org.biojava.bio.seq.homol

Interface SimilarityPairFeature

All Superinterfaces:

Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature

All Known Implementing Classes:

SimpleSimilarityPairFeature

public interface SimilarityPairFeature
extends StrandedFeature

SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature). It is analagous to, and based on, the BioPerl Bio::SeqFeature::SimilarityPair.

It is different from HomologyFeature in that it expresses a relationship between only two sequence regions (rather than >= 2), with one clearly defined as the query sequence and the other as the subject (database hit). These are identified by constant labels in the Alignment. HomologyFeature identifies the related sequence regions by means of an Homology instance which contains an Alignment which uses the HomologyFeatures themselves as labels.

In cases where there is no alignment available, for example when MSPCrunch output or GFF have been used, the EmptyPairwiseAlignment in the EMPTY_PAIRWISE field may be used. This may also be useful if an implementation elides the alignment data for some reason.

Since:

1.2

Author:

Keith James

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	SimilarityPairFeature.EmptyPairwiseAlignment EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.
static class	SimilarityPairFeature.Template Template for construction of SimilarityPairFeatures.

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand

Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

Feature.ByLocationComparator

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static Alignment	EMPTY_PAIRWISE Constant EMPTY_PAIRWISE is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.
static String	QUERY_LABEL Constant QUERY_LABEL is the alignment label used for all query sequences.
static ChangeType	SIBLING The sibling of this feature has altered.
static String	SUBJECT_LABEL Constant SUBJECT_LABEL is the alignment label used for all subject sequences.

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method and Description
Alignment	getAlignment() getAlignment returns the Alignment of two similar features.
double	getScore() getScore returns the alignment score.
SimilarityPairFeature	getSibling() getSibling returns the sibling Feature, query for subject and vice versa.
void	setSibling(SimilarityPairFeature sibling) setSibling sets the sibling feature of the pair.

Methods inherited from interface org.biojava.bio.seq.StrandedFeature

getStrand, getSymbols, setStrand

Methods inherited from interface org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

SIBLING

static final ChangeType SIBLING

The sibling of this feature has altered.

QUERY_LABEL

static final String QUERY_LABEL

Constant QUERY_LABEL is the alignment label used for all query sequences.

See Also:

Constant Field Values

SUBJECT_LABEL

static final String SUBJECT_LABEL

Constant SUBJECT_LABEL is the alignment label used for all subject sequences.

See Also:

Constant Field Values

EMPTY_PAIRWISE

static final Alignment EMPTY_PAIRWISE

Constant EMPTY_PAIRWISE is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.

Method Detail

getSibling

SimilarityPairFeature getSibling()

getSibling returns the sibling Feature, query for subject and vice versa.

Returns:

a Feature.

setSibling

void setSibling(SimilarityPairFeature sibling)
         throws ChangeVetoException

setSibling sets the sibling feature of the pair. This is used to set the reciprocal SimilarityPairFeature as both cannot be set using the Template.

Throws:

ChangeVetoException

getAlignment

Alignment getAlignment()

getAlignment returns the Alignment of two similar features.

Returns:

an Alignment value.

getScore

double getScore()

getScore returns the alignment score.

Returns:

a double.