHTMLSupport
Create an HTML container for the online resource.
inHtml() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
initializeConnection(URI) - Method in class org.opentox.toxotis.client.AbstractClient
Initiate a connection to the remote location identified by the provided URI and using the already specified header parameters.
initializeConnection(URI) - Method in class org.opentox.toxotis.client.http.GetHttpClient
 
initializeConnection(URI) - Method in class org.opentox.toxotis.client.http.PostHttpClient
Initialize a connection to the target URI
initializeConnection(URI) - Method in class org.opentox.toxotis.client.https.DeleteHttpsClient
 
initializeConnection(URI) - Method in class org.opentox.toxotis.client.https.GetHttpsClient
 
initializeConnection(URI) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
Initialize a connection to the target URI
initializeSSLConnection() - Static method in class org.opentox.toxotis.util.aa.SSLConfiguration
 
initRdfWriter(XMLStreamWriter) - Method in class org.opentox.toxotis.core.OTComponent
 
inModel(OntModel) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
inModel(OntModel) - Method in class org.opentox.toxotis.ontology.LiteralValue
Creates a typed literal in an ontological data model.
inModel(OntModel) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
inModel(OntModel) - Method in class org.opentox.toxotis.ontology.ResourceValue
 
INotFound - Interface in org.opentox.toxotis.exceptions
 
inproceedings() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
An article published in conference proceedings.
inputParam() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
inputParameter() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters.
inputParameterCompound() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters that admit compound URIs as values.
inputParameterDataset() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters that admit Dataset URIs as values.
inputParameterDatasetService() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters that admit dataset base URIs as values and serve as dataset service URIs.
inputParameterFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters that admit feature URIs as values.
inputParameterOpenTox() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for OpenTox-style Input Parameters.
inputParameterResultDataset() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters that admit (resulting) dataset URIs as values.
inputParameterSimple() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for single-valued simple Input Parameters.
inputParameterTarget() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for Input Parameters that admit target URIs as values.
InternalServerError - Exception in org.opentox.toxotis.exceptions.impl
 
InternalServerError(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.InternalServerError
 
InternalServerError(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.InternalServerError
 
InternalServerError(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.InternalServerError
 
InternalServerError() - Constructor for exception org.opentox.toxotis.exceptions.impl.InternalServerError
 
invalidate() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Sends an invalidation request to the remote server.
inVitroReproductiveToxicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
In-Vitro Reproductive Toxicity.
inVivoPreNatalDevelopmentToxicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
In vivo pre-natal-developmental toxicity
inVivoPrePeriPostNatalDevelopment() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
In-Vivo Pre/Peri/Post-Natal Development.
IOnlineResource - Interface in org.opentox.toxotis.core
Interface for an OpenTox component that can be made available online.
IOntologyServiceSupport<T extends OTOnlineResource> - Interface in org.opentox.toxotis.core
Declares that a class is supported by the ontology service.
IOTComponent<T extends IOTComponent> - Interface in org.opentox.toxotis.core
Generic interface for all OpenTox components in ToxOtis that can be represented as individuals in an RDF graph.
IOverload - Interface in org.opentox.toxotis.exceptions
 
IPolicy - Interface in org.opentox.toxotis.util.aa.policy
 
IPolicyRule - Interface in org.opentox.toxotis.util.aa.policy
Interface for Policy Rules.
IPolicyWrapper - Interface in org.opentox.toxotis.util.aa.policy
A Policy Wrapper is a bundle of policies that can be sent/posted as one object to the openSSO server.
IPostClient - Interface in org.opentox.toxotis.client
Interface for clients that perform POST requests.
IRemoteServiceException - Interface in org.opentox.toxotis.exceptions
 
IRestOperation - Interface in org.opentox.toxotis.core
Interface documentation for a web service.
isAcceptAllCerts() - Static method in class org.opentox.toxotis.util.aa.SSLConfiguration
 
isAllowDelete() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Whether the DELETE method is allowed
isAllowDelete() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
isAllowGet() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Whether the GET method is allowed
isAllowGet() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
isAllowPost() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Whether the POST method is allowed
isAllowPost() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
isAllowPut() - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Whether the PUT method is allowed
isAllowPut() - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
isCursorFirst() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
isCursorFirst() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
isCursorLast() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
isCursorLast() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
ISecurityException - Interface in org.opentox.toxotis.exceptions
 
isEmpty() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
isEmpty() - Method in interface org.opentox.toxotis.ontology.MetaInfo
Check whether the meta info object is empty.
isEnabled() - Method in interface org.opentox.toxotis.core.IOTComponent
Whether the current entity is enabled.
isEnabled() - Method in class org.opentox.toxotis.core.OTComponent
When a component is deleted, then it is disabled.
IServerException - Interface in org.opentox.toxotis.exceptions
 
IServerFailure - Interface in org.opentox.toxotis.exceptions
 
IServiceInvocationException - Interface in org.opentox.toxotis.exceptions
 
isOpentoxParameter() - Method in class org.opentox.toxotis.core.component.HttpParameter
 
isParamOptional() - Method in class org.opentox.toxotis.core.component.HttpParameter
 
isRetrieveConformers() - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
isRetrieveDepiction() - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
isRowEmpty() - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
isRowEmpty() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
IStAXWritable - Interface in org.opentox.toxotis.core
An interface for components that can be written to an output stream using the Java streaming API for XML (StAX) using in particular some implementation of javax.xml.stream.XMLStreamWriter.
IUnauthorized - Interface in org.opentox.toxotis.exceptions
 
IUPACName() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 

J

joelib() - Static method in class org.opentox.toxotis.client.collection.Services.DescriptorCalculation
JOElib service.

K

KnoufBibTex - Class in org.opentox.toxotis.ontology.collection
A collection of all ontological classes defined by the Knouf BibTeX ontology.
KnoufDatatypeProperties - Class in org.opentox.toxotis.ontology.collection
A collection of all ontological datatype properties specified by the Knouf BibTeX ontology.

L

lazyLearning() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Lazy learning algorithm.
LDAP_Type - Variable in class org.opentox.toxotis.util.aa.policy.PolicySubject
 
learning() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Generic learning algorithm
leverage() - Static method in class org.opentox.toxotis.client.collection.Services.NtuaAlgorithms
Leverage DoA.
linkUrlsInText(String) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Detects all URLs in a given text and replaces them with HTML links using the a tag.
listAllFeatures(VRI, int, AuthenticationToken) - Static method in class org.opentox.toxotis.factory.FeatureFactory
Lists all features available from a feature service providing also an authentication token.
listAllFeatures(VRI, int, int, AuthenticationToken) - Static method in class org.opentox.toxotis.factory.FeatureFactory
Lists all features available from a feature service providing also an authentication token.
listAvailableFeatures() - Method in class org.opentox.toxotis.core.component.Compound
Performs a GET operation on /compound/{id}/feature and obtains the set of available features for this compound.
listConformers(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
Performs a HTTP GET request on /compound/{id} to acquire a URI list of all conformers providing also an authentication token (set it to null if you think there's no need for Authentication.
listElement() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
ListModelRequest - Class in org.opentox.toxotis.ontology
 
ListModelRequest() - Constructor for class org.opentox.toxotis.ontology.ListModelRequest
 
listPolicyUris(VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
List all policies that are hosted in the provided policy service.
LiteralValue<T> - Class in org.opentox.toxotis.ontology
A simple wrapper for a value (usually String) and its datatype according to the XSD specidcation (find online documentation at RNC and the complete specification at the W3C web page.
LiteralValue() - Constructor for class org.opentox.toxotis.ontology.LiteralValue
Dummy constructor for the class LiteralValue which initializes a new instance of it with null value and default class java.lang.String, or in terms of xsd datatypes, XSDDatatype.XSDstring.
LiteralValue(T, XSDDatatype) - Constructor for class org.opentox.toxotis.ontology.LiteralValue
Create a new typed value with given value and XSD datatype.
LiteralValue(T) - Constructor for class org.opentox.toxotis.ontology.LiteralValue
Create a Typed value with no explicit type declaration.
loadDefaultProperties() - Static method in class org.opentox.toxotis.core.html.GoogleAnalytics
 
loadFromRemote(InputStream, VRI) - Method in class org.opentox.toxotis.core.component.Algorithm
Allows algorithms to be created from arbitrary input sources (in general files, URLs or other).Note that this is still an experimental method.
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Algorithm
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.BibTeX
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
This method is not implemented yet!
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Conformer
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Dataset
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Feature
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Model
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Task
 
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.User
 
loadFromRemote() - Method in class org.opentox.toxotis.core.OTOnlineResource
Update the current component according to some remote resource.
loadFromRemote(AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
Downloads and parses a component that is hosted on a remote location identified by the URI of the underlying component as returned by the method OTComponent.getUri().
loadFromRemote(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTOnlineResource
Loads an OpenTox component from a remote location identified by its uri and parses it into an instance of T.
LoggingConfiguration - Class in org.opentox.toxotis.util
Helper for LOG4J global configuration.
LoggingConfiguration() - Constructor for class org.opentox.toxotis.util.LoggingConfiguration
 
login(String, String) - Method in class org.opentox.toxotis.util.aa.TokenPool
 
login(File) - Method in class org.opentox.toxotis.util.aa.TokenPool
Login and acquire an authentication token that you can use to access OpenTox services
login(String) - Method in class org.opentox.toxotis.util.aa.TokenPool
 
logout(String) - Method in class org.opentox.toxotis.util.aa.TokenPool
Logs out a user identified by its username.
logoutAll() - Method in class org.opentox.toxotis.util.aa.TokenPool
 
lookUpComponent(VRI, String) - Method in class org.opentox.toxotis.factory.CompoundFactory
 
lookupSameAs(VRI, OntologicalClass, AuthenticationToken) - Static method in class org.opentox.toxotis.factory.FeatureFactory
Retrieve a collection of Feature URIs that are same as a certain ECHA endpoint as these are formalized using the OpenTox ontology.
lookupSameAs(OntologicalClass, AuthenticationToken) - Static method in class org.opentox.toxotis.factory.FeatureFactory
Retrieve a collection of Feature URIs by querying a default Feature Service, that are same as a certain ECHA endpoint as these are formalized using the OpenTox ontology.

