de.zimek.proteinfeatures.attributeAssigner
Class MotifAssigner

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

All Implemented Interfaces:

ArffAttributeAssigner

public class MotifAssigner

extends AbstractArffRealAttributeAssigner

MotifAssigner assigns numbers of occuring motifs to given proteins, based on a motif map. It has to be initialized using a file providing a motif map. Such a file requires as entries: domainID=(comma separated list of motifIDs (integer)) [one per line]
maximum=(maximal occuring motif id)

Author:

Arthur Zimek

Field Summary

private int	max
static java.lang.String	MAXIMUM
private java.util.regex.Pattern	motifSeparator
private java.util.Properties	properties

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

WHITESPACE

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

ATTRIBUTE_MARK

Constructor Summary

MotifAssigner()

Method Summary

protected double[]	attributes(Protein protein) Returns the attributes according to the actual attribute-assigner.
java.lang.String	getAttributeDefinition() Provides the attribute-definition in arff-format with an ending newline.
void	init(java.io.File motifMap)

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

Field Detail

MAXIMUM

public static java.lang.String MAXIMUM

properties

private java.util.Properties properties

motifSeparator

private java.util.regex.Pattern motifSeparator

max

private int max

Constructor Detail

MotifAssigner

public MotifAssigner()

Method Detail

init

public void init(java.io.File motifMap)

attributes

protected double[] attributes(Protein protein)

Description copied from class: AbstractArffRealAttributeAssigner

Returns the attributes according to the actual attribute-assigner.

Specified by:

attributes in class AbstractArffRealAttributeAssigner

Parameters:

protein -

Returns:

double[]

See Also:

AbstractArffRealAttributeAssigner.attributes(Protein)

getAttributeDefinition

public java.lang.String getAttributeDefinition()

Description copied from interface: ArffAttributeAssigner

Provides the attribute-definition in arff-format with an ending newline.

Returns:

String

See Also:

ArffAttributeAssigner.getAttributeDefinition()