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A B C D E F G I K L M N O P R S T U

A

ActivationFactory - interface com.penguinwerks.jodene.ActivationFactory.: A factory to create activation functions.
ActivationFunction - interface com.penguinwerks.jodene.ActivationFunction.: This is a generic ativation function.
Axon - class com.penguinwerks.jodene.Axon.: An axon connects two neurons.
Axon() - Constructor for class com.penguinwerks.jodene.Axon: Constructor - Creates a new Axon with a unique name.
Axon(Integer) - Constructor for class com.penguinwerks.jodene.Axon: Constructor - creates an Axon with the given name.
accumulateError(Map, Map) - Method in class com.penguinwerks.jodene.ErrorManager: Calculates the error using the available error calculators.
activation(double) - Method in interface com.penguinwerks.jodene.ActivationFunction: The activation level given the input.
activation(double) - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction: Calculates the activation value as per the sigmoid function.
activation(double) - Method in class com.penguinwerks.jodene.activation.TanhActivationFunction: Returns the tanh activation.
addCalculator(String, ErrorCalculator) - Method in class com.penguinwerks.jodene.ErrorManager: Adds a new calculator with the given name to the error manager.
addCalculator(ErrorCalculator) - Method in class com.penguinwerks.jodene.Trainer: The error calculator computes the error from the input values and the output values.
addCalculator(String, ErrorCalculator) - Method in class com.penguinwerks.jodene.Trainer: The error calculator computes the error from the input values and the output values.
addDataFile(ExampleSet, DataStorageTag, String) - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Adds a new example set to the vault with the given name and the given storage tag.
addDataFile(ExampleSet, String) - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Adds a new example set to the vault.
addEpochEventListener(EpochEventListener) - Method in class com.penguinwerks.jodene.Trainer: Adds an epoch event listener to the list of listeners.
addError(String) - Method in class com.penguinwerks.jodene.Pocket: Adds a new error to monitor in the pocket.
addErrorCalculator(ErrorCalculator) - Method in class com.penguinwerks.jodene.Evaluator: Adds a new error calculator to the evaluator.
addErrorCalculator(ErrorCalculator, String) - Method in class com.penguinwerks.jodene.Evaluator: Add an error calculator with the given name, as opposed to the default name of the calculator.
addExample(Example) - Method in class com.penguinwerks.jodene.ExampleSet: Adds an example to this example set.
addFeature(String, Serializable) - Method in class com.penguinwerks.jodene.managers.DataStorageTag: Adds a feature to the meta-data.
addHiddenLayer(int) - Method in class com.penguinwerks.jodene.NetworkBuilder: Adds a hidden layer to build with the given size.
addInputAxon(Axon) - Method in class com.penguinwerks.jodene.Neuron: Add a new input axon to the neuron.
addInputData(List, DataStorageTag, String) - Method in class com.penguinwerks.jodene.managers.InputDataManager: Adds data to the manager.
addInputData(List, String) - Method in class com.penguinwerks.jodene.managers.InputDataManager: Adds data to the data manager.
addInputData(ResultSet, DataStorageTag, String) - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Adds a result set to the vault with the given storage tag.
addInputData(ResultSet, String) - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Add result sets to the vault.
addInputNeuron(Neuron) - Method in class com.penguinwerks.jodene.Network: Add input neuron.
addInputNeuron(String) - Method in class com.penguinwerks.jodene.NetworkBuilder: Adds an input neuron to the builder.
addInputNeurons(List) - Method in class com.penguinwerks.jodene.NetworkBuilder: Adds a list of input neurons to the network builder.
addInternalNeuron(Neuron) - Method in class com.penguinwerks.jodene.Network: Adds a "hidden layer" neuron.
addKey(String) - Method in class com.penguinwerks.jodene.data.Translator: Adds a new key to translate - note that all necessary keys must be defined in the translator.
addNetwork(DataReader, DataStorageTag, String) - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Add a new data reader to the vault.
addNetwork(DataReader, String) - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Add a data reader to the vault, using the default data storage tag.
addNetwork(Network, DataStorageTag, String) - Method in class com.penguinwerks.jodene.managers.NetworkManager: Add a new network to the vault.
addNetwork(Network, String) - Method in class com.penguinwerks.jodene.managers.NetworkManager: Add a network to the vault, using the default data storage tag.
addObject(Serializable, DataStorageTag, String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Add a managed object, passing in the object, the storage tag and the object name as a string.
addObject(Serializable, String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Add an object to be managed by the manager, passing in the object and the name.
addOutputAxon(Axon) - Method in class com.penguinwerks.jodene.Neuron: Adds a new output axon to the neuron.
addOutputNeuron(Neuron) - Method in class com.penguinwerks.jodene.Network: Add output neuron.
addOutputNeuron(String) - Method in class com.penguinwerks.jodene.NetworkBuilder: Adds an output neuron to the builder.
addOutputNeurons(List) - Method in class com.penguinwerks.jodene.NetworkBuilder: Adds a list of output neurons to the builder.
addResult(Result) - Method in class com.penguinwerks.jodene.ResultSet: Add a result to the result set.
addScaler(Scaler) - Method in class com.penguinwerks.jodene.data.Scaler: Chaines another scaler to this scaler.
adjustWeights() - Method in class com.penguinwerks.jodene.Network: Called during training to periodically adjust the weights on the network.
adjustWeights() - Method in class com.penguinwerks.jodene.Neuron: Adjust the weights.
adjustWeights(double[]) - Method in class com.penguinwerks.jodene.NeuronTraining: Called to adjust the weights.