M

main(String...) - Static method in class org.opentox.toxotis.profiler.ProfileMe
 
main(String...) - Static method in class org.opentox.toxotis.util.aa.PasswordFileManager
 
main(String...) - Static method in class org.opentox.toxotis.util.PolicyCreator
 
manual() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A user's manual
mastersThesis() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A master's thesis.
MAX_FORWARDS - Static variable in class org.opentox.toxotis.client.RequestHeaders
Provides a mechanism with the TRACE and OPTIONS methods to limit the number of proxies or gateways that can forward the request to the next inbound server.
Media - Enum in org.opentox.toxotis.client.collection
A collection of useful mediatypes.
mediaType() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for MIME types.
meltingPoint() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Melting Point at atmospheric pressure.
MEMBER - Static variable in class org.opentox.toxotis.util.aa.policy.GroupSubject
All OpenTox members as a group, including the user guest:guest.
message() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
A message returned by an exceptional event providing very essential information about it.
meta - Variable in class org.opentox.toxotis.core.OTComponent
Meta information (including DC and OT meta) about the component
MetaInfo - Interface in org.opentox.toxotis.ontology
Interface describing meta-information for a resource.
MetaInfoBlobber - Class in org.opentox.toxotis.ontology
 
MetaInfoBlobber(MetaInfo) - Constructor for class org.opentox.toxotis.ontology.MetaInfoBlobber
 
MetaInfoDeblobber - Class in org.opentox.toxotis.ontology
 
MetaInfoDeblobber(Blob) - Constructor for class org.opentox.toxotis.ontology.MetaInfoDeblobber
 
MetaInfoImpl - Class in org.opentox.toxotis.ontology.impl
 
MetaInfoImpl() - Constructor for class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
MetaInfoSpider - Class in org.opentox.toxotis.util.spiders
Parser of meta information over a given resource in an RDF graph.
MetaInfoSpider(OntModel, String) - Constructor for class org.opentox.toxotis.util.spiders.MetaInfoSpider
 
MetaInfoSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.MetaInfoSpider
 
METHOD - Static variable in class org.opentox.toxotis.client.https.DeleteHttpsClient
The method that this client applies
METHOD - Static variable in interface org.opentox.toxotis.client.IGetClient
 
METHOD - Static variable in interface org.opentox.toxotis.client.IPostClient
The method that this client applies
MethodNotAllowed - Exception in org.opentox.toxotis.exceptions.impl
 
MethodNotAllowed(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.MethodNotAllowed
 
MethodNotAllowed(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.MethodNotAllowed
 
MethodNotAllowed(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.MethodNotAllowed
 
MethodNotAllowed() - Constructor for exception org.opentox.toxotis.exceptions.impl.MethodNotAllowed
 
mimeChemicalInchi() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the InChI MIME type.
mimeChemicalMol() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the chemical/MOL MIME type.
mimeChemicalSdf() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the chemical/SDF MIME type.
mimeChemicalSmiles() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the chemical/SMILES MIME type.
mimeJson() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the JSON MIME type.
mimeRdfJson() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the RDF/JSON MIME type.
mimeRdfN3() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the RDF/N3 MIME type.
mimeRdfTurtle() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the RDF/Turtle MIME type.
mimeRdfXml() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the RDF/XML MIME type.
mimeTextCsv() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the text/CSV MIME type.
mimeTextHtml() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the text/HTML MIME type.
mimeTextPlain() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the plain-text MIME type.
mimeTextUriList() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the text/URI-list MIME type.
mimeWekaArff() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the Weka ARFF MIME type.
miscellaneous() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
Miscellaneous.
mlr() - Static method in class org.opentox.toxotis.client.collection.Services.NtuaAlgorithms
Multiple Linear Regression.
Model - Class in org.opentox.toxotis.core.component
QSAR, DoA or other OpenTox models.
Model(VRI) - Constructor for class org.opentox.toxotis.core.component.Model
Create a new empty Model with a given URI.
Model() - Constructor for class org.opentox.toxotis.core.component.Model
Creates an empty model.
model() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
A model.
model() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
model - Variable in class org.opentox.toxotis.util.spiders.Tarantula
The data model which is used in the parsing procedure and also hold the base resource
ModelSpider - Class in org.opentox.toxotis.util.spiders
Downloader and Parser for RDF representation of OpenTox Model resources.
ModelSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.ModelSpider
 
ModelSpider(VRI, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.spiders.ModelSpider
 
ModelSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.ModelSpider
 
ModelSpider(OntModel, String) - Constructor for class org.opentox.toxotis.util.spiders.ModelSpider
 
moveCursorAt(int) - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
moveCursorAt(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
msdmTox() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
MultiParameter - Class in org.opentox.toxotis.core.component
 
MultiParameter() - Constructor for class org.opentox.toxotis.core.component.MultiParameter
 
multiParameter() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
multiParameter() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
Assigns a multi-parameter (ot:MultiParameter) to a Model or an Algorithm
MultiParameterSpider - Class in org.opentox.toxotis.util.spiders
 
MultiParameterSpider() - Constructor for class org.opentox.toxotis.util.spiders.MultiParameterSpider
 
multipleTargets() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
Multiple Targets Trainer.
multiTaskTemplate() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An OpenTox APIv1.2-compliant URI-template for Multi-Tasks.
mutagenicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Mutagenicity.

N

nextBibTeX() - Method in class org.opentox.toxotis.util.ROG
 
nextBoolean() - Method in class org.opentox.toxotis.util.ROG
 
nextBytes(byte[]) - Method in class org.opentox.toxotis.util.ROG
 
nextData() - Method in class org.opentox.toxotis.util.arff.RemoteArffRertiever
 
nextDouble() - Method in class org.opentox.toxotis.util.ROG
 
nextErrorReport(int) - Method in class org.opentox.toxotis.util.ROG
 
nextFloat() - Method in class org.opentox.toxotis.util.ROG
 
nextGaussian() - Method in class org.opentox.toxotis.util.ROG
 
nextInt(int) - Method in class org.opentox.toxotis.util.ROG
 
nextInt() - Method in class org.opentox.toxotis.util.ROG
 
nextLong() - Method in class org.opentox.toxotis.util.ROG
 
nextMeta() - Method in class org.opentox.toxotis.util.ROG
 
nextModel() - Method in class org.opentox.toxotis.util.ROG
 
nextReport(int) - Method in class org.opentox.toxotis.util.ROG
 
nextRow() - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
nextRow() - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
nextString(int) - Method in class org.opentox.toxotis.util.ROG
 
nextTask(int) - Method in class org.opentox.toxotis.util.ROG
 
nextTaskStatus() - Method in class org.opentox.toxotis.util.ROG
 
nextUser() - Method in class org.opentox.toxotis.util.ROG
 
nextVri() - Method in class org.opentox.toxotis.util.ROG
 
nominal() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
nominalFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
normalization() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
normalizeTextForHtml(String) - Static method in class org.opentox.toxotis.core.html.HTMLUtils
Normalizes a text for use in HTML.
NotFound - Exception in org.opentox.toxotis.exceptions.impl
 
NotFound(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.NotFound
 
NotFound(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.NotFound
 
NotFound(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.NotFound
 
NotFound() - Constructor for exception org.opentox.toxotis.exceptions.impl.NotFound
 
NS - Static variable in class org.opentox.toxotis.ontology.collection.KnoufBibTex
 
NS - Static variable in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
NameSpace of all algorithm ontological classes.
NS - Static variable in class org.opentox.toxotis.ontology.collection.OTClasses
The OpenTox ontology NameSpace.
NS - Static variable in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
 
NS - Static variable in class org.opentox.toxotis.ontology.collection.OTFeatures
 
NS - Static variable in class org.opentox.toxotis.ontology.collection.OTRestClasses
NameSpace of the OpenTox ontology.
NS - Static variable in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
NameSpace of the OpenTox REST ontology.
ntua() - Static method in class org.opentox.toxotis.client.collection.Services
URI of the NTUA (National Technical University of Athens) resources.
numeric() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
numericFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 

O

OntologicalClass - Interface in org.opentox.toxotis.ontology
ToxOtis interface for ontological classes.
OntologicalClassImpl - Class in org.opentox.toxotis.ontology.impl
 
OntologicalClassImpl() - Constructor for class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
Construct an empty instance of OntologicalClass.
OntologicalClassImpl(String) - Constructor for class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
Create a new Ontological Class with given name.
OntologicalClassImpl(String, String) - Constructor for class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
Constructs a new Ontological class with given name and namespace.
opentox() - Static method in class org.opentox.toxotis.client.collection.Services
The OpenTox main URI.
OpenToxAlgorithms - Enum in org.opentox.toxotis.client.collection
 
openToxResource() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
Superclass for all OpenTox resources.
operationAlgorithm() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation on an algorithm.
operationFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation on a feature.
operationInputCompound() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that requires compounds as input.
operationInputDataset() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that requires datasets as input.
operationInputFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that processes features or in any other way uses features as input.
operationModel() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Any operation on a Model.
operationNoResult() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that does not necessarily return some response such as a DELETE operation.
operationResultAlgorithm() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that results in an algorithm that is returned to the client.
operationResultDataset() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that results in a dataset being created.
operationResultFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that results in a feature being created.
operationResultModel() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that results in a model being created.
operationResultTask() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation that results in a task being created.
operationTask() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An operation on a Task resource.
OPTIONS - Static variable in class org.opentox.toxotis.ontology.collection.HttpMethods
 
org.opentox.toxotis - package org.opentox.toxotis
Container package for all classes and packages in ToxOtis.
org.opentox.toxotis.client - package org.opentox.toxotis.client
Clients used to access remote resources and perform elaborate RESTful requests.
org.opentox.toxotis.client.collection - package org.opentox.toxotis.client.collection
Collection of useful URIs and MIME Types, ready to use.
org.opentox.toxotis.client.http - package org.opentox.toxotis.client.http
HTTP Client implementations of the client API of ToxOtis.
org.opentox.toxotis.client.https - package org.opentox.toxotis.client.https
Secure Client implementations of the client API of ToxOtis.
org.opentox.toxotis.core - package org.opentox.toxotis.core
Core package of ToxOtis where the most important classes and interfaces are found.
org.opentox.toxotis.core.component - package org.opentox.toxotis.core.component
Basic components of the project which fall in one or more categories specified by the interfaces in oeg.opentox.toxotis.core.
org.opentox.toxotis.core.component.qprf - package org.opentox.toxotis.core.component.qprf
 
org.opentox.toxotis.core.html - package org.opentox.toxotis.core.html
Interfaces for the manipulation and creation of HTML documents.
org.opentox.toxotis.core.html.impl - package org.opentox.toxotis.core.html.impl
Implementations of the interfaces in org.opentox.toxotis.core.html.
org.opentox.toxotis.exceptions - package org.opentox.toxotis.exceptions
 
org.opentox.toxotis.exceptions.impl - package org.opentox.toxotis.exceptions.impl
 
org.opentox.toxotis.factory - package org.opentox.toxotis.factory
Factories for the creation of ToxOtis components (implementations of IOTComponent).
org.opentox.toxotis.ontology - package org.opentox.toxotis.ontology
Facilitate the manipulation of ontological entities using this package.
org.opentox.toxotis.ontology.collection - package org.opentox.toxotis.ontology.collection
A collection of ontological specifications like the OpenTox ontology for algorithms (OTA) and the Knouf BibTeX ontology.
org.opentox.toxotis.ontology.impl - package org.opentox.toxotis.ontology.impl
Implementations for ontological entities like models, properties and classes.
org.opentox.toxotis.profiler - package org.opentox.toxotis.profiler
 
org.opentox.toxotis.training - package org.opentox.toxotis.training
Trainers for models exploiting remote OpenTox web services.
org.opentox.toxotis.util - package org.opentox.toxotis.util
Utilities for toxotis including AA functionality and spiders (parsers).
org.opentox.toxotis.util.aa - package org.opentox.toxotis.util.aa
Security facilities for ToxOtis like Authentication and Authorization against an SSo server providing the User's credentials.
org.opentox.toxotis.util.aa.policy - package org.opentox.toxotis.util.aa.policy
Policy management tools for listing, creating, deleting and retrieving the owner of a policy.
org.opentox.toxotis.util.arff - package org.opentox.toxotis.util.arff
 
org.opentox.toxotis.util.spiders - package org.opentox.toxotis.util.spiders
Downloaders and RDF parsers for ToxOtis components.
OTAlgorithmTypes - Class in org.opentox.toxotis.ontology.collection
A collection of all algorithm types specified in OpenTox.
OTClasses - Class in org.opentox.toxotis.ontology.collection
Collection of all Ontological Classes defined in OpenTox.
OTComponent<T extends IOTComponent> - Class in org.opentox.toxotis.core
Abstract class that includes all OpenTox components.
OTComponent() - Constructor for class org.opentox.toxotis.core.OTComponent
Constructor for an empty OpenTox Component
OTComponent(VRI) - Constructor for class org.opentox.toxotis.core.OTComponent
 
OTDatatypeProperties - Class in org.opentox.toxotis.ontology.collection
Collection of datatype properties used in OpenTox.
OTDatatypeProperty - Interface in org.opentox.toxotis.ontology

According to the OWL specification provided by W3C, datatype properties link individuals to data values.

