org.knime.base.node.mine.pca
Class SettingsModelPCADimensions

java.lang.Object
  extended by org.knime.core.node.defaultnodesettings.SettingsModel
      extended by org.knime.base.node.mine.pca.SettingsModelPCADimensions

public class SettingsModelPCADimensions
extends SettingsModel

Settings model, where either an integer (like number of dimensions) or a double like reproduction percentage can be chosen.

Author:
uwe, University of Konstanz

Nested Class Summary
 class SettingsModelPCADimensions.ArraySpinnerModel
           
 
Constructor Summary
SettingsModelPCADimensions(String configName, int intDefault, double doubleDefault, boolean intChoosen)
           
 
Method Summary
 void configureQualitySlider(JSpinner spinner)
           
protected  SettingsModelPCADimensions createClone()
          
protected  String getConfigName()
          
 int getDimensions()
           
 boolean getDimensionsSelected()
           
 double[] getEigenvalues()
           
 String getInformationPreservation(int dim)
           
 double getMinQuality()
           
protected  String getModelTypeID()
          Each settings model provides an ID which will be stored with its values.
 String getNeededDimensionDescription()
           
 int getNeededDimensions(int maxDimensions)
          get number of dimensions to reduce to based on these settings.
protected  void loadSettingsForDialog(NodeSettingsRO settings, PortObjectSpec[] specs)
          Read the value(s) of this settings model from configuration object.
protected  void loadSettingsForModel(NodeSettingsRO settings)
          Read value(s) of this settings model from the configuration object.
protected  void saveSettingsForDialog(NodeSettingsWO settings)
          Write value(s) of this component model to configuration object.
protected  void saveSettingsForModel(NodeSettingsWO settings)
          Write value(s) of this settings model to configuration object.
NOTE: Don't call this method directly, rather call saveSettingsTo.
 void setDimensions(int intValue)
           
 void setDimensionsSelected(boolean intChoosen)
           
 void setEigenValues(double[] eigenvalues)
           
 void setMinQuality(double doubleValue)
           
(package private)  void setValues(double quality, int dimensions, boolean dimensionsSelected)
          set all values of the model.
 String toString()
          Derived classes should print their class name plus the config name for nice and useful error messages.
protected  void validateSettingsForModel(NodeSettingsRO settings)
          Read the expected values from the settings object, without assigning them to the internal variables! (Is not called when the model was disabled at the time the settings were saved.)
 
Methods inherited from class org.knime.core.node.defaultnodesettings.SettingsModel
addChangeListener, createCloneWithValidatedValue, isEnabled, loadSettingsFrom, notifyChangeListeners, prependChangeListener, removeChangeListener, saveSettingsTo, setEnabled, validateSettings
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SettingsModelPCADimensions

public SettingsModelPCADimensions(String configName,
                                  int intDefault,
                                  double doubleDefault,
                                  boolean intChoosen)
Parameters:
configName - key for the config
intDefault - default for integer value
doubleDefault - default for double value
intChoosen - default for "is integer value configured?"
Method Detail

getDimensionsSelected

public boolean getDimensionsSelected()
Returns:
is reduction determined by number of dimensions

setDimensionsSelected

public void setDimensionsSelected(boolean intChoosen)
Parameters:
intChoosen - set info by number of dimensions

getDimensions

public int getDimensions()
Returns:
dimensions to reduce to

setDimensions

public void setDimensions(int intValue)
Parameters:
intValue - dimensions to reduce to

getMinQuality

public double getMinQuality()
Returns:
minimum information to preserve

setMinQuality

public void setMinQuality(double doubleValue)
Parameters:
doubleValue - minimum information to preserve

createClone

protected SettingsModelPCADimensions createClone()

Specified by:
createClone in class SettingsModel
Returns:
a new instance of the same object with identical state and value(s).

getConfigName

protected String getConfigName()

Specified by:
getConfigName in class SettingsModel
Returns:
the name provided at settings model construction time. The id associated with the value.

getModelTypeID

protected String getModelTypeID()
Each settings model provides an ID which will be stored with its values. This is to ensure that the same type of model is used to read the values back. Otherwise an assertion will go off. Make sure to provide a unique ID - and to re-use that ID in all compatible models. IntegerModels for example should use the same ID as BoundedInteger models.