B

beginTraining(Trainer) - Method in class com.penguinwerks.jodene.Network: Attaches a trainer to the network and establishes any necessary structures for training.
buildNetwork() - Method in class com.penguinwerks.jodene.NetworkBuilder: Build a network.

C

ClassificationErrorCalculator - class com.penguinwerks.jodene.calculators.ClassificationErrorCalculator.: This error calculator assumes that your are measuring memership in a class.
ClassificationErrorCalculator() - Constructor for class com.penguinwerks.jodene.calculators.ClassificationErrorCalculator: Creates a new instance of ClassificationErrorCalculator
ClassificationScaler - class com.penguinwerks.jodene.data.ClassificationScaler.: This scaler is used to translate an input value for a classifier, 1.0 or 0.0 usually, to an intermediate value like 0.1 and 0.9.
ClassificationScaler() - Constructor for class com.penguinwerks.jodene.data.ClassificationScaler: Constructor - no argument constructor.
ClassificationScaler(double, double) - Constructor for class com.penguinwerks.jodene.data.ClassificationScaler: Constructor - sets the min and the max.
Column - class com.penguinwerks.jodene.data.Column.: Represents a column in the output data set.
Column() - Constructor for class com.penguinwerks.jodene.data.Column: The constructor for the comment.
calculateDelta(double, double, double) - Method in class com.penguinwerks.jodene.NeuronTraining: Calculates the delta given the expected values, the actual values and the derivative of the activation value.
calculateDelta(double[], double) - Method in class com.penguinwerks.jodene.NeuronTraining: Calcuates the delta given the deltas of the subsequent layers and the weight connecting this neuron to the next neuron.
calculateError(Map, Map) - Method in class com.penguinwerks.jodene.ErrorCalculator: Given an expected value and an input value the error is returned.
calculateError(Map, Map) - Method in class com.penguinwerks.jodene.calculators.ClassificationErrorCalculator: Calculates the error by rounding the expected values and the actual values and subtracting.
calculateError(Map, Map) - Method in class com.penguinwerks.jodene.calculators.MSEErrorCalculator: Calculates the mean squared error.
calculateError(Map, Map) - Method in class com.penguinwerks.jodene.calculators.SSEErrorCalculator: Calculates the error based on the sum of squares where the total error is equal to the sum of the squares of the differences between the actual and expected values.
calculatePartials(double[], double) - Method in class com.penguinwerks.jodene.NeuronTraining: Initializes the partials, if necessary.
cleanVault() - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Cleans the vault of all data readers.
cleanVault() - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Cleans out the example sets from the vault.
cleanVault(String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Cleans out the vault for the given file extension.
cleanVault() - Method in class com.penguinwerks.jodene.managers.InputDataManager: Cleans the vault.
cleanVault() - Method in class com.penguinwerks.jodene.managers.NetworkManager: Cleans the vault of all networks.
cleanVault() - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Cleans the results sets from the vault.
cleanup() - Method in class com.penguinwerks.jodene.managers.PocketManager: Clean up the pocket contents at the end of training.
clearErrors() - Method in class com.penguinwerks.jodene.ErrorManager: Clears the error report, moving it to the error History.
clearPartials() - Method in class com.penguinwerks.jodene.NeuronTraining: Clears the partial derivatives, called after weights are adjusted.
closeError(String) - Method in class com.penguinwerks.jodene.Pocket: Closes named error, cleaning up the pocket.
com.penguinwerks.jodene - package com.penguinwerks.jodene
com.penguinwerks.jodene.activation - package com.penguinwerks.jodene.activation
com.penguinwerks.jodene.calculators - package com.penguinwerks.jodene.calculators
com.penguinwerks.jodene.data - package com.penguinwerks.jodene.data
com.penguinwerks.jodene.listeners - package com.penguinwerks.jodene.listeners
com.penguinwerks.jodene.managers - package com.penguinwerks.jodene.managers
connect(String, String) - Method in class com.penguinwerks.jodene.Network: Connect two nuerons by their name.
connect(Neuron, Neuron) - Method in class com.penguinwerks.jodene.Network: Connect two neurons.