OTDatatypePropertyImpl - Class in org.opentox.toxotis.ontology.impl
 
OTDatatypePropertyImpl() - Constructor for class org.opentox.toxotis.ontology.impl.OTDatatypePropertyImpl
 
OTDatatypePropertyImpl(String) - Constructor for class org.opentox.toxotis.ontology.impl.OTDatatypePropertyImpl
 
OTEchaEndpoints - Class in org.opentox.toxotis.ontology.collection
Collection of ECHA endpoints.
OTEchaEndpoints() - Constructor for class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
 
OTFeatures - Class in org.opentox.toxotis.ontology.collection
Collection of all features defined in the OpenTox ontology.
OTFeatures() - Constructor for class org.opentox.toxotis.ontology.collection.OTFeatures
 
other() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Other (e.g.
OTObjectProperties - Class in org.opentox.toxotis.ontology.collection
Collection of all object propertied used in OpenTox (API version 1.1).
OTObjectProperty - Interface in org.opentox.toxotis.ontology
Object properties link individuals to individuals.
OTObjectPropertyImpl - Class in org.opentox.toxotis.ontology.impl
 
OTObjectPropertyImpl() - Constructor for class org.opentox.toxotis.ontology.impl.OTObjectPropertyImpl
 
OTObjectPropertyImpl(String) - Constructor for class org.opentox.toxotis.ontology.impl.OTObjectPropertyImpl
 
OTObjectPropertyImpl(String, String) - Constructor for class org.opentox.toxotis.ontology.impl.OTObjectPropertyImpl
 
OTOnlineResource<T extends OTOnlineResource> - Class in org.opentox.toxotis.core
Any OTComponent that can be available online and has a URL.
OTOnlineResource(VRI) - Constructor for class org.opentox.toxotis.core.OTOnlineResource
Construct an OpenTox online resource providing its URI.
OTOnlineResource() - Constructor for class org.opentox.toxotis.core.OTOnlineResource
Construct a new instance of OTOnlineResource.
OTProperty - Interface in org.opentox.toxotis.ontology
An interface for ontological properties used in OpenTox web services.
OTPropertyImpl - Class in org.opentox.toxotis.ontology.impl
 
OTPropertyImpl() - Constructor for class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
OTPropertyImpl(String) - Constructor for class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
OTPropertyImpl(String, String) - Constructor for class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
OTPublishable<T extends OTPublishable> - Class in org.opentox.toxotis.core

An OpenTox component is OTPublishable if it is a class of online resources that can be created by clients, i.e.

OTPublishable() - Constructor for class org.opentox.toxotis.core.OTPublishable
Create a new empty publishable object
OTPublishable(VRI) - Constructor for class org.opentox.toxotis.core.OTPublishable
Create a new publishable object providing its URI
OTResource - Interface in org.opentox.toxotis.ontology
Interface for resources that appear in ontological represnetations in OpenTox.
OTRestClasses - Class in org.opentox.toxotis.ontology.collection
Collection of ontological classes needed to define the REST interface operations over a URI that provides access to web services.
OTRestDatatypeProperties - Class in org.opentox.toxotis.ontology.collection
 
OTRestDatatypeProperties() - Constructor for class org.opentox.toxotis.ontology.collection.OTRestDatatypeProperties
 
OTRestObjectProperties - Class in org.opentox.toxotis.ontology.collection
OpenTox REST Object Properties.
OTRestObjectProperties() - Constructor for class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 

P

Pair<K extends Serializable,V extends Serializable> - Class in org.opentox.toxotis.client
A Pair is a simple implementation of the interface Map.Entry.
Pair(K, V) - Constructor for class org.opentox.toxotis.client.Pair
Construct a new pair with a key and a value.
Pair() - Constructor for class org.opentox.toxotis.client.Pair
Dummy constructor which is protected to allow for subclassing of this class.
paramContent() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
paramContentOpenTox() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
paramContentSimple() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
Parameter<T> - Class in org.opentox.toxotis.core.component
A parameter of an Algorithm characterized by its name, value and scope.
Parameter() - Constructor for class org.opentox.toxotis.core.component.Parameter
 
Parameter(VRI) - Constructor for class org.opentox.toxotis.core.component.Parameter
 
Parameter(String, LiteralValue) - Constructor for class org.opentox.toxotis.core.component.Parameter
 
Parameter(VRI, String, LiteralValue) - Constructor for class org.opentox.toxotis.core.component.Parameter
 
parameter() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
Parameter.ParameterScope - Enum in org.opentox.toxotis.core.component
The scope of the parameter of an Algorithm that can either be Mandatory or Optional.
parameters() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
ParameterSpider - Class in org.opentox.toxotis.util.spiders
Parser for Parameter resources in a given RDF graph.
ParameterSpider(OntModel, Resource) - Constructor for class org.opentox.toxotis.util.spiders.ParameterSpider
ParameterSpider constructor with an ontological resource and an ontological model.
ParameterValue - Class in org.opentox.toxotis.core.component
 
ParameterValue() - Constructor for class org.opentox.toxotis.core.component.ParameterValue
 
ParameterValue(VariableValue...) - Constructor for class org.opentox.toxotis.core.component.ParameterValue
 
ParameterValue(int, VariableValue...) - Constructor for class org.opentox.toxotis.core.component.ParameterValue
 
parameterValue() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
parameterValues() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
paramName() - Static method in class org.opentox.toxotis.ontology.collection.OTRestDatatypeProperties
 
paramOptional() - Static method in class org.opentox.toxotis.ontology.collection.OTRestDatatypeProperties
 
paramScope() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
 
paramValue() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
A parameter value.
parse() - Method in class org.opentox.toxotis.util.spiders.AlgorithmSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.BibTeXSprider
 
parse() - Method in class org.opentox.toxotis.util.spiders.CompoundSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.ConformerSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.DataEntrySpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.DatasetSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.ErrorReportSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.FeatureSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.FeatureValueSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.MetaInfoSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.ModelSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.ParameterSpider
 
parse() - Method in class org.opentox.toxotis.util.spiders.Tarantula
Parse the data model of an OpenTox entity and create an ToxOtis object according to the data content of the data model.
parse() - Method in class org.opentox.toxotis.util.spiders.TaskSpider
 
parsePolicy(String, VRI, AuthenticationToken) - Static method in class org.opentox.toxotis.util.aa.policy.PolicyManager
 
parseTime - Variable in class org.opentox.toxotis.util.spiders.Tarantula
Computational time needed for the parsing of the data model.
PARTNER - Static variable in class org.opentox.toxotis.util.aa.policy.GroupSubject
Group of all partners in OpenTox.
PasswordFileManager - Class in org.opentox.toxotis.util.aa

Create highly secure password files to store your credentials.

percentageCompleted() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
The percentage to which a task is complete.
phdThesis() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A PhD thesis.
photoCarcinogenicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Photo-carcinogenicity.
photoMutagenicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Photo-mutagenicity.
photoSensitisation() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Photo-sensitisation.
physicoChemicalEffects() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Physicochemical Effects
Policy - Class in org.opentox.toxotis.util.aa.policy
An authentication/authorization policy defines explicitly the way in which clients are granted permissions to access certain resource and perform HTTP requests.
Policy() - Constructor for class org.opentox.toxotis.util.aa.policy.Policy
New empty policy.
Policy(String) - Constructor for class org.opentox.toxotis.util.aa.policy.Policy
New policy with a policy name.
PolicyCreator - Class in org.opentox.toxotis.util
 
PolicyCreator() - Constructor for class org.opentox.toxotis.util.PolicyCreator
 
PolicyManager - Class in org.opentox.toxotis.util.aa.policy
Utilities for policy creation, deletion and parsing.
PolicyRule - Class in org.opentox.toxotis.util.aa.policy
A Rule in a policy that defined the behavior of the SSO service when permission is asked on a target URI for some method.
PolicyRule(String) - Constructor for class org.opentox.toxotis.util.aa.policy.PolicyRule
 
PolicySubject - Class in org.opentox.toxotis.util.aa.policy
Any subject of a policy that can either be an individual user or a group of such.
PolicySubject() - Constructor for class org.opentox.toxotis.util.aa.policy.PolicySubject
 
PolicyWrapper - Class in org.opentox.toxotis.util.aa.policy
 
PolicyWrapper() - Constructor for class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
PolicyWrapper(Policy...) - Constructor for class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
post() - Method in class org.opentox.toxotis.client.http.PostHttpClient
According to the the configuration of the PostHttpClient, performs a remote POST request to the server identified by the URI provided in the constructor.
post() - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
post() - Method in interface org.opentox.toxotis.client.IPostClient
According to the the configuration of the PostHttpClient, permorms a remote POST request to the server identified by the URI provided in the contructor.
POST - Static variable in class org.opentox.toxotis.ontology.collection.HttpMethods
 
postAlgorithmCreateModel() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for a POST operation on an algorithm that creates a model.
postAlgorithmProcessCompound() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for a POST operation on an algorithm that processes a compound.
postAlgorithmProcessDataset() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for a POST operation on an algorithm that (pre)processes a dataset.
postFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for an POST operation on a feature.
PostHttpClient - Class in org.opentox.toxotis.client.http
A client used to perform POST operations.
PostHttpClient() - Constructor for class org.opentox.toxotis.client.http.PostHttpClient
 
PostHttpClient(VRI) - Constructor for class org.opentox.toxotis.client.http.PostHttpClient
 
