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
HomologyFeature
s 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
Field Summary |
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 java.lang.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 java.lang.String |
SUBJECT_LABEL
Constant SUBJECT_LABEL is the alignment label used
for all subject sequences. |
Methods inherited from interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
SIBLING
static final ChangeType SIBLING
- The sibling of this feature has altered.
QUERY_LABEL
static final java.lang.String QUERY_LABEL
- Constant
QUERY_LABEL
is the alignment label used
for all query sequences.
- See Also:
- Constant Field Values
SUBJECT_LABEL
static final java.lang.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.
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
.