D

DataReader - class com.penguinwerks.jodene.data.DataReader.: This is an abstract data reader.
DataReader() - Constructor for class com.penguinwerks.jodene.data.DataReader
DataReaderManager - class com.penguinwerks.jodene.managers.DataReaderManager.
DataReadingException - exception com.penguinwerks.jodene.data.DataReadingException.: A DataReadingException is thrown to indicate an error during data reading.
DataReadingException() - Constructor for class com.penguinwerks.jodene.data.DataReadingException: Default constructor.
DataReadingException(String) - Constructor for class com.penguinwerks.jodene.data.DataReadingException: Constructor with the message.
DataReadingException(String, Throwable) - Constructor for class com.penguinwerks.jodene.data.DataReadingException: Constructor with the message and the exception which generated this exception.
DataReadingException(Throwable) - Constructor for class com.penguinwerks.jodene.data.DataReadingException: Constructor with the generating exception.
DataStorageTag - class com.penguinwerks.jodene.managers.DataStorageTag.: The data storage tags stores the meta data that belongs to an item in the vault.
DataStorageTag() - Constructor for class com.penguinwerks.jodene.managers.DataStorageTag: Creates a new instance of DataStorageTag
DuplicateNeuronException - exception com.penguinwerks.jodene.DuplicateNeuronException.: This exception is thrown when an attempt is made to enter two neurons with the same name to the same network.
DuplicateNeuronException() - Constructor for class com.penguinwerks.jodene.DuplicateNeuronException
DuplicateNeuronException(String) - Constructor for class com.penguinwerks.jodene.DuplicateNeuronException
DuplicateNeuronException(String, Throwable) - Constructor for class com.penguinwerks.jodene.DuplicateNeuronException
DuplicateNeuronException(Throwable) - Constructor for class com.penguinwerks.jodene.DuplicateNeuronException
defineColumn(String, Scaler) - Method in class com.penguinwerks.jodene.data.DataReader: Define a new column in the output set with the given name and scaler.
defineColumn(String) - Method in class com.penguinwerks.jodene.data.DataReader: Define a column in the output set, that does not scale.
defineRealInputField(String) - Method in class com.penguinwerks.jodene.data.DataReader: Defines a real valued input field in the data set with the given name.
defineTranslatedInputField(String, Translator) - Method in class com.penguinwerks.jodene.data.DataReader: Defines a translated input field with the given name.
derivative(double) - Method in interface com.penguinwerks.jodene.ActivationFunction: The derivative of the activation value.
derivative(double) - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction: Calculate the derivative of the activation value.
derivative(double) - Method in class com.penguinwerks.jodene.activation.TanhActivationFunction: Returns the tanh derivative.
divideLinear(int[]) - Method in class com.penguinwerks.jodene.ExampleSet: Divides the example set into sub sets based on the sizes in the size array.
divideLinear(double[]) - Method in class com.penguinwerks.jodene.ExampleSet: Same as dividLinear using integer sizes, except the sizes are expressed as percentages.
divideRandom(int[]) - Method in class com.penguinwerks.jodene.ExampleSet: Divide this data set (without modifying it) into two data sets.
divideRandom(double[]) - Method in class com.penguinwerks.jodene.ExampleSet: Sames as divideRandom using integer sizes, except the sizes are expressed as percentages.

E

EpochEventListener - interface com.penguinwerks.jodene.EpochEventListener.: The Epoch Event Listener interface is used to receive epoch end events.
ErrorCalculator - class com.penguinwerks.jodene.ErrorCalculator.: The error calculator calculates the error based on some agorithm, for example, sum of squares.
ErrorCalculator() - Constructor for class com.penguinwerks.jodene.ErrorCalculator: Default constructor.
ErrorManager - class com.penguinwerks.jodene.ErrorManager.: The error manager allows you to configure error calculators and maintains a history of errors.
ErrorManager() - Constructor for class com.penguinwerks.jodene.ErrorManager: Creates a new instance of ErrorManager
Evaluator - class com.penguinwerks.jodene.Evaluator.: Evaluates the network, using the error calculators to accumulate error information.
Evaluator() - Constructor for class com.penguinwerks.jodene.Evaluator: Creates a new instance of Evaluator
Example - class com.penguinwerks.jodene.Example.: Encapsulates an example - which is a set of inputs and a set of expected values.
Example() - Constructor for class com.penguinwerks.jodene.Example
ExampleSet - class com.penguinwerks.jodene.ExampleSet.: An example set is a set of examples.
ExampleSet() - Constructor for class com.penguinwerks.jodene.ExampleSet
ExampleSetException - exception com.penguinwerks.jodene.ExampleSetException.: Thrown if there is an error with the example set.
ExampleSetException() - Constructor for class com.penguinwerks.jodene.ExampleSetException: Creates a new instance of ExampleSetException
ExampleSetException(String) - Constructor for class com.penguinwerks.jodene.ExampleSetException: Constructor that sets the message.
ExampleSetException(String, Throwable) - Constructor for class com.penguinwerks.jodene.ExampleSetException: Constructor with name and exception chain.
ExampleSetException(Throwable) - Constructor for class com.penguinwerks.jodene.ExampleSetException: Constructor with exception change.
ExampleSetManager - class com.penguinwerks.jodene.managers.ExampleSetManager.: This manager handles the storing and retrieval of example sets.
endEpoch() - Method in class com.penguinwerks.jodene.NeuronTraining: Called to end the epoch.
endEpoch(Network) - Method in class com.penguinwerks.jodene.Trainer: Called at the end of an epoch.
endTraining() - Method in class com.penguinwerks.jodene.Network: Completes the training by removing training structures from the network.
epochEnd(TrainingEpochEvent) - Method in interface com.penguinwerks.jodene.EpochEventListener: The end epoch event.
epochEnd(TrainingEpochEvent) - Method in class com.penguinwerks.jodene.listeners.MaxIterationsListener: Implements the listener interface and handles the end of epoch event.
epochEnd(TrainingEpochEvent) - Method in class com.penguinwerks.jodene.listeners.PocketListener: Implements the end epoch method.
epochEnd(TrainingEpochEvent) - Method in class com.penguinwerks.jodene.listeners.StopOnClassificationListener: Implements epoch end listeners.
epochEnd(TrainingEpochEvent) - Method in class com.penguinwerks.jodene.listeners.StopOnErrorListener: An implementation of the EpochEventListener interface.
evaluate(Network, ExampleSet) - Method in class com.penguinwerks.jodene.Evaluator: Evaluates the network, returning the evaluation of the error.