PostHttpsClient - Class in org.opentox.toxotis.client.https
 
PostHttpsClient() - Constructor for class org.opentox.toxotis.client.https.PostHttpsClient
 
PostHttpsClient(VRI) - Constructor for class org.opentox.toxotis.client.https.PostHttpsClient
 
postModel() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for an POST operation on a model.
postOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the POST REST operation.
predictedVariables() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
prediction() - Method in class org.opentox.toxotis.util.SuperPredictor
 
preprocessing() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
previousRow() - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
previousRow() - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
ProfileMe - Class in org.opentox.toxotis.profiler
 
ProfileMe() - Constructor for class org.opentox.toxotis.profiler.ProfileMe
 
PROXY_AUTHORIZATION - Static variable in class org.opentox.toxotis.client.RequestHeaders
Used by a client to identify itself (or its user) to a proxy which requires authentication.
publish(VRI, AuthenticationToken, ExecutorService) - Method in class org.opentox.toxotis.core.OTPublishable
 
publish(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTPublishable
 
publish(VRI, AuthenticationToken) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyWrapper
Publish this policy to a remote server and acquire a URI for it.
publish(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.util.aa.policy.Policy
Publish this policy to a remote server and acquire a URI for it.
publish(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
publishFromFile(File, String, AuthenticationToken) - Method in class org.opentox.toxotis.factory.CompoundFactory
POSTs a file to a default compound service using a specified Content-type header in order to create a new Compound.
publishFromFile(File, Media, AuthenticationToken) - Method in class org.opentox.toxotis.factory.CompoundFactory
POSTs a file to a default compound service using a specified Content-type header in order to create a new Compound.
publishFromFile(File, String, AuthenticationToken, String) - Method in class org.opentox.toxotis.factory.CompoundFactory
POSTs a file to a specified compound service using a specified Content-type header in order to create a new Compound.
publishFromFile(File, Media, AuthenticationToken, String) - Method in class org.opentox.toxotis.factory.CompoundFactory
POSTs a file to a specified compound service using a specified Content-type header in order to create a new Compound.
publishFromFile(File, String, AuthenticationToken, VRI) - Method in class org.opentox.toxotis.factory.DatasetFactory
Publishes a dataset reading from a file.
publishFromFile(File, Media, AuthenticationToken, VRI) - Method in class org.opentox.toxotis.factory.DatasetFactory
 
publishFromFile(File, Media, AuthenticationToken) - Method in class org.opentox.toxotis.factory.DatasetFactory
 
publishFromStream(InputStream, String, AuthenticationToken, String) - Method in class org.opentox.toxotis.factory.CompoundFactory
 
publishFromStream(InputStream, Media, AuthenticationToken, String) - Method in class org.opentox.toxotis.factory.CompoundFactory
 
publishFromStream(InputStream, Media, AuthenticationToken) - Method in class org.opentox.toxotis.factory.CompoundFactory
 
publishFromStream(InputStream, String, AuthenticationToken) - Method in class org.opentox.toxotis.factory.CompoundFactory
 
publishFromStream(InputStream, String, AuthenticationToken, VRI) - Method in class org.opentox.toxotis.factory.DatasetFactory
 
publishFromStream(InputStream, Media, AuthenticationToken) - Method in class org.opentox.toxotis.factory.DatasetFactory
 
publishOnline(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.BibTeX
 
publishOnline(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.BibTeX
Publishes the BibTeX object to the bibtex service that corresponds to the URI that is returned by the method getUri().
publishOnline(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
 
publishOnline(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Compound
 
publishOnline(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Dataset
 
publishOnline(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Dataset
 
publishOnline(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Feature
 
publishOnline(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Feature
 
publishOnline(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
publishOnline(AuthenticationToken) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
publishOnline(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.OTPublishable
Publish the component to a proper server identified by the uri of the publishing service provided in this method.
publishOnline(AuthenticationToken) - Method in class org.opentox.toxotis.core.OTPublishable
Publish the component to a standard (default) server.
publishToOntService(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Algorithm
 
publishToOntService(VRI, AuthenticationToken) - Method in class org.opentox.toxotis.core.component.Model
 
publishToOntService(VRI, AuthenticationToken) - Method in interface org.opentox.toxotis.core.IOntologyServiceSupport
Publishes the underlying component to the ontology service.
PUT - Static variable in class org.opentox.toxotis.ontology.collection.HttpMethods
 
putFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
A PUT operation on a feature.
putOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the PUT REST operation.

Q

QprfAuthor - Class in org.opentox.toxotis.core.component.qprf
 
QprfAuthor() - Constructor for class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
QprfAuthor(String, String, String, String, String, String, String) - Constructor for class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
QprfReport - Class in org.opentox.toxotis.core.component.qprf
 
QprfReport() - Constructor for class org.opentox.toxotis.core.component.qprf.QprfReport
 
QprfReport(VRI) - Constructor for class org.opentox.toxotis.core.component.qprf.QprfReport
 
qprfReport() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
A QPRF report.
QprfReportMeta - Class in org.opentox.toxotis.core.component.qprf
 
QprfReportMeta() - Constructor for class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
QprfReportMetaDeserializer - Class in org.opentox.toxotis.core.component.qprf
 
QprfReportMetaDeserializer(Blob) - Constructor for class org.opentox.toxotis.core.component.qprf.QprfReportMetaDeserializer
 
QprfReportMetaSerializer - Class in org.opentox.toxotis.core.component.qprf
 
QprfReportMetaSerializer(QprfReportMeta) - Constructor for class org.opentox.toxotis.core.component.qprf.QprfReportMetaSerializer
 

R

RANGE - Static variable in class org.opentox.toxotis.client.RequestHeaders
Restricts the request to some part(s), specified as range(s) of octets, in the resource.
RDF_ABOUT - Static variable in class org.opentox.toxotis.core.OTComponent
 
RDF_RDF - Static variable in class org.opentox.toxotis.core.OTComponent
 
RDF_RESOURCE - Static variable in class org.opentox.toxotis.core.OTComponent
 
RDF_TYPE - Static variable in class org.opentox.toxotis.core.OTComponent
 
REACHRegistrationDate() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
readRemoteTime - Variable in class org.opentox.toxotis.util.spiders.Tarantula
Time in ms that was needed for the reading the data model from the remote location identified by the URI of the parsed entity.
readString(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Create a new BibTeX resource from its String representation.
readString(InputStream) - Method in class org.opentox.toxotis.core.component.BibTeX
Create a new BibTeX resource from its String representation.
readString(Reader) - Method in class org.opentox.toxotis.core.component.BibTeX
Create a new BibTeX resource from its String representation.
readString(File) - Method in class org.opentox.toxotis.core.component.BibTeX
Reads from a file and parses a BibTeX document into an instance of BibTeX.
receptorBinding() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Receptor Binding.
receptorBindingAndGeneExpression() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Receptor Binding and Gene Expression.
REFERER - Static variable in class org.opentox.toxotis.client.RequestHeaders
Used by a client to specify, for the server's benefit, the address (URI) of the resource from which the Request-URI was obtained.
regression() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
RemoteArffRertiever - Class in org.opentox.toxotis.util.arff
 
RemoteArffRertiever(VRI) - Constructor for class org.opentox.toxotis.util.arff.RemoteArffRertiever
 
RemoteServiceException - Exception in org.opentox.toxotis.exceptions.impl
 
RemoteServiceException(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.RemoteServiceException
 
RemoteServiceException(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.RemoteServiceException
 
RemoteServiceException(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.RemoteServiceException
 
RemoteServiceException() - Constructor for exception org.opentox.toxotis.exceptions.impl.RemoteServiceException
 
removeFeatureValue(int) - Method in class org.opentox.toxotis.core.component.DataEntry
 
removeUrlParameter(String) - Method in class org.opentox.toxotis.client.VRI
Removes all parameters that match the given parameter name.
repeatedDoseToxicity() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Repeated-dose toxicity.
report() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
Any kind of report (QPRF, QMRP or other).
RequestHeaders - Class in org.opentox.toxotis.client
This is a collection of some HTTP Request and Entity Headers gathered from the W3C specifications at http://www.w3.org/Protocols/rfc2616/rfc2616.html.
RequestHeaders() - Constructor for class org.opentox.toxotis.client.RequestHeaders
 
resource() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
resource - Variable in class org.opentox.toxotis.util.spiders.Tarantula
The core resource that is to be parsed out of the datamodel into an OpenTox component object.
ResourceValue - Class in org.opentox.toxotis.ontology
A wrapper for a Resource assigned to some other resource through an Object property acting as a value for that property.
ResourceValue(VRI, OntologicalClass) - Constructor for class org.opentox.toxotis.ontology.ResourceValue
 
respiratorySensitisation() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Respiratory sensitisation.
RestOperation - Class in org.opentox.toxotis.core.component
An implementation of IRestOperation
RestOperation() - Constructor for class org.opentox.toxotis.core.component.RestOperation
Dummy constructor for the class RestOperation that creates an empty instance of it.
RestOperation(VRI) - Constructor for class org.opentox.toxotis.core.component.RestOperation
 
restOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for REST operations (using HTTP methods).
restTemplate() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An OpenTox APIv1.2-compliant URI-template.
restTemplateAttribute() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
 
result() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
resultURI() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
The result URI of a task.
RetriableRequest<T> - Class in org.opentox.toxotis.util
An invocation that will be repeated after a certain time if it fails.
RetriableRequest(Method, Object) - Constructor for class org.opentox.toxotis.util.RetriableRequest
 
retrievePropertyLiterals(Property) - Method in class org.opentox.toxotis.util.spiders.Tarantula
 
retrievePropertyNodes(Property) - Method in class org.opentox.toxotis.util.spiders.Tarantula
 
retry(int, long, Object...) - Method in class org.opentox.toxotis.util.RetriableRequest
 
retry(int, long) - Method in class org.opentox.toxotis.util.RetriableRequest
 
ROG - Class in org.opentox.toxotis.util
Random Object Generator
ROG() - Constructor for class org.opentox.toxotis.util.ROG
 

S

ServiceInvocationException - Exception in org.opentox.toxotis.exceptions.impl
Generic exception includes all kinds of possible exceptional events that might
ServiceInvocationException() - Constructor for exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
Creates a new instance of ServiceInvocationException without detail message.
ServiceInvocationException(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
Constructs an instance of ServiceInvocationException with the specified detail message.
ServiceInvocationException(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
ServiceInvocationException(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
ServiceRestDocumentation - Class in org.opentox.toxotis.core.component
Provides a machine-readable documentation for the consumption of all available services provided including information about diffferent HTTP methods, possible status codes, input parameters and more.
ServiceRestDocumentation(IOTComponent) - Constructor for class org.opentox.toxotis.core.component.ServiceRestDocumentation
A ServiceRestDocumentation object should be initialized with an OpenTox component.
Services - Class in org.opentox.toxotis.client.collection
A collection of URIs of services that participate in the OpenTox net.
Services() - Constructor for class org.opentox.toxotis.client.collection.Services
 
