Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
R
S
T
U
V
W
X
Y
_
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
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
R
S
T
U
V
W
X
Y
_