org.biojava.bio.seq.homol

Interface Homology

All Known Implementing Classes:

SimpleHomology

public interface Homology

Signifies that two or more features are homologous.

Blast hits or local multiple-sequence alignments can be represented as a set of features on sequences that have an alignment. The features will probably implement HomologyFeature.

Since:

1.2

Author:

Matthew Pocock, Keith James

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	ALIGNMENT Signals that the alignment describing the homologous sequences has changed.

Method Summary

Methods

Modifier and Type	Method and Description
Alignment	getAlignment() Retrieve the Alignment that specifies how the homologous regions are aligned.
FeatureHolder	getFeatures() Retrieve the set of features that mark homologous regions.

Field Detail

ALIGNMENT

static final ChangeType ALIGNMENT

Signals that the alignment describing the homologous sequences has changed. For implementations which implement Changeable.

Method Detail

getFeatures

FeatureHolder getFeatures()

Retrieve the set of features that mark homologous regions.

Returns:

the FeatureHolder containing each homologous region

getAlignment

Alignment getAlignment()

Retrieve the Alignment that specifies how the homologous regions are aligned. The labels of the alignment are the HomologyFeature objects.

Returns:

the Alignment between the HomologyFeatures