Services.Depiction - Class in org.opentox.toxotis.client.collection
Services that create a depiction of a given chemical.
Services.Depiction() - Constructor for class org.opentox.toxotis.client.collection.Services.Depiction
 
Services.DescriptorCalculation - Class in org.opentox.toxotis.client.collection
Descriptor calculation services.
Services.DescriptorCalculation() - Constructor for class org.opentox.toxotis.client.collection.Services.DescriptorCalculation
 
Services.NtuaAlgorithms - Class in org.opentox.toxotis.client.collection
Algorithms implemented by NTUA.
Services.NtuaAlgorithms() - Constructor for class org.opentox.toxotis.client.collection.Services.NtuaAlgorithms
 
Services.SingleSignOn - Class in org.opentox.toxotis.client.collection
SSO-related services.
Services.SingleSignOn() - Constructor for class org.opentox.toxotis.client.collection.Services.SingleSignOn
 
setAbstract(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the abstract.
setAcceptAllCerts(boolean) - Static method in class org.opentox.toxotis.util.aa.SSLConfiguration
 
setActionUrl(String) - Method in interface org.opentox.toxotis.core.html.HTMLForm
 
setActionUrl(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
setActor(String) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
setActor(String) - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
setActor(String) - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
setActualModel(Serializable) - Method in class org.opentox.toxotis.core.component.Model
Set the actual model.
setAddress(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the address of the publisher or other type of institution.
setAddress(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setAdmissibleValues(Set<LiteralValue>) - Method in class org.opentox.toxotis.core.component.Feature
 
setAffiliation(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setAlgorithm(Algorithm) - Method in class org.opentox.toxotis.core.component.Model
Specify the algorithm that was used to train the model.
setAlgorithm(Algorithm) - Method in class org.opentox.toxotis.training.Trainer
 
setAlignment(Alignment) - Method in interface org.opentox.toxotis.core.html.HTMLContainer
 
setAlignment(Alignment) - Method in interface org.opentox.toxotis.core.html.HTMLParagraph
 
setAlignment(Alignment) - Method in class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
setAlignment(Alignment) - Method in class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
setAllowances(boolean, boolean, boolean, boolean) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
A method to easily set which HTTP methods are allowed and which not.
setAllowances(boolean, boolean, boolean, boolean) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setAllowDelete(boolean) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Set the access regime for the DELETE method.
setAllowDelete(boolean) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setAllowGet(boolean) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Set the access regime for the GET method.
setAllowGet(boolean) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setAllowPost(boolean) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Set the access regime for the POST method.
setAllowPost(boolean) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setAllowPut(boolean) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Set the access regime for the PUT method.
setAllowPut(boolean) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setAnnotation(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the annotation.
setApplicabilityDomainResult(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setAtCursor(HTMLComponent) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setAtCursor(HTMLComponent) - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
setAtCursor(HTMLComponent) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setAtCursor(HTMLComponent) - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
setAudiences(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setAudiences(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setAuthor(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the author(s).
setAuthor(String) - Method in interface org.opentox.toxotis.core.html.HTMLHead
Specify the author(s) of the current HTML document.
setAuthor(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
setAuthors(Set<QprfAuthor>) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setAuthParameters(Set<HttpParameter>) - Method in class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
setBibTeXReferences(VRI...) - Method in class org.opentox.toxotis.core.component.Model
 
setBibTeXReferences(Set<VRI>) - Method in class org.opentox.toxotis.core.component.Model
 
setBibTeXReferences(VRI...) - Method in interface org.opentox.toxotis.core.IBibTexReferencable
 
setBibTeXReferences(Set<VRI>) - Method in interface org.opentox.toxotis.core.IBibTexReferencable
 
setBibType(BibTeX.BibTYPE) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter for the bibliographic type.
setBlob(Blob) - Method in class org.opentox.toxotis.core.component.Model
 
setBookTitle(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the bookTitle.
setCasrn(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setCellPadding(int) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setCellPadding(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setCellSpacing(int) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setCellSpacing(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setChapter(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the chapter of the BibTeX resource.
setColumnWidth(int, int) - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
setColumnWidth(int, int) - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
setColumnWidths(int...) - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
setColumnWidths(int...) - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
setColWidth(int, int) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setColWidth(int, int) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setComment(String) - Method in interface org.opentox.toxotis.core.html.HTMLText
Set a comment instead of a text.
setComment(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
setComments(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setComments(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
Setter for comments as a set.
setCompound(Compound) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setConformer(Compound) - Method in class org.opentox.toxotis.core.component.DataEntry
 
setConformers(Set<Conformer>) - Method in class org.opentox.toxotis.core.component.Compound
 
setConnection(HttpURLConnection) - Method in class org.opentox.toxotis.client.AbstractClient
 
setContactInfo(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setContent(String) - Method in interface org.opentox.toxotis.core.html.HTMLTag
 
setContent(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
setContentType(String) - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
setContentType(Media) - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
setContentType(String) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
setContentType(Media) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
setContentType(String) - Method in interface org.opentox.toxotis.client.IPostClient
Specify the Content-type header value that is the MIME of the POSTed entity.
setContentType(Media) - Method in interface org.opentox.toxotis.client.IPostClient
Specify the Content-type header value that is the MIME of the POSTed entity.
setContributors(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setContributors(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setCopyright(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the copyright notice of the BibTeX resource.
setCreatedBy(User) - Method in class org.opentox.toxotis.core.component.BibTeX
Sets the user who created the current BibTeX object.
setCreatedBy(User) - Method in class org.opentox.toxotis.core.component.Model
Specify who created this model.
setCreatedBy(User) - Method in class org.opentox.toxotis.core.component.Task
 
setCreators(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setCreators(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setCrossref(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the cross-ref of this BibTeX resource.
setCryptoIterations(int) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Set the salting iterations to be used in all encryption/decryption operations of the Password Manager.
setCssUrl(URL) - Method in interface org.opentox.toxotis.core.html.HTMLHead
Set the URL where a CSS document can be found thus defining the style of the HTML document.
setCssUrl(URL) - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
setCurrentColumnWidth(int) - Method in interface org.opentox.toxotis.core.html.HTMLTableRow
 
setCurrentColumnWidth(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
setDataEntries(List<DataEntry>) - Method in class org.opentox.toxotis.core.component.Dataset
 
setDataset(VRI) - Method in class org.opentox.toxotis.core.component.Model
Specify the URI of the training dataset.
setDataset(Dataset) - Method in class org.opentox.toxotis.training.Trainer
 
setDate(LiteralValue) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setDate(LiteralValue) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setDateCurrent() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setDelay(long) - Method in class org.opentox.toxotis.util.TaskRunner
Specify the delay between successive reloads of the task resource from the remote location.
setDependentFeatures(List<Feature>) - Method in class org.opentox.toxotis.core.component.Model
Set the list of dependent features of the current model
setDepiction(ImageIcon) - Method in class org.opentox.toxotis.core.component.Compound
 
setDepictionService(String) - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
setDescriptions(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setDescriptions(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
Provide set of descriptions
setDescriptorDomain(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setDetails(String) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
setDetails(String) - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
setDetails(String) - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
setDisjointWith(Set<OntologicalClass>) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
setDisjointWith(Set<OntologicalClass>) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
setDivClass(String) - Method in interface org.opentox.toxotis.core.html.HTMLContainer
Specify the class for the HTML container.
setDivClass(String) - Method in class org.opentox.toxotis.core.html.HTMLDivBuilder
 
setDivClass(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
setDoAName(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setDoaUri(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setDomain(Collection<OntologicalClass>) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
setDomain(Collection<OntologicalClass>) - Method in interface org.opentox.toxotis.ontology.OTProperty
The following note is copied here from the online OWL reference at http://www.w3.org/TR/owl-ref: For a property one can define (multiple) rdfs:domain axioms.
setDoRedirect(URL) - Method in interface org.opentox.toxotis.core.html.HTMLHead
If this page is a redirection to another URI, set the URL to redirect to.
setDoRedirect(URL) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
setDoRedirect(URL) - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
setDoRefresh(boolean, int) - Method in interface org.opentox.toxotis.core.html.HTMLHead
Set a refresh rate for the HTML page.
setDoRefresh(boolean, int) - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
setDoRefresh(boolean, int) - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
setDownloadDetails(boolean) - Method in class org.opentox.toxotis.util.spiders.CompoundSpider
 
setDuration(Long) - Method in class org.opentox.toxotis.core.component.Task
Setter method for the duration of the task in milliseconds.
setEdition(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter for the edition.
setEditor(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter for the editor(s).
setEinecs(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setEmail(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setEnabled(boolean) - Method in interface org.opentox.toxotis.core.IOTComponent
Sets the status of the current modifiable entity.
setEnabled(boolean) - Method in class org.opentox.toxotis.core.OTComponent
 
setEncoding(String) - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Specify the standard encoding that should be used for the encoding of the token.
setErrorCause(ErrorReport) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
setErrorCode(String) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
setErrorReport(ErrorReport) - Method in class org.opentox.toxotis.core.component.Task
 
setErrorReport(ErrorReport) - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
setErrorReport(ErrorReport) - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
setExperimentalResult(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setExperimentalValues(List<String>) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setExpResultUnits(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setFeature(Feature) - Method in class org.opentox.toxotis.core.component.FeatureValue
 
setFeatureValues(List<FeatureValue>) - Method in class org.opentox.toxotis.core.component.DataEntry
 
setFirstName(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setHash(long) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setHash(long) - Method in class org.opentox.toxotis.ontology.LiteralValue
Required so that the class can be persistent using Hibernate.
setHash(long) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setHash(long) - Method in class org.opentox.toxotis.ontology.ResourceValue
 
setHashedPass(String) - Method in class org.opentox.toxotis.core.component.User
 
setHasSources(Set<ResourceValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setHasSources(Set<ResourceValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setHead(HTMLHead) - Method in interface org.opentox.toxotis.core.html.HTMLPage
Set the header of the HTML page.
setHead(HTMLHead) - Method in class org.opentox.toxotis.core.html.impl.HTMLPageImpl
 
setHtmlBody(HTMLBody) - Method in interface org.opentox.toxotis.core.html.HTMLPage
Set the body of the HTML page.
setHtmlBody(HTMLBody) - Method in class org.opentox.toxotis.core.html.impl.HTMLPageImpl
 
setHttpParameters(Set<HttpParameter>) - Method in class org.opentox.toxotis.core.component.RestOperation
 
setHttpParameters(Set<HttpParameter>) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setHttpStatus(int) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
setHttpStatus(float) - Method in class org.opentox.toxotis.core.component.Task
 
setHttpStatus(int) - Method in exception org.opentox.toxotis.exceptions.impl.ServiceInvocationException
 
setHttpStatus(int) - Method in interface org.opentox.toxotis.exceptions.IServiceInvocationException
 
setHttpStatusClass(OntologicalClass) - Method in class org.opentox.toxotis.core.component.HttpStatus
 
