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

G

GAMMA - Static variable in class org.opentox.algorithm.ConstantParameters
 
GAMMA(double) - Static method in class org.opentox.algorithm.ConstantParameters
 
gamma - Variable in class org.opentox.algorithm.SvmParameters
The kernel parameter gamma used in various kernel functions.
gamma - Variable in class org.opentox.algorithm.trainer.SvcTrainer
The kernel parameter gamma used in various kernel functions.
generateDigest(String, String) - Static method in class org.opentox.auth.DigestGenerator
Gives the SHA or MD5 digest for a given string message.
generatePMML(double[], int) - Method in class org.opentox.algorithm.trainer.MlrTrainer
Generates the PMML representation of the model and stores in the hard disk.
get(Variant) - Method in interface org.opentox.interfaces.IProvidesHttpAccess
 
get(Variant) - Method in class org.opentox.resource.Algorithm
Implementation of the GET method.
get(Variant) - Method in class org.opentox.resource.IndexResource
 
get(Variant) - Method in class org.opentox.resource.ListAlgorithms
 
get(Variant) - Method in class org.opentox.resource.ListModels
Return a text/uri-list or text/html representation of the list of available models.
get(Variant) - Method in class org.opentox.resource.ListTasks
 
get(Variant) - Method in class org.opentox.resource.ModelInfoResource
Returns a text/uri list which corresponds to the requested meta-information.
get(Variant) - Method in class org.opentox.resource.ModelResource
 
get(Variant) - Method in class org.opentox.resource.ShutDownResource
 
get(Variant) - Method in class org.opentox.resource.TaskResource
TODO: Return a representation of the task - use org.opentox.rdf.Task.
get(Variant) - Method in class org.opentox.resource.TestResource
 
getAlgorithm(String) - Method in class org.opentox.database.ModelsTable
Returns an AlgorithmEnum characterization of a given model.
getAlgorithmEnum(String) - Static method in enum org.opentox.algorithm.AlgorithmEnum
Returns the AlgorithmEnum enumeration element which has a certain name.
getAlgorithmName() - Method in enum org.opentox.algorithm.AlgorithmEnum
Returns the name of the algorithm.
getAttributes(Map<Resource, String>) - Method in class org.opentox.ontology.rdf.Dataset
Returns a FastVector for the attributes of the dataset as an Instaces object.
getAuthorizationForUser(String) - Method in class org.opentox.database.UsersTable
 
getClassMemberIteratorFor(AbsOntClass.Class) - Method in class org.opentox.ontology.rdf.RDFHandler
Creates an ExtendedIterator over the set of all resources which correspond to a specific class.
getConnection() - Method in class org.opentox.database.InHouseDB
Establishes a connection to the database.
getCredentialsAsMap(Priviledges) - Method in class org.opentox.database.UsersTable
Returns a Map<String,char[]> for the credentials of a given authorization level.
getDependentFeatureUri() - Method in interface org.opentox.interfaces.IModel
Returns the dependent features of the model.
getDependentFeatureUri() - Method in class org.opentox.ontology.rdf.Model
Returns the dependent features of the model.
getErrorLevel() - Method in class org.opentox.error.ErrorRepresentation
The Error Level is defined to be the number of Error or exception in this object.
getErrorRep() - Method in class org.opentox.algorithm.dataprocessing.InfoGain
 
getErrorRep() - Method in class org.opentox.algorithm.reporting.AlgorithmReporter
 
getErrorRep() - Method in class org.opentox.error.ErrorSource
 
getErrorRep() - Method in interface org.opentox.interfaces.IProne2Error
 
getInstace() - Static method in class org.opentox.Server
 
getInstaces(String, boolean) - Method in interface org.opentox.interfaces.IDataset
This method is used to encapsulate the data of the RDF document in a weka.core.Instances object which can be used to create Regression and classification models using weka algorithms.
getInstaces(String, boolean) - Method in class org.opentox.ontology.rdf.Dataset
This method is used to encapsulate the data of the RDF document in a weka.core.Instances object which can be used to create Regression and classification models using weka algorithms.
getInstance() - Static method in class org.opentox.client.opentoxClient
 
getInstance() - Static method in class org.opentox.database.InHouseDB
 
getInstance() - Static method in class org.opentox.database.ModelsTable
 
getInstance() - Static method in class org.opentox.database.TaskTable
 
getInstance() - Static method in class org.opentox.database.UsersTable
 
getInstance() - Static method in class org.opentox.OpenToxApplication
 
getInstances(String) - Method in interface org.opentox.interfaces.IDataset
Similar to Dataset.getInstaces(java.lang.String, boolean) but the generated Instances is constructed with respect to a certain model.
getInstances(String) - Method in class org.opentox.ontology.rdf.Dataset
Similar to Dataset.getInstaces(java.lang.String, boolean) but the generated Instances is constructed with respect to a certain model.
getIterator() - Static method in enum org.opentox.algorithm.AlgorithmEnum
 
