edu.berkeley.compbio.msensr.label
Class AbstractTaxonomyLabelChooser

java.lang.Object
  edu.berkeley.compbio.msensr.label.AbstractTaxonomyLabelChooser

Direct Known Subclasses:

MergingLabelChooser, NcbiNameRankLabelChooser, NcbiTaxidRankLabelChooser, StrainDirectoryLabelChooser

public class AbstractTaxonomyLabelChooser
extends java.lang.Object

Version:

$Id$

Author:

David Soergel

Field Summary

protected java.util.Set<java.lang.Integer>	mutuallyExclusiveLabels
protected static java.lang.Integer	NO_VALID_LABEL
TaxonomyService<java.lang.Integer>	taxonomyService

Constructor Summary

AbstractTaxonomyLabelChooser()

Method Summary

java.lang.Integer	findEquivalent(java.lang.Integer synonym)
java.util.Set<java.lang.Integer>	getMutuallyExclusiveLabels()
boolean	isEquivalent(java.lang.Integer label, java.lang.Integer synonym)
void	restrict(java.util.Set<java.lang.Integer> restrictionSet)
java.util.Set<java.lang.Integer>	selectEquivalent(java.util.Set<java.lang.Integer> labels, java.lang.Integer id)

Methods inherited from class java.lang.Object

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

Field Detail

mutuallyExclusiveLabels

protected java.util.Set<java.lang.Integer> mutuallyExclusiveLabels

taxonomyService

public TaxonomyService<java.lang.Integer> taxonomyService

NO_VALID_LABEL

protected static final java.lang.Integer NO_VALID_LABEL

Constructor Detail

AbstractTaxonomyLabelChooser

public AbstractTaxonomyLabelChooser()

Method Detail

getMutuallyExclusiveLabels

public java.util.Set<java.lang.Integer> getMutuallyExclusiveLabels()

restrict

public void restrict(java.util.Set<java.lang.Integer> restrictionSet)

isEquivalent

public boolean isEquivalent(java.lang.Integer label,
                            java.lang.Integer synonym)

selectEquivalent

public java.util.Set<java.lang.Integer> selectEquivalent(java.util.Set<java.lang.Integer> labels,
                                                         java.lang.Integer id)

findEquivalent

@NotNull
public java.lang.Integer findEquivalent(java.lang.Integer synonym)
                                 throws LabellerException

Throws:

LabellerException