setHttpStatusCodes(Set<HttpStatus>) - Method in class org.opentox.toxotis.core.component.RestOperation
 
setHttpStatusCodes(Set<HttpStatus>) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setId(String) - Method in interface org.opentox.toxotis.core.html.HTMLContainer
 
setId(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
setIdentifiers(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setIdentifiers(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setInchi(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setInchiKey(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setIndependentFeatures(List<Feature>) - Method in class org.opentox.toxotis.core.component.Model
Set the list of independent features of the current model.
setIndex(int) - Method in class org.opentox.toxotis.core.component.ParameterValue
 
setInputParamClass(Set<OntologicalClass>) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
setIsbn(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the ISBN.
setIssn(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the ISSN.
setIupacName(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setJournal(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter for the journal name.
setKey(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter for the variable key.
setKeyword(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setKeywords(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Set a list of keywords separated by any custom delimiter.
setLastName(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setLocalCode(String) - Method in class org.opentox.toxotis.core.component.Model
Sets the local code of the model.
setLowLevelOntologies(Set<OntologicalClass>) - Method in class org.opentox.toxotis.core.component.Feature
What this method does is that it sets the ontological classes of the current entity to the prescribed values if there are no other ontological classes already defined.
setMail(String) - Method in class org.opentox.toxotis.core.component.User
Checks whethe the provided e-mail address is RDF-2822 compliant and sets the e-mail address of the user accordingly.
setMasterPasswordFile(String) - Method in class org.opentox.toxotis.util.aa.PasswordFileManager
Set the location of the master password file.
setMasterPasswordFile(File) - Static method in class org.opentox.toxotis.util.aa.TokenPool
 
setMasterPasswordFile(String) - Static method in class org.opentox.toxotis.util.aa.TokenPool
 
setMaxBibTeX(int) - Method in class org.opentox.toxotis.core.component.User
 
setMaxLength(int) - Method in interface org.opentox.toxotis.core.html.HTMLInput
 
setMaxLength(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
setMaxModels(int) - Method in class org.opentox.toxotis.core.component.User
 
setMaxParallelTasks(int) - Method in class org.opentox.toxotis.core.component.User
 
setMechanismDomain(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setMediaType(String) - Method in class org.opentox.toxotis.client.AbstractClient
Specify the mediatype to be used in the Accept header.
setMediaType(Media) - Method in class org.opentox.toxotis.client.AbstractClient
Specify the mediatype to be used in the Accept header providing an instance of Media.
setMediaType(String) - Method in interface org.opentox.toxotis.client.IClient
Specify the mediatype to be used in the Accept header.
setMediaType(Media) - Method in interface org.opentox.toxotis.client.IClient
Specify the media-type to be used in the Accept header providing an instance of Media.
setMediaTypes(Set<HttpMediatype>) - Method in class org.opentox.toxotis.core.component.RestOperation
 
setMediaTypes(Set<HttpMediatype>) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setMessage(String) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
setMeta(MetaInfo) - Method in interface org.opentox.toxotis.core.IOTComponent
Set the meta-information of the component
setMeta(MetaInfo) - Method in class org.opentox.toxotis.core.OTComponent
Set the meta-information of the component
setMetabolicDomain(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setMetaInfo(MetaInfo) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
setMetaInfo(MetaInfo) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
setMetaInfo(MetaInfo) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
setMetaInfo(MetaInfo) - Method in interface org.opentox.toxotis.ontology.OTProperty
Provide meta-information about the property
setMethod(HttpMethod) - Method in class org.opentox.toxotis.core.component.RestOperation
Update the REST Operation automatic documentation setting the corresponding method to which the specifications refer.
setMethod(HttpMethods.MethodsEnum) - Method in class org.opentox.toxotis.core.component.RestOperation
 
setMethod(String) - Method in interface org.opentox.toxotis.core.html.HTMLForm
 
setMethod(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
setMethod(HttpMethod) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setMethod(HttpMethods.MethodsEnum) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setModel(Model) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setModelDate(long) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setModelVersion(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setMolecularStructure(String) - Method in class org.opentox.toxotis.core.component.Compound
Define the molecular structure or a compound (MOL file, SDF etc).
setMultiParameters(Set<MultiParameter>) - Method in class org.opentox.toxotis.core.component.Algorithm
 
setMultiParameters(List<MultiParameter>) - Method in class org.opentox.toxotis.core.component.Model
 
setName(String) - Method in class org.opentox.toxotis.core.component.Parameter
 
setName(String) - Method in class org.opentox.toxotis.core.component.User
 
setName(String) - Method in interface org.opentox.toxotis.core.html.HTMLInput
 
setName(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
setName(String) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
setName(String) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
setName(String) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
setName(String) - Method in interface org.opentox.toxotis.ontology.OTProperty
Set the local name of the property (namespace not included).
setName(String) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Specify the name of the rule.
setName(String) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setNameSpace(String) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
setNameSpace(String) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
setNameSpace(String) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
setNameSpace(String) - Method in interface org.opentox.toxotis.ontology.OTProperty
Specify a namespace for the ontological property
setNumber(Integer) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the number of the current BibTeX object.
setOntologicalClass(OntologicalClass) - Method in class org.opentox.toxotis.ontology.ResourceValue
 
setOntologicalClasses(Set<OntologicalClass>) - Method in interface org.opentox.toxotis.core.IOTComponent
A simple setter for the ontological classes of the current OT-component.
setOntologicalClasses(Set) - Method in class org.opentox.toxotis.core.OTComponent
 
setOntologies(Set<OntologicalClass>) - Method in class org.opentox.toxotis.core.component.Algorithm
Specify the ontologies for this algorithm.
setOpentoxParameter(boolean) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
setPages(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the pages of the current BibTeX object.
setParamContent(Set<OntologicalClass>) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
setParameters(Set<Parameter>) - Method in class org.opentox.toxotis.core.component.Algorithm
ParameterValue the parameters of the algorithm.
setParameters(Set<Parameter>) - Method in class org.opentox.toxotis.core.component.Model
Specify the set of parameters for the current model.
setParameterValues(List<ParameterValue>) - Method in class org.opentox.toxotis.core.component.MultiParameter
 
setParamName(String) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
setParamOptional(boolean) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
setPercentageCompleted(float) - Method in class org.opentox.toxotis.core.component.Task
 
setPolicies(Set<Policy>) - Method in class org.opentox.toxotis.util.aa.policy.PolicyWrapper
 
setPolicyName(String) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
Specify the policy name,
setPolicyName(String) - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
setPostable(OntModel) - Method in class org.opentox.toxotis.client.http.PostHttpClient
Set an ontological data model which is to be posted to the remote location as application/rdf+xml.
setPostable(IStAXWritable) - Method in class org.opentox.toxotis.client.http.PostHttpClient
Set a StAX-writeable component to be posted to the remote location
setPostable(File) - Method in class org.opentox.toxotis.client.http.PostHttpClient
Set a file whose contents are to be posted to the remote server specified in the constructor of this class.
setPostable(String, boolean) - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
setPostable(InputStream) - Method in class org.opentox.toxotis.client.http.PostHttpClient
 
setPostable(String, boolean) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
setPostable(OntModel) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
Set an ontological data model which is to be posted to the remote location as application/rdf+xml.
setPostable(IStAXWritable) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
Set a StAX-writeable component to be posted to the remote location
setPostable(File) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
Set a file whose contents are to be posted to the remote server specified in the constructor of this class.
setPostable(InputStream) - Method in class org.opentox.toxotis.client.https.PostHttpsClient
 
setPostable(OntModel) - Method in interface org.opentox.toxotis.client.IPostClient
Set an ontological data model which is to be posted to the remote location as application/rdf+xml.
setPostable(InputStream) - Method in interface org.opentox.toxotis.client.IPostClient
 
setPostable(IStAXWritable) - Method in interface org.opentox.toxotis.client.IPostClient
Set a StAX-writeable component to be posted to the remote location
setPostable(File) - Method in interface org.opentox.toxotis.client.IPostClient
Set a file whose contents are to be posted to the remote server specified in the constructor of this class.
setPostable(String, boolean) - Method in interface org.opentox.toxotis.client.IPostClient
Provide a POSTable object as a string.
setPredictedFeatures(List<Feature>) - Method in class org.opentox.toxotis.core.component.Model
Set the list of predicted features of the current model.
setPredictionFeature(Feature) - Method in class org.opentox.toxotis.training.Trainer
 
setPredictionResult(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setPredResultUnits(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setProtectedResource(boolean) - Method in class org.opentox.toxotis.core.component.RestOperation
 
setProtectedResource(boolean) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setPublishers(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setPublishers(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setQMRFreference(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setQMRFReportDiscussion(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setQMRFReportReference(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setRange(Collection<XSDDatatype>) - Method in class org.opentox.toxotis.ontology.impl.OTDatatypePropertyImpl
 
setRange(Collection<OntologicalClass>) - Method in class org.opentox.toxotis.ontology.impl.OTObjectPropertyImpl
 
setRange(Collection<XSDDatatype>) - Method in interface org.opentox.toxotis.ontology.OTDatatypeProperty
Set the range for this datatype property
setRange(Collection<OntologicalClass>) - Method in interface org.opentox.toxotis.ontology.OTObjectProperty
Setter method for the range of the current object property.
setRegistrationDate(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setReportDate(long) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setReportMeta(QprfReportMeta) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setRestClasses(Set<OntologicalClass>) - Method in class org.opentox.toxotis.core.component.RestOperation
 
setRestClasses(Set<OntologicalClass>) - Method in interface org.opentox.toxotis.core.IRestOperation
 
setRestOperations(Set<IRestOperation>) - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
setResultUri(VRI) - Method in class org.opentox.toxotis.core.component.Task
 
setRetrieveConformers(boolean) - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
setRetrieveDepiction(boolean) - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
setRights(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setRights(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setSameAs(Set<ResourceValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setSameAs(Set<ResourceValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setScope(Parameter.ParameterScope) - Method in class org.opentox.toxotis.core.component.MultiParameter
 
setScope(Parameter.ParameterScope) - Method in class org.opentox.toxotis.core.component.Parameter
 
setScope(Parameter.ParameterScope) - Method in class org.opentox.toxotis.core.component.VariableInfo
 
setSec32e(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec33c(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec34(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec35(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec41(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec42(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec43(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSec44(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSeeAlso(Set<ResourceValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setSeeAlso(Set<ResourceValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setSeries(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the series of the BibTeX entry.
setServiceName(String) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Setter method for the service name.
setServiceName(String) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setSimilarityLevel(double) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setSize(int) - Method in interface org.opentox.toxotis.core.html.HTMLInput
 
setSize(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
setSmiles(String) - Method in class org.opentox.toxotis.core.component.Compound
 
setStatus(Task.Status) - Method in class org.opentox.toxotis.core.component.Task
ParameterValue the status of a task.
setStereoFeatures(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setStructuralAnalogues(List<Compound>) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
setStructuralDomain(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMeta
 