Specified by:
getModelTypeID in class SettingsModel
Returns:
a string that identifies all models that are able (and empowered) to read the values stored by this model.

loadSettingsForDialog

protected void loadSettingsForDialog(NodeSettingsRO settings,
                                     PortObjectSpec[] specs)
                              throws NotConfigurableException
Read the value(s) of this settings model from configuration object. If the value is not stored in the config, the objects value must remain unchanged. Called only from within the components using this model. If the model is disabled it should not throw the exception.
This method must always notify change listeners!!
NOTE: Do not call this method directly, rather call dlgLoadSettingsFrom

Specified by:
loadSettingsForDialog in class SettingsModel
Parameters:
settings - The NodeSettings to read from.
specs - The input specs.
Throws:
NotConfigurableException - if the specs are not good enough to

setValues

void setValues(double quality,
               int dimensions,
               boolean dimensionsSelected)
set all values of the model.

Parameters:
quality - min quality
dimensions - dimensions to reduce to
dimensionsSelected - selection by dimension

loadSettingsForModel

protected void loadSettingsForModel(NodeSettingsRO settings)
                             throws InvalidSettingsException
Read value(s) of this settings model from the configuration object. If the value is not stored in the config, an exception will be thrown.
NOTE: Don't call this method directly, rather call loadSettingsFrom.

Specified by:
loadSettingsForModel in class SettingsModel
Parameters:
settings - The NodeSettings to read from.
Throws:
InvalidSettingsException - if load fails.

saveSettingsForDialog

protected void saveSettingsForDialog(NodeSettingsWO settings)
                              throws InvalidSettingsException
Write value(s) of this component model to configuration object. Called only from within the components using this model.
NOTE: Don't call this method directly, rather use dlgSaveSettingsTo.

Specified by:
saveSettingsForDialog in class SettingsModel
Parameters:
settings - The NodeSettings to read from.
Throws:
InvalidSettingsException - if the user has entered wrong values.

saveSettingsForModel

protected void saveSettingsForModel(NodeSettingsWO settings)
Write value(s) of this settings model to configuration object.
NOTE: Don't call this method directly, rather call saveSettingsTo.

Specified by:
saveSettingsForModel in class SettingsModel
Parameters:
settings - The NodeSettings to write into.

toString

public String toString()
Derived classes should print their class name plus the config name for nice and useful error messages. Like that,
return getClass().getSimpleName() + " ('" + m_configName + "')";

Specified by:
toString in class SettingsModel

validateSettingsForModel

protected void validateSettingsForModel(NodeSettingsRO settings)
                                 throws InvalidSettingsException
Read the expected values from the settings object, without assigning them to the internal variables! (Is not called when the model was disabled at the time the settings were saved.)

Specified by:
validateSettingsForModel in class SettingsModel
Parameters:
settings - the object to read the value(s) from
Throws:
InvalidSettingsException - if the value(s) in the settings object are invalid.

setEigenValues

public void setEigenValues(double[] eigenvalues)
Parameters:
eigenvalues - eigenvalues of pca matrix

getEigenvalues

public double[] getEigenvalues()

getNeededDimensions

public int getNeededDimensions(int maxDimensions)
get number of dimensions to reduce to based on these settings.

Parameters:
maxDimensions - dimensionality of input data
Returns:
number of output dimensions as configured, or -1 of it cannot be determined (i.e. evs==null and selection by quality with quality <100)

getNeededDimensionDescription

public String getNeededDimensionDescription()

configureQualitySlider

public void configureQualitySlider(JSpinner spinner)
Parameters:
spinner - spinner component to be updated

getInformationPreservation

public String getInformationPreservation(int dim)
Parameters:
dim - dimensions to reduce to
Returns:
preserved information int percent, based on eigenvalues


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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