F

FactorScaler - class com.penguinwerks.jodene.data.FactorScaler.: A factor scaler is an instance of scaler that divides the input value by the given factor.
FactorScaler() - Constructor for class com.penguinwerks.jodene.data.FactorScaler: Constructors - empty contructor;
FactorScaler(double) - Constructor for class com.penguinwerks.jodene.data.FactorScaler: Constructor that takes a factor as an argument.
Field - class com.penguinwerks.jodene.data.Field.: A field used to read in values.
Field() - Constructor for class com.penguinwerks.jodene.data.Field
FileDataReader - class com.penguinwerks.jodene.data.FileDataReader.: Reads in data from a file.
FileDataReader() - Constructor for class com.penguinwerks.jodene.data.FileDataReader
feedback(double) - Method in class com.penguinwerks.jodene.Axon: When training feedback is fired from the dendrite neuron back to the base.
finalize() - Method in class com.penguinwerks.jodene.Pocket
fireEpochEvent(Network) - Method in class com.penguinwerks.jodene.Trainer: Fires an epoch training event to all the listeners.

G

GenericManager - class com.penguinwerks.jodene.managers.GenericManager.: This is generic manager of objects inside the vault.
GenericManager() - Constructor for class com.penguinwerks.jodene.managers.GenericManager: Creates a new instance of GenericManager
get(int) - Method in class com.penguinwerks.jodene.ExampleSet: Returns the example at a given index.
getActivationFactory() - Method in class com.penguinwerks.jodene.Network: Returns the activaiton factory.
getActivationFactory() - Method in class com.penguinwerks.jodene.NetworkBuilder: Returns the activation factory for this builder.
getBase() - Method in class com.penguinwerks.jodene.Axon: Returns the base of the Axon.
getCalculator(String) - Method in class com.penguinwerks.jodene.ErrorManager: Returns an error calculator with a given name.
getContents(String) - Method in class com.penguinwerks.jodene.Pocket: Returns the contents of the pocket or null if there is no network in the pocket.
getCreateDate() - Method in class com.penguinwerks.jodene.managers.DataStorageTag: Returns the date this vault item was created.
getData(String) - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Returns the example set for the given name.
getDefaultName() - Method in class com.penguinwerks.jodene.ErrorCalculator: Returns the default name for this error calculator.
getDefaultName() - Method in class com.penguinwerks.jodene.calculators.ClassificationErrorCalculator: Returns the the default name of the classification error calculator.
getDefaultName() - Method in class com.penguinwerks.jodene.calculators.MSEErrorCalculator: Returns the default name of the mean squared error calculator.
getDefaultName() - Method in class com.penguinwerks.jodene.calculators.SSEErrorCalculator: Returns the default name of the sum of squares error calculator
getDelimiter() - Method in class com.penguinwerks.jodene.data.FileDataReader: The delimiter used to separate inputs in a line.
getDendrite() - Method in class com.penguinwerks.jodene.Axon: Returns the dendrite of the Axon.
getDescription() - Method in class com.penguinwerks.jodene.managers.DataStorageTag: Returns the description
getEpochCount() - Method in class com.penguinwerks.jodene.Trainer: Returns the epoch count so far.
getEpochSize() - Method in class com.penguinwerks.jodene.Trainer: The epoch size is the number of examples to present during training before the error is saved and the weights are adjusted.
getError(String) - Method in class com.penguinwerks.jodene.ErrorManager: Returns the error for a given error calculator.
getError(String) - Method in class com.penguinwerks.jodene.Evaluator: Return the error for the given name.
getError() - Method in class com.penguinwerks.jodene.listeners.StopOnErrorListener: Returns the error threshold.
getErrorHistorySize() - Method in class com.penguinwerks.jodene.ErrorManager: Returns the size of the error history.
getErrorManager() - Method in class com.penguinwerks.jodene.Trainer: Returns the error manager used by the trainer when calculating training error.
getErrorName() - Method in class com.penguinwerks.jodene.listeners.StopOnClassificationListener: The name of this error listener.
getErrorName() - Method in class com.penguinwerks.jodene.listeners.StopOnErrorListener: Returns the name of the error to listen to.
getErrorNames() - Method in class com.penguinwerks.jodene.Evaluator: Returns the error names.
getErrors() - Method in class com.penguinwerks.jodene.Pocket: Returns the names of the errors that are managed the this pocket.
getExpected() - Method in class com.penguinwerks.jodene.Example: Returns the expected values for this example.
getExtension() - Method in class com.penguinwerks.jodene.managers.GenericManager: Returns the extension the manager will use.
getFactor() - Method in class com.penguinwerks.jodene.data.FactorScaler: The factor to use.
getFeature(String) - Method in class com.penguinwerks.jodene.managers.DataStorageTag: Returns a feature for a given name.
getHardMax() - Method in class com.penguinwerks.jodene.Trainer: If no EpochEventListeners are added to the network the hardMax limit is used to safely stop training.
getHistoricalErrors(String) - Method in class com.penguinwerks.jodene.ErrorManager: Returns the error history for a given error calculator.
getId() - Method in class com.penguinwerks.jodene.Axon: Returns the Id of the axon.
getInputData(String) - Method in class com.penguinwerks.jodene.managers.InputDataManager: Returns the data set.
getInputData(String) - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Returns the named result set.
getInputs() - Method in class com.penguinwerks.jodene.Example: The inputs expected to produce the given expected values.
getInputs() - Method in class com.penguinwerks.jodene.Result: Returns the inputs for this result.
getLastError(String) - Method in class com.penguinwerks.jodene.ErrorManager: Returns the last error value for a given calculator.
getLastErrors() - Method in class com.penguinwerks.jodene.ErrorManager: Returns the last error report in history.
getLastUpdateEpoch(String) - Method in class com.penguinwerks.jodene.Pocket: Return the epoch the pocket was updated.
getLastUpdateEpoch() - Method in class com.penguinwerks.jodene.managers.PocketManager: Returns the epoch number when the pocket was last updated.
getLastUpdateError(String) - Method in class com.penguinwerks.jodene.Pocket: Returns the last update error for the network in the pocket or the MAX_VALUE of double if there is no network in the pocket.
getLastUpdateError() - Method in class com.penguinwerks.jodene.managers.PocketManager: Returns the error of the network in the pocket.
getLearningRate() - Method in class com.penguinwerks.jodene.NeuronTraining: The learning rate used by this Neuron trainer.
