de.zimek.proteinfeatures.attributeAssigner
Class AutoCorrelationFunction

java.lang.Object
  de.zimek.proteinfeatures.attributeAssigner.AbstractArffRealAttributeAssigner
      de.zimek.proteinfeatures.attributeAssigner.AutoCorrelationFunction

All Implemented Interfaces:

ArffAttributeAssigner

public class AutoCorrelationFunction

extends AbstractArffRealAttributeAssigner

implements ArffAttributeAssigner

Provides the AutoCorrelationFunction for an AAIndex and a set m. The function is according to Bu et al.: Prediction of protein (domain) structural classes based on amino-acid index (Eur. J. Biochem. 266, 1043-1049), 1999.

Author:

Arthur Zimek

Field Summary

private AAIndex	aaIndex
private int	m

Fields inherited from class de.zimek.proteinfeatures.attributeAssigner.AbstractArffRealAttributeAssigner

WHITESPACE

Fields inherited from interface de.zimek.proteinfeatures.attributeAssigner.ArffAttributeAssigner

ATTRIBUTE_MARK

Constructor Summary

AutoCorrelationFunction()
Default constructor constructs no aaIndex.

Method Summary

protected double[]	attributes(Protein protein) Returns a list of attributes of length m according to the currently set AAIndex.
java.lang.String	getAttributeDefinition() If m is not set, the description-String will be empty.
void	setAaIndex(AAIndex aaIndex) Sets the aaIndex.
void	setM(int m) Sets the m.

Methods inherited from class de.zimek.proteinfeatures.attributeAssigner.AbstractArffRealAttributeAssigner

getAttribute

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface de.zimek.proteinfeatures.attributeAssigner.ArffAttributeAssigner

getAttribute

Field Detail

aaIndex

private AAIndex aaIndex

m

private int m

Constructor Detail

AutoCorrelationFunction

public AutoCorrelationFunction()

Default constructor constructs no aaIndex. The aaIndex is to be set separately, as is the variable m.

Method Detail

getAttributeDefinition

public java.lang.String getAttributeDefinition()

If m is not set, the description-String will be empty.

Specified by:

getAttributeDefinition in interface ArffAttributeAssigner

Returns:

String

See Also:

ArffAttributeAssigner.getAttributeDefinition()

setAaIndex

public void setAaIndex(AAIndex aaIndex)

Sets the aaIndex.

Parameters:

aaIndex - The aaIndex to set

setM

public void setM(int m)

Sets the m.

Parameters:

m - The m to set

attributes

protected double[] attributes(Protein protein)

Returns a list of attributes of length m according to the currently set AAIndex.

Specified by:

attributes in class AbstractArffRealAttributeAssigner

Parameters:

protein -

Returns:

double[]

Throws:

java.lang.NullPointerException - if aaIndex is not set.

See Also:

AbstractArffRealAttributeAssigner.attributes(Protein)