setSubjectName(String) - Method in class org.opentox.toxotis.util.aa.policy.PolicySubject
 
setSubjects(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setSubjects(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setSubjectsCollectionName(String) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
Specify the name of the collection of subjects in the policy.
setSubjectsCollectionName(String) - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
setSubjectsDescription(String) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicy
Provide some description for the subjects.
setSubjectsDescription(String) - Method in class org.opentox.toxotis.util.aa.policy.Policy
 
setSummary(String) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setSummary(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setSuperClasses(Set<OntologicalClass>) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
setSuperClasses(Set<OntologicalClass>) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
setSuperProperties(Collection<OTProperty>) - Method in class org.opentox.toxotis.ontology.impl.OTPropertyImpl
 
setSuperProperties(Collection<OTProperty>) - Method in interface org.opentox.toxotis.ontology.OTProperty
 
setSuperServiceUri(VRI) - Method in class org.opentox.toxotis.util.SuperPredictor
 
setSynonyms(List<String>) - Method in class org.opentox.toxotis.core.component.Compound
 
setTableBorder(int) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setTableBorder(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setTableWidth(int) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setTableWidth(int) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setTag(String) - Method in interface org.opentox.toxotis.core.html.HTMLTag
 
setTag(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
setTargetUri(String) - Method in interface org.opentox.toxotis.util.aa.policy.IPolicyRule
Setter method for the URI of the target resource.
setTargetUri(String) - Method in class org.opentox.toxotis.util.aa.policy.PolicyRule
 
setTask(Task) - Method in class org.opentox.toxotis.util.TaskRunner
 
setText(String) - Method in interface org.opentox.toxotis.core.html.HTMLText
Set the content of the text element.
setText(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
setTextAtCursor(String) - Method in interface org.opentox.toxotis.core.html.HTMLTable
 
setTextAtCursor(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
setTitle(String) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the title.
setTitle(String) - Method in interface org.opentox.toxotis.core.html.HTMLHead
Setter for the title of the HTML document, which is inccluded in the <head> section of the document.
setTitle(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
setTitles(Set<LiteralValue>) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
setTitles(Set<LiteralValue>) - Method in interface org.opentox.toxotis.ontology.MetaInfo
 
setToken(AuthenticationToken) - Method in class org.opentox.toxotis.util.TaskRunner
 
setType(HTMLInput.HTMLInputType) - Method in interface org.opentox.toxotis.core.html.HTMLInput
 
setType(HTMLInput.HTMLInputType) - Method in class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
setType(XSDDatatype) - Method in class org.opentox.toxotis.ontology.LiteralValue
 
setTypedValue(LiteralValue<T>) - Method in class org.opentox.toxotis.core.component.Parameter
 
setUid(String) - Method in class org.opentox.toxotis.core.component.User
 
setUnits(String) - Method in class org.opentox.toxotis.core.component.Feature
Setter method for the units of the feature.
setUri(VRI) - Method in class org.opentox.toxotis.client.AbstractClient
Set the URI on which the GET method is applied.
setUri(String) - Method in class org.opentox.toxotis.client.AbstractClient
Provide the target URI as a String
setUri(VRI) - Method in interface org.opentox.toxotis.client.IClient
Set the URI on which the GET method is applied.
setUri(String) - Method in interface org.opentox.toxotis.client.IClient
Provide the target URI as a String
setUri(String) - Method in class org.opentox.toxotis.client.VRI
 
setUri(VRI) - Method in class org.opentox.toxotis.core.OTComponent
Set the URI of the component which has to be an instance of VRI
setUri(String) - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
setUri(String) - Method in interface org.opentox.toxotis.ontology.OntologicalClass
 
setUri(VRI) - Method in class org.opentox.toxotis.ontology.ResourceValue
 
setUrl(String) - Method in class org.opentox.toxotis.core.component.BibTeX
 
setURL(String) - Method in class org.opentox.toxotis.core.component.qprf.QprfAuthor
 
setValidatable(OntModel) - Method in class org.opentox.toxotis.ontology.WonderWebValidator
 
setValidatable(IStAXWritable) - Method in class org.opentox.toxotis.ontology.WonderWebValidator
 
setValue(V) - Method in class org.opentox.toxotis.client.Pair
Replaces the value corresponding to this entry with the specified value (optional operation).
setValue(LiteralValue) - Method in class org.opentox.toxotis.core.component.FeatureValue
 
setValue(LiteralValue<T>) - Method in class org.opentox.toxotis.core.component.VariableValue
 
setValue(String) - Method in interface org.opentox.toxotis.core.html.HTMLInput
 
setValue(String) - Method in class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
setValue(T) - Method in class org.opentox.toxotis.ontology.LiteralValue
 
setValueAsString(String) - Method in class org.opentox.toxotis.ontology.LiteralValue
 
setValuedParameter() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
setValues(List<VariableValue>) - Method in class org.opentox.toxotis.core.component.ParameterValue
 
setVariableInfo(VariableInfo) - Method in class org.opentox.toxotis.core.component.VariableValue
 
setVolume(Integer) - Method in class org.opentox.toxotis.core.component.BibTeX
Setter method for the volume of a journal or multivolume book.
setYear(Integer) - Method in class org.opentox.toxotis.core.component.BibTeX
Set the year of publication.
similarCompounds() - Method in class org.opentox.toxotis.util.SimilarityRetriever
 
SimilarityRetriever - Class in org.opentox.toxotis.util
 
SimilarityRetriever(double, Compound) - Constructor for class org.opentox.toxotis.util.SimilarityRetriever
 
SimpleOntModelImpl - Class in org.opentox.toxotis.ontology.impl
 
SimpleOntModelImpl() - Constructor for class org.opentox.toxotis.ontology.impl.SimpleOntModelImpl
 
SimpleOntModelImpl(OntModelSpec) - Constructor for class org.opentox.toxotis.ontology.impl.SimpleOntModelImpl
 
SimpleOntModelImpl(OntModelSpec, Model) - Constructor for class org.opentox.toxotis.ontology.impl.SimpleOntModelImpl
 
singleResourceOperation() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
A simple single-resource operation.
SingleSubject - Class in org.opentox.toxotis.util.aa.policy
An individual user as it is defined and used for the purposes of an SSO Policy.
SingleSubject() - Constructor for class org.opentox.toxotis.util.aa.policy.SingleSubject
 
SingleSubject(String) - Constructor for class org.opentox.toxotis.util.aa.policy.SingleSubject
 
singleTarget() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
size() - Method in class org.opentox.toxotis.util.aa.TokenPool
 
skinIrritationCorrosion() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Skin Irritation/Corrosion.
skinSensitisation() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Skin Sensitisation.
SMILES() - Static method in class org.opentox.toxotis.ontology.collection.OTFeatures
 
SSLConfiguration - Class in org.opentox.toxotis.util.aa
Manages your SSL connections.
SSLConfiguration() - Constructor for class org.opentox.toxotis.util.aa.SSLConfiguration
 
sso() - Static method in class org.opentox.toxotis.client.collection.Services
URI of the central SSO server.
SSO_AUTHORIZATION - Static variable in class org.opentox.toxotis.client.RequestHeaders
Header used within OpenTox for exchanging authorization tokens (between services and the central SSO server as well)
SSO_HOST - Static variable in class org.opentox.toxotis.client.collection.Services
 
ssoAttributes() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO Attributes service.
ssoAuthenticate() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO Authentication service
ssoAuthorize() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO authorization service.
ssoIdentity() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO Identity service.
ssoInvalidate() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO logout/token-invalidation service.
ssoPolicy() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO policy service.
ssoPolicyOld() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
Deprecated.  
ssoValidate() - Static method in class org.opentox.toxotis.client.collection.Services.SingleSignOn
SSO identity validation service.
status() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
status200() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 200.
status201() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 201.
status202() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 202.
status303() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 303.
status400() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 400.
status401() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 401.
status403() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 403.
status404() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 404.
status500() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 500.
status502() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 502.
status503() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for the HTTP Status 503.
string() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
stringFeature() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
stringValue() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Returns the token as a String (not URL encoded).
SuperPredictor - Class in org.opentox.toxotis.util
 
SuperPredictor(Compound, Model, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.SuperPredictor
 
SuperPredictor(VRI, VRI, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.SuperPredictor
 
supervised() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
svm() - Static method in class org.opentox.toxotis.client.collection.Services.NtuaAlgorithms
Support Vector Machine.

T

Tarantula<Result> - Class in org.opentox.toxotis.util.spiders
A generic parser for OpenTox components.
Tarantula(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.Tarantula
Constructor of a generic parsing processor with a given data model and a base resource which is the target of the parsing processor.
Tarantula() - Constructor for class org.opentox.toxotis.util.spiders.Tarantula
 
Task - Class in org.opentox.toxotis.core.component
An asynchronous job running on a remote service.
Task() - Constructor for class org.opentox.toxotis.core.component.Task
 
Task(VRI) - Constructor for class org.opentox.toxotis.core.component.Task
 
task() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
Task.Status - Enum in org.opentox.toxotis.core.component
Status of the task revealing information about the asynchronous job with which the task is related and runs on a server.
TaskRunner - Class in org.opentox.toxotis.util
Reloads a task until its status is no longer Task.Status.RUNNING.
TaskRunner(Task) - Constructor for class org.opentox.toxotis.util.TaskRunner
 
TaskRunner(Task, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.TaskRunner
 
TaskSpider - Class in org.opentox.toxotis.util.spiders
 
TaskSpider() - Constructor for class org.opentox.toxotis.util.spiders.TaskSpider
 
TaskSpider(VRI) - Constructor for class org.opentox.toxotis.util.spiders.TaskSpider
 
TaskSpider(VRI, AuthenticationToken) - Constructor for class org.opentox.toxotis.util.spiders.TaskSpider
 