getLearningRate() - Method in class com.penguinwerks.jodene.Trainer: Returns the default learning rate set for training.
getManager() - Static method in class com.penguinwerks.jodene.managers.DataReaderManager: Returns an instance of the data reader manager.
getManager() - Static method in class com.penguinwerks.jodene.managers.ExampleSetManager: Used to obtain a reference to the example set manager, a singleton in this system.
getManager() - Static method in class com.penguinwerks.jodene.managers.InputDataManager: Returns the input data manager.
getManager() - Static method in class com.penguinwerks.jodene.managers.NetworkManager: Returns an instance of the network manager.
getManager() - Static method in class com.penguinwerks.jodene.managers.ResultSetManager: Returns an instance of the result set manager.
getMax() - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction: The maximum value for activation.
getMax() - Method in class com.penguinwerks.jodene.data.RangeScaler: The maximum value for the scale.
getMaxIterations() - Method in class com.penguinwerks.jodene.listeners.MaxIterationsListener: The maximum number of iterations.
getMaxScale() - Method in class com.penguinwerks.jodene.data.ClassificationScaler: This is the maximum value for a classifier, usually considered the "on" or "yes" value.
getMin() - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction: The minimum value for activation.
getMin() - Method in class com.penguinwerks.jodene.data.RangeScaler: The minimum value for the scale.
getMinScale() - Method in class com.penguinwerks.jodene.data.ClassificationScaler: This is the minimum value for a classifier, usually considered the "off" or "no" value.
getMomentum() - Method in class com.penguinwerks.jodene.NeuronTraining: The momentum rate used by this Neuron trainer.
getMomentum() - Method in class com.penguinwerks.jodene.Trainer: Returns the momentum used during training.
getName() - Method in class com.penguinwerks.jodene.Neuron: Returns the name of this neuron.
getName() - Method in class com.penguinwerks.jodene.data.Column: This will be the name of the column in the output data set.
getName() - Method in class com.penguinwerks.jodene.data.Field: The field name.
getNetwork() - Method in class com.penguinwerks.jodene.TrainingEpochEvent: Returns the network which is being trained.
getNetwork(String) - Method in class com.penguinwerks.jodene.managers.NetworkManager: Returns the named network from the vault.
getNetwork() - Method in class com.penguinwerks.jodene.managers.PocketManager: Returns the network from the pocket.
getObject(String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Return an object from the vault.
getOutputSize() - Method in class com.penguinwerks.jodene.data.KClassTranslator: Indicates the size of K.
getOutputSize() - Method in class com.penguinwerks.jodene.data.NMinusOneClassTranslator: The numer of doubles in the output array.
getOutputSize() - Method in class com.penguinwerks.jodene.data.Translator: Abstract method that returns the size of an encoded class.
getOutputValue() - Method in class com.penguinwerks.jodene.Neuron: Returns the output value for this neuron.
getOutputs() - Method in class com.penguinwerks.jodene.Result: The outputs for this result
getPartials() - Method in class com.penguinwerks.jodene.NeuronTraining: Return the partial derivatives.
getReader(String) - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Returns the named data reader from the vault.
getReport() - Method in class com.penguinwerks.jodene.ErrorManager: Returns the error report, which contains the errors, organized by name.
getResult(int) - Method in class com.penguinwerks.jodene.ResultSet: Returns the result at the given index.
getScaler() - Method in class com.penguinwerks.jodene.data.Column: This will be the scaler used to scale the value.
getSize() - Method in class com.penguinwerks.jodene.ErrorManager: Returns the number of error calculators configured.
getSize() - Method in class com.penguinwerks.jodene.ExampleSet: Returns the size of the example set.
getSize() - Method in class com.penguinwerks.jodene.ResultSet: Returns the size of the result set.
getSizes() - Method in class com.penguinwerks.jodene.NetworkBuilder: Return the sizes of the layers of the network to build
getStopValue() - Method in class com.penguinwerks.jodene.listeners.StopOnClassificationListener: Returns the number of missclassifications that will stop training.
getStorageTag(String) - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Returns the data storage tag for the named data reader.
getStorageTag(String) - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Returns the data storage tage associates with a given example set.
getStorageTag(String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Returns the data storage tag for this object.
getStorageTag(String) - Method in class com.penguinwerks.jodene.managers.InputDataManager: Returns the data storage tag.
getStorageTag(String) - Method in class com.penguinwerks.jodene.managers.NetworkManager: Returns the data storage tag for the named network.
getStorageTag(String) - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Returns the data storage tag for the result set.
getTrainer(String) - Method in class com.penguinwerks.jodene.Network: Returns the trainer attached to this network.
getTrainer() - Method in class com.penguinwerks.jodene.Neuron: Returns the affiliated neuron trainer.
getTrainer() - Method in class com.penguinwerks.jodene.NeuronTraining: The trainer that owns this neuron trainer.
getTraining() - Method in class com.penguinwerks.jodene.Trainer: Returns the default neuron training for this trainer.
getTrainingExamples() - Method in class com.penguinwerks.jodene.Trainer: The training examples are set of known inputs and their outputs used to train the network.
getTranslator() - Method in class com.penguinwerks.jodene.data.TranslatedField: The translator that actually translates the value.
getValue() - Method in class com.penguinwerks.jodene.data.OutputField: The value.
getVaulDirectory() - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Returns the current directory for the example set vault.
getVaultDirectory() - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Returns the base directory for the vault.
getVaultDirectory() - Method in class com.penguinwerks.jodene.managers.GenericManager: Returns the vault directory.
getVaultDirectory() - Method in class com.penguinwerks.jodene.managers.InputDataManager: Returns the vault directory.
getVaultDirectory() - Method in class com.penguinwerks.jodene.managers.NetworkManager: Returns the base directory for the vault.
getVaultDirectory() - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Returns the vault directory for the result sets.
getWeightUpdates() - Method in class com.penguinwerks.jodene.NeuronTraining: Returns the weight updates - anther specious function.

