org.knime.base.node.mine.bfn
Class BasisFunctionPredictorNodeModel

java.lang.Object
  extended by org.knime.core.node.NodeModel
      extended by org.knime.base.node.mine.bfn.BasisFunctionPredictorNodeModel
Direct Known Subclasses:
FuzzyBasisFunctionPredictorNodeModel, RadialBasisFunctionPredictorNodeModel

public abstract class BasisFunctionPredictorNodeModel
extends NodeModel

The basis function predictor model performing a prediction on the data from the first input and the radial basisfunction model from the second.

Author:
Thomas Gabriel, University of Konstanz
See Also:
BasisFunctionPredictorCellFactory

Constructor Summary
protected BasisFunctionPredictorNodeModel(PortType model)
          Creates a new basisfunction predictor model with two inputs, the first one which contains the data and the second with the model.
 
Method Summary
 boolean appendClassProbabilities()
           
 DataTableSpec[] configure(PortObjectSpec[] portObjSpec)
          Configure method for general port types.
 ColumnRearranger createRearranger(DataTableSpec dataSpec, String[] modelSpec)
          Creates a column rearranger based on the data spec.
 DataColumnSpec[] createSpec(DataTableSpec dataSpec, DataTableSpec modelSpec, int modelClassIdx)
          Creates the output model spec.
 BufferedDataTable[] execute(PortObject[] portObj, ExecutionContext exec)
          Execute method for general port types.
 String getApplyColumn()
           
 double getDontKnowClassDegree()
           
 void loadInternals(File internDir, ExecutionMonitor exec)
          Load internals into the derived NodeModel.
 void loadValidatedSettingsFrom(NodeSettingsRO settings)
          Sets new settings from the passed object in the model.
abstract  boolean normalizeClassification()
           
 void reset()
          Override this function in the derived model and reset your NodeModel.
 void saveInternals(File internDir, ExecutionMonitor exec)
          Save internals of the derived NodeModel.
 void saveSettingsTo(NodeSettingsWO settings)
          Adds to the given NodeSettings the model specific settings.
 void validateSettings(NodeSettingsRO settings)
          Validates the settings in the passed NodeSettings object.
 
Methods inherited from class org.knime.core.node.NodeModel
addWarningListener, configure, continueLoop, execute, executeModel, getInHiLiteHandler, getLoopEndNode, getLoopStartNode, getNrInPorts, getNrOutPorts, getOutHiLiteHandler, getWarningMessage, notifyViews, notifyWarningListeners, peekFlowVariableDouble, peekFlowVariableInt, peekFlowVariableString, peekScopeVariableDouble, peekScopeVariableInt, peekScopeVariableString, pushFlowVariableDouble, pushFlowVariableInt, pushFlowVariableString, pushScopeVariableDouble, pushScopeVariableInt, pushScopeVariableString, removeWarningListener, setInHiLiteHandler, setWarningMessage, stateChanged
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BasisFunctionPredictorNodeModel

protected BasisFunctionPredictorNodeModel(PortType model)
Creates a new basisfunction predictor model with two inputs, the first one which contains the data and the second with the model.

Parameters:
model - type of the basisfunction model at the in-port
Method Detail

execute

public BufferedDataTable[] execute(PortObject[] portObj,
                                   ExecutionContext exec)
                            throws CanceledExecutionException,
                                   InvalidSettingsException
Execute method for general port types. The argument objects represent the input objects and are guaranteed to be subclasses of the PortObject classes that are defined through the PortTypes given in the constructor. Similarly, the returned output objects need to comply with their port types object class (otherwise an error is reported by the framework).

For a general description of the execute method refer to the description of the specialized NodeModel.execute(BufferedDataTable[], ExecutionContext) methods as it addresses more use cases.

Overrides:
execute in class NodeModel
Parameters:
portObj - The input objects.
exec - For BufferedDataTable creation and progress.
Returns:
The output objects.
Throws:
CanceledExecutionException
InvalidSettingsException

createSpec

public final DataColumnSpec[] createSpec(DataTableSpec dataSpec,
                                         DataTableSpec modelSpec,
                                         int modelClassIdx)
Creates the output model spec.

