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

C

CACHESIZE - Static variable in class org.opentox.algorithm.ConstantParameters
 
CACHESIZE(int) - Static method in class org.opentox.algorithm.ConstantParameters
 
cacheSize - Variable in class org.opentox.algorithm.SvmParameters
The cahed memory used in model training.
cacheSize - Variable in class org.opentox.algorithm.trainer.SvcTrainer
The cahed memory used in model training.
call() - Method in class org.opentox.algorithm.trainer.CallableTrainer
 
CallableTrainer - Class in org.opentox.algorithm.trainer
 
CallableTrainer(AbstractTrainer) - Constructor for class org.opentox.algorithm.trainer.CallableTrainer
 
checkDirs() - Static method in class org.opentox.resource.OTResource.Directories
Checks if the necessary directories already exist.
checkParameters() - Method in class org.opentox.algorithm.dataprocessing.InfoGain
 
checkParameters() - Method in class org.opentox.algorithm.trainer.MlrTrainer
Check wether the dataset and target values are valid URIs.
checkParameters() - Method in class org.opentox.algorithm.trainer.SvcTrainer
 
checkParameters() - Method in class org.opentox.algorithm.trainer.SvmTrainer
Check the consistency of the POSTed svm parameters and assign default values to the parameters that where not posted.
checkParameters() - Method in interface org.opentox.interfaces.IFeatureSelection
Check the consistency of the posted parameters.
checkParameters() - Method in interface org.opentox.interfaces.ITrainer
Check the consistency of the posted parameters.
CHEMICAL_CML - Static variable in class org.opentox.media.OpenToxMediaType
 
CHEMICAL_MDLMOL - Static variable in class org.opentox.media.OpenToxMediaType
 
CHEMICAL_MDLSDF - Static variable in class org.opentox.media.OpenToxMediaType
 
CHEMICAL_SMILES - Static variable in class org.opentox.media.OpenToxMediaType
 
ClassificationEagerMultipleTargets - Static variable in class org.opentox.ontology.namespaces.AlgorithmTypes
 
ClassificationEagerSingleTarget - Static variable in class org.opentox.ontology.namespaces.AlgorithmTypes
 
close() - Method in class org.opentox.database.InHouseDB
 
close() - Method in class org.opentox.database.ModelsTable.JteratorImpl
 
close() - Method in interface org.opentox.interfaces.Jterator
 
COEFF0 - Static variable in class org.opentox.algorithm.ConstantParameters
 
COEFF0(double) - Static method in class org.opentox.algorithm.ConstantParameters
 
coeff0 - Variable in class org.opentox.algorithm.SvmParameters
The bias of the support vector model.
coeff0 - Variable in class org.opentox.algorithm.trainer.SvcTrainer
The bias of the support vector model.
COL_ALGORITHM_ID - Static variable in class org.opentox.database.ModelsTable
 
COL_MODEL_ID - Static variable in class org.opentox.database.ModelsTable
 
COL_MODEL_URI - Static variable in class org.opentox.database.ModelsTable
 
COL_USER_AUTH - Static variable in class org.opentox.database.UsersTable
 
COL_USER_NAME - Static variable in class org.opentox.database.UsersTable
 
COL_USER_PASSWRD - Static variable in class org.opentox.database.UsersTable
 
column - Variable in class org.opentox.database.ModelsTable.JteratorImpl
 
compareTo(IAuthorizationHierarchy) - Method in class org.opentox.auth.Priviledges
Compares two authorization levels.
Implements the ordering:
compareTo(IAuthorizationHierarchy) - Method in interface org.opentox.interfaces.IAuthorizationHierarchy
Compares two Access Levels and returns an integer that describes a comparison relationship between them.
compatibleWith(Instances) - Method in interface org.opentox.interfaces.IModel
Check the assertion that a certain weka.core.Instances object is compatible with this model in terms of having proper features.
compatibleWith(Instances) - Method in class org.opentox.ontology.rdf.Model
Check the assertion that a certain weka.core.Instances object is compatible with this model in terms of having proper features.
component - Static variable in class org.opentox.Server
 
Compound - Static variable in class org.opentox.ontology.namespaces.OTClass
 
compound - Static variable in class org.opentox.ontology.namespaces.OTProperties
 
Conformer - Static variable in class org.opentox.ontology.namespaces.OTClass
 
conformer - Static variable in class org.opentox.ontology.namespaces.OTProperties
 
connection - Static variable in class org.opentox.database.InHouseDB
Static Connection to the databse.
ConstantParameters - Class in org.opentox.algorithm
 