getJenaModel() - Method in class org.opentox.ontology.rdf.RDFHandler
Returns the jena Model.
getLevel() - Method in class org.opentox.auth.Priviledges
Returns the identifier of a Priviledge.
getLevel() - Method in interface org.opentox.interfaces.IAuthorizationHierarchy
The priviledges as a string, i.e.
getListOfParameters() - Method in class org.opentox.algorithm.SvmParameters
Returns the SVM parameters as a list of AlgorithmParameter objects.
getMessages() - Method in class org.opentox.error.ErrorRepresentation
The explanatory messages about the errors.
getModelsStack() - Method in class org.opentox.database.ModelsTable
TODO: IMPORTANT!!! Rewrite this method!!! Returns the number of models currently in the database.
getOntClass(OntModel) - Method in interface org.opentox.interfaces.IOntClass
Returns the corresponding Ontological Class (i.e.
getOntClass(OntModel) - Method in class org.opentox.ontology.namespaces.AbsOntClass.Class
Returns the corresponding Ontological Class (i.e.
getOntClass(OntModel) - Method in class org.opentox.ontology.namespaces.AbsOntClass
Returns the corresponding Ontological Class (i.e.
getPredictedFeatureUri() - Method in interface org.opentox.interfaces.IModel
Get the URI of the predicted feature of the model.
getPredictedFeatureUri() - Method in class org.opentox.ontology.rdf.Model
Get the URI of the predicted feature of the model.
getRepresentation(MediaType) - Method in class org.opentox.formatters.AbstractAlgorithmFormatter
Returns the Corresponding Representation.
getRepresentation(MediaType) - Method in class org.opentox.formatters.AbstractModelFormatter
 
getRepresentation(MediaType) - Method in class org.opentox.formatters.AlgorithmJsonFormatter
 
getRepresentation(MediaType) - Method in class org.opentox.formatters.AlgorithmRdfFormatter
 
getRepresentation(MediaType) - Method in class org.opentox.formatters.AlgorithmXmlFormatter
 
getRepresentation(MediaType) - Method in class org.opentox.formatters.AlgorithmYamlFormatter
 
getRepresentation(MediaType) - Method in class org.opentox.formatters.ModelFormatter
 
getRepresentation(MediaType) - Method in interface org.opentox.interfaces.IFormatter
 
getRepresentationForMetaInf(AlgorithmMeta, MediaType) - Method in class org.opentox.algorithm.reporting.AlgorithmReporter
 
getResource() - Method in interface org.opentox.interfaces.IOntClass
Returns the Resource of this class ( IOntClass ).
getResource() - Method in class org.opentox.ontology.namespaces.AbsOntClass.Class
Returns the Resource of this class ( AbsOntClass.Class ).
getResource() - Method in class org.opentox.ontology.namespaces.AbsOntClass
Returns the Resource of this class ( AbsOntClass.Class ).
getRidOf() - Method in class org.opentox.database.ModelsTable
 
getRidOf() - Method in class org.opentox.database.TaskTable
 
getRidOf() - Method in class org.opentox.database.UsersTable
 
getRidOf() - Method in interface org.opentox.interfaces.ITable
Removes completely the table from the database.
getRs() - Method in class org.opentox.database.ModelsTable.JteratorImpl
 
getScaledFileName() - Method in class org.opentox.util.libSVM.svm_scale
 
getSetOfIndependentFeatures() - Method in interface org.opentox.interfaces.IModel
The set of independent variables of the model.
getSetOfIndependentFeatures() - Method in class org.opentox.ontology.rdf.Model
The set of independent variables of the model.
getStatus() - Method in class org.opentox.error.ErrorRepresentation
Returns the status that accompanies the ErrorRepresentaiton.
getStream() - Method in class org.opentox.error.ErrorRepresentation
Returns a stream with the content of the representation.
getText() - Method in class org.opentox.error.ErrorRepresentation
Returns the representation as plain text.
getURI() - Method in interface org.opentox.interfaces.IOntClass
Returns the URI of the class
getURI() - Method in class org.opentox.ontology.namespaces.AbsOntClass.Class
Returns the URI of the class
getURI() - Method in class org.opentox.ontology.namespaces.AbsOntClass
Returns the URI of the class
GuardDog - Class in org.opentox.auth
 
GuardDog() - Constructor for class org.opentox.auth.GuardDog
 
GuardDog.ChallengeAuthenticatorImpl - Class in org.opentox.auth
An Implementation of ChallengeAuthenticator
GuardDog.ChallengeAuthenticatorImpl(Context, boolean, ChallengeScheme, String) - Constructor for class org.opentox.auth.GuardDog.ChallengeAuthenticatorImpl
 
GUEST - Static variable in class org.opentox.auth.Priviledges
Guest Users with no priviledges.

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