TaskSpider(Resource, OntModel) - Constructor for class org.opentox.toxotis.util.spiders.TaskSpider
 
taskTemplate() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
An OpenTox APIv1.2-compliant URI-template for tasks.
techReport() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
A technical report.
thing() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
Every individual in the OWL world is a member of the class owl:Thing.
thing() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Every individual in the OWL world is a member of the class owl:Thing.
toBlob() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMetaSerializer
 
toBlob() - Method in class org.opentox.toxotis.ontology.MetaInfoBlobber
 
TokenPool - Class in org.opentox.toxotis.util.aa
Serves as a pool of tokens you can use in your project to best manage your tokens and not create multiple tokens for the same user.
toMetaInfo() - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMetaDeserializer
 
toMetaInfo() - Method in class org.opentox.toxotis.ontology.MetaInfoDeblobber
 
toObject(byte[]) - Method in class org.opentox.toxotis.core.component.Model
 
toObject(byte[]) - Method in class org.opentox.toxotis.core.component.qprf.QprfReportMetaDeserializer
 
toObject(byte[]) - Method in class org.opentox.toxotis.ontology.MetaInfoDeblobber
 
toString() - Method in enum org.opentox.toxotis.client.collection.Media
 
toString() - Method in class org.opentox.toxotis.client.VRI
 
toString() - Method in class org.opentox.toxotis.core.component.BibTeX
 
toString() - Method in class org.opentox.toxotis.core.component.ErrorReport
 
toString() - Method in class org.opentox.toxotis.core.component.Feature
 
toString() - Method in class org.opentox.toxotis.core.component.Parameter
 
toString() - Method in class org.opentox.toxotis.core.component.Task
 
toString() - Method in class org.opentox.toxotis.core.component.User
 
toString() - Method in enum org.opentox.toxotis.core.html.HTMLInput.HTMLInputType
 
toString() - Method in class org.opentox.toxotis.core.html.HTMLPageBuilder
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLAppendableTableImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLBodyImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLContainerImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLFormImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLHeadImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLInputImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLPageImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLParagraphImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLTableRowFixedLength
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLTagImpl
 
toString() - Method in class org.opentox.toxotis.core.html.impl.HTMLTextImpl
 
toString() - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
toString() - Method in class org.opentox.toxotis.ontology.impl.OntologicalClassImpl
 
toString() - Method in class org.opentox.toxotis.ontology.LiteralValue
 
toString() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
 
toURI() - Method in class org.opentox.toxotis.client.VRI
Converts the VRI object into the corresponding java.net.URI
toxicoKinetics() - Static method in class org.opentox.toxotis.ontology.collection.OTEchaEndpoints
Toxico-Kinetics.
ToxOtisException - Exception in org.opentox.toxotis.exceptions.impl
 
ToxOtisException(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ToxOtisException
 
ToxOtisException(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.ToxOtisException
 
ToxOtisException(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.ToxOtisException
 
ToxOtisException() - Constructor for exception org.opentox.toxotis.exceptions.impl.ToxOtisException
 
trace() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
train(AuthenticationToken) - Method in class org.opentox.toxotis.training.Trainer
 
Trainer - Class in org.opentox.toxotis.training
 
Trainer(Algorithm, Dataset, Feature) - Constructor for class org.opentox.toxotis.training.Trainer
 
trainingDataset() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
tumDev() - Static method in class org.opentox.toxotis.client.collection.Services
Development version of TUM resources.

U

Unauthorized - Exception in org.opentox.toxotis.exceptions.impl
 
Unauthorized(String, Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.Unauthorized
 
Unauthorized(Throwable) - Constructor for exception org.opentox.toxotis.exceptions.impl.Unauthorized
 
Unauthorized(String) - Constructor for exception org.opentox.toxotis.exceptions.impl.Unauthorized
 
Unauthorized() - Constructor for exception org.opentox.toxotis.exceptions.impl.Unauthorized
 
units() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
Units of measure.
unpublished() - Static method in class org.opentox.toxotis.ontology.collection.KnoufBibTex
Unpublished material.
unsupervised() - Static method in class org.opentox.toxotis.ontology.collection.OTAlgorithmTypes
 
uri() - Static method in class org.opentox.toxotis.ontology.collection.OTRestObjectProperties
 
URL_ENCODING - Static variable in interface org.opentox.toxotis.client.IClient
Standard UTF-8 Encoding
urlParameter() - Static method in class org.opentox.toxotis.ontology.collection.OTRestClasses
Ontological class for URL parameters.
User - Class in org.opentox.toxotis.core.component
An individual User and its publicly available attributes.
User() - Constructor for class org.opentox.toxotis.core.component.User
 
USER_AGENT - Static variable in class org.opentox.toxotis.client.RequestHeaders
Contains information about the user agent (client) originating the request
UserGroup - Class in org.opentox.toxotis.util.aa
A group of users.
UserGroup() - Constructor for class org.opentox.toxotis.util.aa.UserGroup
 

V

validate(WonderWebValidator.OWL_SPECIFICATION) - Method in class org.opentox.toxotis.ontology.WonderWebValidator
 
validate() - Method in class org.opentox.toxotis.util.aa.AuthenticationToken
Ask the remote SSO server whether this token is valid.
validate(String) - Static method in class org.opentox.toxotis.util.aa.EmailValidator
Validate an email address
value() - Static method in class org.opentox.toxotis.ontology.collection.OTDatatypeProperties
An actual value.
valueOf(String) - Static method in enum org.opentox.toxotis.client.collection.Media
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.client.collection.OpenToxAlgorithms
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.client.HttpStatusCodes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.core.component.BibTeX.BibTYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.core.component.Parameter.ParameterScope
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.core.component.Task.Status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.core.html.Alignment
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.core.html.HTMLInput.HTMLInputType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.ontology.collection.HttpMethods.MethodsEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.ontology.WonderWebValidator.OWL_SPECIFICATION
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.opentox.toxotis.util.aa.AuthenticationToken.TokenStatus
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.opentox.toxotis.client.collection.Media
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.client.collection.OpenToxAlgorithms
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.client.HttpStatusCodes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.core.component.BibTeX.BibTYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.core.component.Parameter.ParameterScope
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.core.component.Task.Status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.core.html.Alignment
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.core.html.HTMLInput.HTMLInputType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.ontology.collection.HttpMethods.MethodsEnum
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
values() - Static method in enum org.opentox.toxotis.ontology.WonderWebValidator.OWL_SPECIFICATION
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.opentox.toxotis.util.aa.AuthenticationToken.TokenStatus
Returns an array containing the constants of this enum type, in the order they are declared.
variable() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
VariableInfo - Class in org.opentox.toxotis.core.component
 
VariableInfo() - Constructor for class org.opentox.toxotis.core.component.VariableInfo
 
variableInfo() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
variableInfo() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
VariableValue<T> - Class in org.opentox.toxotis.core.component
 
VariableValue() - Constructor for class org.opentox.toxotis.core.component.VariableValue
 
VariableValue(String, T, Parameter.ParameterScope) - Constructor for class org.opentox.toxotis.core.component.VariableValue
 
VariableValue(String, T) - Constructor for class org.opentox.toxotis.core.component.VariableValue
 
variableValue() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
variableValues() - Static method in class org.opentox.toxotis.ontology.collection.OTObjectProperties
 
vectorParameter() - Static method in class org.opentox.toxotis.ontology.collection.OTClasses
 
VRI - Class in org.opentox.toxotis.client
VRI is an alternative to URI.
VRI() - Constructor for class org.opentox.toxotis.client.VRI
Dummy constructor
VRI(String) - Constructor for class org.opentox.toxotis.client.VRI
Construct a new VRI providing its String representation.
VRI(VRI) - Constructor for class org.opentox.toxotis.client.VRI
Creates a VRI as a clone of a given VRI.
VRI(String, String...) - Constructor for class org.opentox.toxotis.client.VRI
Create a new VRI object providing its URI as String (can possibly include a query part which will be parsed) and a set of parameters (name-value pairs).

W

WONDERWEB_VLD - Static variable in class org.opentox.toxotis.ontology.WonderWebValidator
The URI that identifies the online OWL-DL validation service.
WonderWebValidator - Class in org.opentox.toxotis.ontology

Validate an ontological model against the online OWL validator at http://www.mygrid.org.uk/OWL/Validator.

WonderWebValidator() - Constructor for class org.opentox.toxotis.ontology.WonderWebValidator
Dummy constructor for an WonderWebValidator object.
WonderWebValidator(OntModel) - Constructor for class org.opentox.toxotis.ontology.WonderWebValidator
Construct a WonderWebValidator object providing an OntModel which is to be checked for compliance against some OWL specification.
WonderWebValidator(IStAXWritable) - Constructor for class org.opentox.toxotis.ontology.WonderWebValidator
 
WonderWebValidator.OWL_SPECIFICATION - Enum in org.opentox.toxotis.ontology
An enumeration of supported OWL specifications.
wrapInDataset(VRI) - Method in class org.opentox.toxotis.core.component.Compound
Wraps the compound in a dataset object.
writeAnnotationProperty(XMLStreamWriter, String) - Method in class org.opentox.toxotis.core.OTComponent
 
writeClass(XMLStreamWriter, OntologicalClass) - Method in class org.opentox.toxotis.core.OTComponent
 
writeDatatypeProperty(XMLStreamWriter, OTDatatypeProperty) - Method in class org.opentox.toxotis.core.OTComponent
 
writeMetaDataProperties(XMLStreamWriter) - Method in class org.opentox.toxotis.core.OTComponent
Appends declarations for all metadata properties at the current cursor position of the writer.
writeObjectProperty(XMLStreamWriter, OTObjectProperty) - Method in class org.opentox.toxotis.core.OTComponent
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.AASpecifications
Deprecated.  
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Algorithm
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.BibTeX
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Bookmark
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Compound
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.DataEntry
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Dataset
Due to the large size of some dataset objects, it is advisable to use this method for serializing dataset objects to RDF/XML rather than the method OntModel#write(OutputStream).
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.DummyComponent
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.ErrorReport
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Feature
This method is still under development, so maybe the created RDF/XML representation is not fully compliant to the OpenTox API.
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.FeatureValue
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.HttpMediatype
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.HttpMethod
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.HttpParameter
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.HttpStatus
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Model
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.MultiParameter
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Parameter
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.ParameterValue
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.qprf.QprfReport
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.RestOperation
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.ServiceRestDocumentation
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.Task
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.User
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.VariableInfo
 
writeRdf(XMLStreamWriter) - Method in class org.opentox.toxotis.core.component.VariableValue
 
writeRdf(Writer) - Method in interface org.opentox.toxotis.core.IStAXWritable
Serializes the Dataset object into an RDF/XML document and writes it to an output stream using a java.io.Writer.
writeRdf(OutputStream) - Method in interface org.opentox.toxotis.core.IStAXWritable
Serializes the Dataset object into an RDF/XML document and writes it to a given output stream.
writeRdf(XMLStreamWriter) - Method in interface org.opentox.toxotis.core.IStAXWritable
Due to the large size of some objects like datasets, it is advisable to use this method for serializing large objects to RDF/XML rather than the method OntModel#write(OutputStream).
writeRdf(Writer) - Method in class org.opentox.toxotis.core.OTComponent
 
writeRdf(OutputStream) - Method in class org.opentox.toxotis.core.OTComponent
 
writeSuperClassRelationships(XMLStreamWriter) - Method in class org.opentox.toxotis.core.OTComponent
 
writeToStAX(XMLStreamWriter) - Method in class org.opentox.toxotis.ontology.impl.MetaInfoImpl
 
writeToStAX(XMLStreamWriter) - Method in interface org.opentox.toxotis.ontology.MetaInfo
Write the meta information in RDF/XML format using an XML Stream Writer.

X

XSD_DATATYPE_LINKS - Static variable in class org.opentox.toxotis.core.OTOnlineResource
Assigns a documentation link to each XSDDataType element.

Y

YAQPservice - Static variable in class org.opentox.toxotis.util.aa.policy.SingleSubject
 

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