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M

m_model - Static variable in class org.opentox.ontology.namespaces.AbsOntClass
 
main(String[]) - Static method in class org.opentox.database.ModelsTable
 
main(String[]) - Static method in class org.opentox.database.UsersTable
 
Main - Class in org.opentox
 
Main() - Constructor for class org.opentox.Main
 
main(String[]) - Static method in class org.opentox.Main
Usage: Server --port PORT --serverName SERVER_NAME --dataBase DATABASE_NAME
main(String[]) - Static method in class org.opentox.ontology.rdf.Dataset
 
main(String[]) - Static method in class org.opentox.util.libSVM.svm_predict
Usage:
-b 1
test_file model_file output_file
main(String[]) - Static method in class org.opentox.util.libSVM.svm_train
Usage: svm_train [options] training_set_file [model_file]"
options:
-s svm_type : set type of SVM (default 0)
0 -- C-SVC 1 -- nu-SVC 2 -- one-class SVM 3 -- epsilon-SVR 4 -- nu-SVR -t kernel_type : set type of kernel function (default 2)
0 -- linear: u'*v 1 -- polynomial: (gamma*u'*v + coef0)^degree 2 -- radial basis function: exp(-gamma*|u-v|^2) 3 -- sigmoid: tanh(gamma*u'*v + coef0) 4 -- precomputed kernel (kernel values in training_set_file) -d degree : set degree in kernel function (default 3)

-g gamma : set gamma in kernel function (default 1/k)

-r coef0 : set coef0 in kernel function (default 0)

-c cost : set the parameter C of C-SVC, epsilon-SVR, and nu-SVR (default 1)

-n nu : set the parameter nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5)\n"

-p epsilon : set the epsilon in loss function of epsilon-SVR (default 0.1)\n"

-m cachesize : set cache memory size in MB (default 100)

-e epsilon : set tolerance of termination criterion (default 0.001)

-h shrinking : whether to use the shrinking heuristics, 0 or 1 (default 1)

-b probability_estimates : whether to train a SVC or SVR model for probability estimates, 0 or 1 (default 0)

-wi weight : set the parameter C of class i to weight*C, for C-SVC (default 1)

-v n : n-fold cross validation mode

-q : quiet mode (no outputs)
map - Variable in class org.opentox.error.ErrorRepresentation
Maps a Throwable to a corresponding explanation.
max - Variable in class org.opentox.resource.ListModels
 
max_index - Variable in class org.opentox.util.libSVM.svm_scale
 
MAX_RESULTS_QUERY - Static variable in class org.opentox.resource.ListModels
 
MD2 - Static variable in class org.opentox.auth.DigestGenerator.DigestAlgorithm
The MD2 message digest algorithm as defined in RFC 1319.
MD5 - Static variable in class org.opentox.auth.DigestGenerator.DigestAlgorithm
The MD5 message digest algorithm as defined in RFC 1321.
metainf - Variable in class org.opentox.formatters.AbstractAlgorithmFormatter
 
mime - Static variable in class org.opentox.formatters.AlgorithmJsonFormatter
 
mime - Static variable in class org.opentox.formatters.AlgorithmXmlFormatter
 
mime - Static variable in class org.opentox.formatters.AlgorithmYamlFormatter
 
mlrAlgorithmURI - Static variable in class org.opentox.resource.OTResource.URIs
URI for Multiple Linear Regression Algorithm.
MlrPredictor - Class in org.opentox.prediction
Applies a dataset on an MLR model to predict a feature.
MlrPredictor() - Constructor for class org.opentox.prediction.MlrPredictor
Constructor.
MlrTrainer - Class in org.opentox.algorithm.trainer
Trainer for MLR models.
MlrTrainer(Form, ServerResource) - Constructor for class org.opentox.algorithm.trainer.MlrTrainer
 
Model - Static variable in class org.opentox.ontology.namespaces.OTClass
 
model - Static variable in class org.opentox.ontology.namespaces.OTProperties
 
Model - Class in org.opentox.ontology.rdf
This class is used to parse and generate RDF representations of Models.
Model() - Constructor for class org.opentox.ontology.rdf.Model
 
Model(InputStream) - Constructor for class org.opentox.ontology.rdf.Model
Initialized a new instance of Model reading its content from an input stream which can be a FileInputStream or an InputStream pointing to a web Resource.
model - Variable in class org.opentox.util.libSVM.svm_train
 
model_file_name - Variable in class org.opentox.util.libSVM.svm_train
 
model_id - Variable in class org.opentox.algorithm.trainer.SvcTrainer
The id of the generated model.
model_id - Variable in class org.opentox.algorithm.trainer.SvmTrainer
The id of the generated model.
model_id - Variable in class org.opentox.formatters.AbstractModelFormatter
 
model_id - Variable in class org.opentox.ontology.meta.ModelMeta
Identification number of the model.
model_id - Variable in class org.opentox.resource.ModelInfoResource
 
model_id - Variable in class org.opentox.resource.ModelResource
 
MODEL_INFO_TABLE - Static variable in class org.opentox.database.ModelsTable
 
modelDir - Static variable in class org.opentox.resource.OTResource.Directories
Folder where all model-related files are stored.
ModelFormatter - Class in org.opentox.formatters
Reads a stored or online model (in RDF format) and returns it in a prefered MIME type (format).
ModelFormatter(int) - Constructor for class org.opentox.formatters.ModelFormatter
 
ModelInfoResource - Class in org.opentox.resource
This resource return meta information about a model such as its dependent variables , its independent and predicted variables.
ModelInfoResource() - Constructor for class org.opentox.resource.ModelInfoResource
 
ModelMeta - Class in org.opentox.ontology.meta
Meta information about a Model.
ModelMeta(String, String, Instances, List<AlgorithmParameter>, String) - Constructor for class org.opentox.ontology.meta.ModelMeta
 
modelPmmlDir - Static variable in class org.opentox.resource.OTResource.Directories
Folder where all PMML documents are stored.
modelRdfDir - Static variable in class org.opentox.resource.OTResource.Directories
Folder where all RDF representations of models are stored.
ModelResource - Class in org.opentox.resource
This resource, returns a representation of a model and supports the POST operation for prediction.
ModelResource() - Constructor for class org.opentox.resource.ModelResource
 
ModelsTable - Class in org.opentox.database
 
ModelsTable() - Constructor for class org.opentox.database.ModelsTable
 
ModelsTable.JteratorImpl - Class in org.opentox.database
A private implementation of Jterator.
ModelsTable.JteratorImpl(String, String) - Constructor for class org.opentox.database.ModelsTable.JteratorImpl
 
modelURI - Static variable in class org.opentox.resource.OTResource.URIs
URI for all models stored in the server.
modelWekaDir - Static variable in class org.opentox.resource.OTResource.Directories
Folder where all RAW (dsd-like) files are stored.
MSDMTox - Static variable in class org.opentox.ontology.namespaces.AlgorithmTypes
 
MultipleTargets - Static variable in class org.opentox.ontology.namespaces.AlgorithmTypes
 

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