ConstantParameters() - Constructor for class org.opentox.algorithm.ConstantParameters
 
contributor - Variable in class org.opentox.ontology.meta.DCMeta
 
convert(Instances, File) - Method in interface org.opentox.interfaces.IConverter
Converts an Instances object into a DSD file.
convert(File, Instances) - Method in interface org.opentox.interfaces.IConverter
Creates an Instances object using a DSD file.
convert(InputStream, Instances) - Method in interface org.opentox.interfaces.IConverter
Using the InputStream provided by a remote or local resource (file, URL etc) produces an Instances object accepted by weka.
convert(Instances, File) - Method in class org.opentox.util.converters.Converter
Saves a given Instances object in a DSD file.
convert(File, Instances) - Method in class org.opentox.util.converters.Converter
Will be supported in some next version.
convert(InputStream, Instances) - Method in class org.opentox.util.converters.Converter
 
Converter - Class in org.opentox.util.converters
 
Converter() - Constructor for class org.opentox.util.converters.Converter
 
Converter() - Method in class org.opentox.util.converters.Converter
 
COST - Static variable in class org.opentox.algorithm.ConstantParameters
 
COST(double) - Static method in class org.opentox.algorithm.ConstantParameters
 
cost - Variable in class org.opentox.algorithm.SvmParameters
The Cost coefficient.
cost - Variable in class org.opentox.algorithm.trainer.SvcTrainer
The Cost coefficient.
count - Variable in class org.opentox.algorithm.AlgorithmEnum.IteratorImpl
 
create() - Method in class org.opentox.database.ModelsTable
Generates the table that contains information about models.
create() - Method in class org.opentox.database.TaskTable
 
create() - Method in class org.opentox.database.UsersTable
Generates the table which contains a/a data.
create() - Method in interface org.opentox.interfaces.ITable
Creates the table.
createDataBase() - Static method in class org.opentox.database.InHouseDB
If the database does not exist, it is created.
createGuard(OpenToxApplication, Verifier, boolean, List<Method>, List<Method>, Class<?>) - Method in class org.opentox.auth.GuardDog
 
createModel(ModelMeta, OutputStream) - Method in interface org.opentox.interfaces.IModel
Creates the RDF representation for an OpenTox model given its name, the uri of the dataset used to train it, its target feature, the Data and a List of tuning parameters for the training algorithm.
createModel() - Static method in class org.opentox.ontology.namespaces.AbsOntClass
Creates an OWL-DL Ontological Model which includes the definition of some AbsOntClass prefices such as ot, dc and owl.
createModel(ModelMeta, OutputStream) - Method in class org.opentox.ontology.rdf.Model
Creates the RDF representation for an OpenTox model given its name, the uri of the dataset used to train it, its target feature, the Data and a List of tuning parameters for the training algorithm.
createNewFeature(String, OutputStream) - Method in interface org.opentox.interfaces.IFeature
Creates a new Feature and writes it to an OutputStream.
createNewFeature(String, URI) - Method in interface org.opentox.interfaces.IFeature
Generates a new Feature and POSTs it to a feature service
createNewFeature(String, OutputStream) - Method in class org.opentox.ontology.rdf.Feature
Creates a new Feature and writes it to an OutputStream.
createNewFeature(String, URI) - Method in class org.opentox.ontology.rdf.Feature
Generates a new Feature and POSTs it to a feature service
createOntClass(OntModel) - Method in interface org.opentox.interfaces.IOntClass
Creates a new Ontological class for an Ontological Model.
createOntClass(OntModel) - Method in class org.opentox.ontology.namespaces.AbsOntClass.Class
Creates a new Ontological class for an Ontological Model.
createOntClass(OntModel) - Method in class org.opentox.ontology.namespaces.AbsOntClass
Creates a new Ontological class for an Ontological Model.
createProperty(OntModel) - Method in interface org.opentox.interfaces.IOntClass
Generates a property out of a given model.
createProperty(OntModel) - Method in class org.opentox.ontology.namespaces.AbsOntClass.Class
Generates a property out of a given model.
createProperty(OntModel) - Method in class org.opentox.ontology.namespaces.AbsOntClass
Generates a property out of a given model.
createRandomDataset(int, int, OutputStream, String) - Static method in class org.opentox.ontology.rdf.Dataset
Generates a random dataset of prescribed dimensions.
createRoot() - Method in class org.opentox.OpenToxApplication
Creates a root Restlet that will receive all incoming calls.
creator - Variable in class org.opentox.ontology.meta.DCMeta
 
CredentialsVerifier - Class in org.opentox.auth
Verifies if some given credentials are valid performing a database query.
CredentialsVerifier(OpenToxApplication) - Constructor for class org.opentox.auth.CredentialsVerifier
Initialize the CredentialsVerifier.
CredentialsVerifier(OpenToxApplication, Priviledges) - Constructor for class org.opentox.auth.CredentialsVerifier
Verifies credentials only if their corresponding authorization level is equal or greater to a specified level.
cross_validation - Variable in class org.opentox.util.libSVM.svm_train
 

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