Parameters:
dataSpec - input data spec
modelSpec - input model spec
modelClassIdx - index with reflects the class column
Returns:
the new model spec

normalizeClassification

public abstract boolean normalizeClassification()
Returns:
true if normalization is required for output

getApplyColumn

public String getApplyColumn()
Returns:
the column name contained the winner prediction

getDontKnowClassDegree

public double getDontKnowClassDegree()
Returns:
the don't know class probability between 0.0 and 1.0

appendClassProbabilities

public boolean appendClassProbabilities()
Returns:
true if class probability columns should be appended

configure

public DataTableSpec[] configure(PortObjectSpec[] portObjSpec)
                          throws InvalidSettingsException
Configure method for general port types. The argument specs represent the input object specs and are guaranteed to be subclasses of the PortObjectSpecs that are defined through the PortTypes given in the constructor. Similarly, the returned output specs need to comply with their port types spec class (otherwise an error is reported by the framework). They may also be null.

For a general description of the configure method refer to the description of the specialized NodeModel.configure(DataTableSpec[]) methods as it addresses more use cases.

Overrides:
configure in class NodeModel
Parameters:
portObjSpec - The input object specs.
Returns:
The output objects specs or null.
Throws:
InvalidSettingsException - If this node can't be configured.

createRearranger

public final ColumnRearranger createRearranger(DataTableSpec dataSpec,
                                               String[] modelSpec)
                                        throws InvalidSettingsException
Creates a column rearranger based on the data spec. The new apply column is appended.

Parameters:
dataSpec - data spec
modelSpec - model spec
Returns:
column rearranger from data spec
Throws:
InvalidSettingsException - if the settings are not valid against data and/or model spec

reset

public void reset()
Override this function in the derived model and reset your NodeModel. All components should unregister themselves from any observables (at least from the hilite handler right now). All internally stored data structures should be released. User settings should not be deleted/reset though.

Specified by:
reset in class NodeModel

loadValidatedSettingsFrom

public void loadValidatedSettingsFrom(NodeSettingsRO settings)
                               throws InvalidSettingsException
Sets new settings from the passed object in the model. You can safely assume that the object passed has been successfully validated by the #validateSettings(NodeSettings) method. The model must set its internal configuration according to the settings object passed.

Specified by:
loadValidatedSettingsFrom in class NodeModel
Parameters:
settings - The settings to read.
Throws:
InvalidSettingsException - If a property is not available.
See Also:
NodeModel.saveSettingsTo(NodeSettingsWO), NodeModel.validateSettings(NodeSettingsRO)

saveSettingsTo

public void saveSettingsTo(NodeSettingsWO settings)
Adds to the given NodeSettings the model specific settings. The settings don't need to be complete or consistent. If, right after startup, no valid settings are available this method can write either nothing or invalid settings.

Method is called by the Node if the current settings need to be saved or transfered to the node's dialog.

Specified by:
saveSettingsTo in class NodeModel
Parameters:
settings - The object to write settings into.
See Also:
NodeModel.loadValidatedSettingsFrom(NodeSettingsRO), NodeModel.validateSettings(NodeSettingsRO)

validateSettings

public void validateSettings(NodeSettingsRO settings)
                      throws InvalidSettingsException
Validates the settings in the passed NodeSettings object. The specified settings should be checked for completeness and consistency. It must be possible to load a settings object validated here without any exception in the #loadValidatedSettings(NodeSettings) method. The method must not change the current settings in the model - it is supposed to just check them. If some settings are missing, invalid, inconsistent, or just not right throw an exception with a message useful to the user.

Specified by:
validateSettings in class NodeModel
Parameters:
settings - The settings to validate.
Throws:
InvalidSettingsException - If the validation of the settings failed.
See Also:
NodeModel.saveSettingsTo(NodeSettingsWO), NodeModel.loadValidatedSettingsFrom(NodeSettingsRO)

loadInternals

public void loadInternals(File internDir,
                          ExecutionMonitor exec)
Load internals into the derived NodeModel. This method is only called if the Node was executed. Read all your internal structures from the given file directory to create your internal data structure which is necessary to provide all node functionalities after the workflow is loaded, e.g. view content and/or hilite mapping.

Specified by:
loadInternals in class NodeModel
Parameters:
internDir - The directory to read from.
exec - Used to report progress and to cancel the load process.
See Also:
NodeModel.saveInternals(File,ExecutionMonitor)

saveInternals

public void saveInternals(File internDir,
                          ExecutionMonitor exec)
Save internals of the derived NodeModel. This method is only called if the Node is executed. Write all your internal structures into the given file directory which are necessary to recreate this model when the workflow is loaded, e.g. view content and/or hilite mapping.

Specified by:
saveInternals in class NodeModel
Parameters:
internDir - The directory to write into.
exec - Used to report progress and to cancel the save process.
See Also:
NodeModel.loadInternals(File,ExecutionMonitor)


Copyright, 2003 - 2010. All rights reserved.
University of Konstanz, Germany.
Chair for Bioinformatics and Information Mining, Prof. Dr. Michael R. Berthold.
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