I

InputDataManager - class com.penguinwerks.jodene.managers.InputDataManager.: Stores and retrieves input data files.
InvalidInputsException - exception com.penguinwerks.jodene.InvalidInputsException.: This exception is thrown when the inputs do not match the expected values in the network.
InvalidInputsException() - Constructor for class com.penguinwerks.jodene.InvalidInputsException
InvalidInputsException(String) - Constructor for class com.penguinwerks.jodene.InvalidInputsException
InvalidInputsException(String, Throwable) - Constructor for class com.penguinwerks.jodene.InvalidInputsException
InvalidInputsException(Throwable) - Constructor for class com.penguinwerks.jodene.InvalidInputsException
isScaling() - Method in class com.penguinwerks.jodene.data.Column: Identifies the column as performing scaling.

K

KClassTranslator - class com.penguinwerks.jodene.data.KClassTranslator.: This translates one of a set of strings into an array of values, such that there is a member for each possible string.
KClassTranslator() - Constructor for class com.penguinwerks.jodene.data.KClassTranslator

L

listCalculators() - Method in class com.penguinwerks.jodene.ErrorManager: Returns the list of calculator names.
listDataFiles() - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Lists the example sets in this vault.
listDataSets() - Method in class com.penguinwerks.jodene.managers.InputDataManager: Lists the data sets in the vault.
listFilenames() - Method in class com.penguinwerks.jodene.managers.GenericManager: Lists the names of the stored objects.
listNetworks() - Method in class com.penguinwerks.jodene.managers.NetworkManager: Lists the networks in the vault.
listReaders() - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Lists the data readers in the vault.
listResultSets() - Method in class com.penguinwerks.jodene.managers.ResultSetManager: Lists the result set in the vaults.

M

MSEErrorCalculator - class com.penguinwerks.jodene.calculators.MSEErrorCalculator.: Mean squared error calculator.
MSEErrorCalculator(int) - Constructor for class com.penguinwerks.jodene.calculators.MSEErrorCalculator: Creates a new instance of MSEErrorCalculator
MaxIterationsListener - class com.penguinwerks.jodene.listeners.MaxIterationsListener.: This epoch event listener requests training termination after maxIterations epochs have expired.
MaxIterationsListener() - Constructor for class com.penguinwerks.jodene.listeners.MaxIterationsListener: Default constructor.
MaxIterationsListener(int) - Constructor for class com.penguinwerks.jodene.listeners.MaxIterationsListener: Constructor that sets the maximum number of iterations.
main(String[]) - Static method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction
main(String[]) - Static method in class com.penguinwerks.jodene.activation.TanhActivationFunction
main(String[]) - Static method in class com.penguinwerks.jodene.data.TestReader: Main method for the test.
makeExamples(List, List, List) - Static method in class com.penguinwerks.jodene.ExampleSet: A static factory function that builds an example set from data, and the list of input and output names.
makeFunction() - Method in interface com.penguinwerks.jodene.ActivationFactory: Returns an activation function.
makeFunction() - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFactory: Creates a new sigmoid activation function.
makeFunction() - Method in class com.penguinwerks.jodene.activation.TanhActivationFactory: This method creates a new Tanh activation function.

N

NMinusOneClassTranslator - class com.penguinwerks.jodene.data.NMinusOneClassTranslator.: This class encodes a set of values using N-1 encoding, that is, if it a class with K members is encoded using K-1 values.
NMinusOneClassTranslator() - Constructor for class com.penguinwerks.jodene.data.NMinusOneClassTranslator
Network - class com.penguinwerks.jodene.Network.: This is a neural network.
Network() - Constructor for class com.penguinwerks.jodene.Network: Create a new instance of a network.
NetworkBuilder - class com.penguinwerks.jodene.NetworkBuilder.: TODO Implement a generic network builder.
NetworkBuilder() - Constructor for class com.penguinwerks.jodene.NetworkBuilder
NetworkManager - class com.penguinwerks.jodene.managers.NetworkManager.: Manages collections of networks.
Neuron - class com.penguinwerks.jodene.Neuron.: A neuron is a basic processing unit in the network.
Neuron() - Constructor for class com.penguinwerks.jodene.Neuron
Neuron(String) - Constructor for class com.penguinwerks.jodene.Neuron: Constructor - requires a name which needs to be unique for the network.
NeuronTraining - class com.penguinwerks.jodene.NeuronTraining.: This class is used by the neuron to facilitate training.
NeuronTraining() - Constructor for class com.penguinwerks.jodene.NeuronTraining: Default constructor.
nameValues(double[]) - Method in class com.penguinwerks.jodene.data.DataReader: Assigns the name to values.
nextExample() - Method in class com.penguinwerks.jodene.ExampleSet: Returns the next example.

O

OutputField - class com.penguinwerks.jodene.data.OutputField.: TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Generation - Code and Comments
OutputField() - Constructor for class com.penguinwerks.jodene.data.OutputField

P

Pocket - class com.penguinwerks.jodene.Pocket.
Pocket(String) - Constructor for class com.penguinwerks.jodene.Pocket: Creates a new instance of Pocket
PocketListener - class com.penguinwerks.jodene.listeners.PocketListener.: This listener invokes the pocket system for the network.
PocketListener(Pocket) - Constructor for class com.penguinwerks.jodene.listeners.PocketListener: Creates a new instance of PocketListener
PocketManager - class com.penguinwerks.jodene.managers.PocketManager.: The pocket manager used to manage the networks in the pocket.
PocketManager(String, String) - Constructor for class com.penguinwerks.jodene.managers.PocketManager: Creates a new instance of PocketManager
process(Map) - Method in class com.penguinwerks.jodene.Network: Process a set of inputs and return a result.
process(String) - Method in class com.penguinwerks.jodene.data.Field: Abstract process method.
process(String) - Method in class com.penguinwerks.jodene.data.RealField: Translates an input string to a result double.
process(String) - Method in class com.penguinwerks.jodene.data.TranslatedField: Processes the input value by returning the translated value.
propagate(double) - Method in class com.penguinwerks.jodene.Axon: Propagates the given signal to the dendrite neuron from the base.

R

RangeScaler - class com.penguinwerks.jodene.data.RangeScaler.: The range scaler scales a raw value between the min an max in a range.
RangeScaler() - Constructor for class com.penguinwerks.jodene.data.RangeScaler
RealField - class com.penguinwerks.jodene.data.RealField.: Translates the input string to a resulting double.
RealField() - Constructor for class com.penguinwerks.jodene.data.RealField
Result - class com.penguinwerks.jodene.Result.: A result is the inputs and their expected values.
Result(Map, Map) - Constructor for class com.penguinwerks.jodene.Result: Creates a new instance of Result
ResultSet - class com.penguinwerks.jodene.ResultSet.: A result set is a collection of inputs and their returned results.
ResultSet() - Constructor for class com.penguinwerks.jodene.ResultSet: Creates a new instance of ResultSet
ResultSetManager - class com.penguinwerks.jodene.managers.ResultSetManager.: Manages result sets, which are the results processed by the network.
readValues() - Method in class com.penguinwerks.jodene.data.DataReader: This is an abstract method that is implemented by a particular data reader, for example a JDBC data reader would read from a database.
readValues() - Method in class com.penguinwerks.jodene.data.FileDataReader: An implementation of DataReader.readValues().
receiveFeedback(double, Axon) - Method in class com.penguinwerks.jodene.Neuron: Receives feedback from subsequent layer neurons.
receiveSignal(Axon, double) - Method in class com.penguinwerks.jodene.Neuron: This receives an input signal from the input axon.
removeDataFile(String) - Method in class com.penguinwerks.jodene.managers.ExampleSetManager: Remove the data file from the vault.
removeFile(String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Removes the object from the vault.
removeNetwork(String) - Method in class com.penguinwerks.jodene.managers.NetworkManager: Remove the network from the vault.
removeReader(String) - Method in class com.penguinwerks.jodene.managers.DataReaderManager: Remove the data reader from the vault.
requestTermination() - Method in class com.penguinwerks.jodene.Trainer: Used primarily by the epoch event listeners to request the neural network to stop training.

S

SSEErrorCalculator - class com.penguinwerks.jodene.calculators.SSEErrorCalculator.: A sum of squares error calculator.
SSEErrorCalculator() - Constructor for class com.penguinwerks.jodene.calculators.SSEErrorCalculator: Default constructor.
Scaler - class com.penguinwerks.jodene.data.Scaler.: An abstract scaler.
Scaler() - Constructor for class com.penguinwerks.jodene.data.Scaler
SigmoidActivationFactory - class com.penguinwerks.jodene.activation.SigmoidActivationFactory.: The sigmoid activation Factory.
SigmoidActivationFactory() - Constructor for class com.penguinwerks.jodene.activation.SigmoidActivationFactory: Creates a new instance of SigmoidActivationFactory
SigmoidActivationFunction - class com.penguinwerks.jodene.activation.SigmoidActivationFunction.: The sigmoid activation function.
SigmoidActivationFunction() - Constructor for class com.penguinwerks.jodene.activation.SigmoidActivationFunction: Default constructor.
StopOnClassificationListener - class com.penguinwerks.jodene.listeners.StopOnClassificationListener.: Stops training when the max number of incorrect classifications is reached.
StopOnClassificationListener() - Constructor for class com.penguinwerks.jodene.listeners.StopOnClassificationListener: Creates a new instance of StopOnCassificationListener
StopOnClassificationListener(double) - Constructor for class com.penguinwerks.jodene.listeners.StopOnClassificationListener: Creates a new listener.
StopOnErrorListener - class com.penguinwerks.jodene.listeners.StopOnErrorListener.: This implementation of the epoch listener interface sets a threshold error.
StopOnErrorListener() - Constructor for class com.penguinwerks.jodene.listeners.StopOnErrorListener: Default constructor.
StopOnErrorListener(double) - Constructor for class com.penguinwerks.jodene.listeners.StopOnErrorListener: Constructor that sets the error threshold.
saveNetwork(String, Network, Trainer) - Method in class com.penguinwerks.jodene.Pocket: Save the network to the pocket with the named error calculator.
saveNetwork(Network, Trainer) - Method in class com.penguinwerks.jodene.managers.PocketManager: Saves the network to the pocket if it has a lower error than the existing version of the network.
scale(double) - Method in class com.penguinwerks.jodene.data.ClassificationScaler: Scales the input value.
scale(double) - Method in class com.penguinwerks.jodene.data.FactorScaler: Scales the input value, dividing by the given factor.
scale(double) - Method in class com.penguinwerks.jodene.data.RangeScaler: Scale the input value so that input values at max are = 1.0 and input values at minumum are 0.0.
scale(double) - Method in class com.penguinwerks.jodene.data.Scaler: The abstract scaling method to implement.
scaleLine(double[]) - Method in class com.penguinwerks.jodene.data.DataReader: Performs the scaling on a line translated into doubles.
setActivationFactory(ActivationFactory) - Method in class com.penguinwerks.jodene.Network: Set the activation factory which will create new activation functions.
setActivationFactory(ActivationFactory) - Method in class com.penguinwerks.jodene.NetworkBuilder: Sets the factory that will create activation functions, therefore building the network with the desired activation function.
setActivationFunction(ActivationFunction) - Method in class com.penguinwerks.jodene.Neuron: Sets the activation function used by this neuron.
setBase(Neuron) - Method in class com.penguinwerks.jodene.Axon: A signal propagates from the base neuron to the dendrite neuron through the axon.
setDefaultErrorName(String) - Method in class com.penguinwerks.jodene.Trainer: Sets the default error name to examine.
setDelimiter(String) - Method in class com.penguinwerks.jodene.data.FileDataReader: The delimiter used to separate inputs in a line.
setDendrite(Neuron) - Method in class com.penguinwerks.jodene.Axon: Sets the dendrite or destination neuron for this axon.
setDescription(String) - Method in class com.penguinwerks.jodene.managers.DataStorageTag: Set the description for this data storage tag.
setEpochSize(int) - Method in class com.penguinwerks.jodene.Trainer: The epoch size is the number of examples to present during training before the error is saved and the weights are adjusted.
setError(Double, Double) - Method in class com.penguinwerks.jodene.Neuron: Set the error using the actual and expected values.
setError(double) - Method in class com.penguinwerks.jodene.listeners.StopOnErrorListener: Sets the error threshold.
setErrorName(String) - Method in class com.penguinwerks.jodene.listeners.StopOnClassificationListener: Sets the error name for the listener.
setErrorName(String) - Method in class com.penguinwerks.jodene.listeners.StopOnErrorListener: Sets the name of the error to listen to.
setExpected(Map) - Method in class com.penguinwerks.jodene.Example: Set the expected results for this example.
setExtension(String) - Method in class com.penguinwerks.jodene.managers.GenericManager: Sets the file extension of the type of data to be stored.
setFactor(double) - Method in class com.penguinwerks.jodene.data.FactorScaler: The factor to use.
setFeedback(Map, Map) - Method in class com.penguinwerks.jodene.Network: During training a network is presented the actual and expected values for a given input.
setFilename(String) - Method in class com.penguinwerks.jodene.data.FileDataReader: The filename to read.
setHardMax(int) - Method in class com.penguinwerks.jodene.Trainer: If no EpochEventListeners are added to the network the hardMax limit is used to safely stop training.
setInput(double) - Method in class com.penguinwerks.jodene.Neuron: If this neuron is an input neuron, then the output value is set by the neural network and the results are propagated to the output axons.
setInputs(Map) - Method in class com.penguinwerks.jodene.Example: The inputs expected to produce the given expected result.
setLearningRate(double) - Method in class com.penguinwerks.jodene.NeuronTraining: The learning rate used by this Neuron trainer.
setLearningRate(double) - Method in class com.penguinwerks.jodene.Trainer: Set the default learning rate used for training.
setMax(double) - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction: The maximum value for output activation.
setMax(double) - Method in class com.penguinwerks.jodene.data.RangeScaler: The maximum value for the scale.
setMaxIterations(int) - Method in class com.penguinwerks.jodene.listeners.MaxIterationsListener: The maximum number of iterations.
setMaxScale(double) - Method in class com.penguinwerks.jodene.data.ClassificationScaler: This is the maximum value for a classifier, usually considered the "on" or "yes" value.
setMin(double) - Method in class com.penguinwerks.jodene.activation.SigmoidActivationFunction: The mimimum output value for activation.
setMin(double) - Method in class com.penguinwerks.jodene.data.RangeScaler: The minimum value for the scale.
setMinScale(double) - Method in class com.penguinwerks.jodene.data.ClassificationScaler: This is the minimum value for a classifier, usually considered the "off" or "no" value.
setMomentum(double) - Method in class com.penguinwerks.jodene.NeuronTraining: The momentum rate used by this Neuron trainer.
setMomentum(double) - Method in class com.penguinwerks.jodene.Trainer: Sets the momentum used during