Interface SimilarityPairFeature
- All Superinterfaces:
Annotatable
,Changeable
,Feature
,FeatureHolder
,StrandedFeature
- All Known Implementing Classes:
SimpleSimilarityPairFeature
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
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class
EmptyPairwiseAlignment
empty pairwise alignment which has labels to empty symbol lists.static class
Template
for construction ofSimilarityPairFeature
s.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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.seq.StrandedFeature
StrandedFeature.Strand
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final Alignment
ConstantEMPTY_PAIRWISE
is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.static final String
ConstantQUERY_LABEL
is the alignment label used for all query sequences.static final ChangeType
The sibling of this feature has altered.static final String
ConstantSUBJECT_LABEL
is the alignment label used for all subject sequences.Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN
-
Method Summary
Modifier and TypeMethodDescriptiongetAlignment
returns theAlignment
of two similar features.double
getScore()
getScore
returns the alignment score.getSibling
returns the siblingFeature
, 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.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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.seq.StrandedFeature
getStrand, getSymbols, setStrand
-
Field Details
-
SIBLING
The sibling of this feature has altered. -
QUERY_LABEL
ConstantQUERY_LABEL
is the alignment label used for all query sequences.- See Also:
-
SUBJECT_LABEL
ConstantSUBJECT_LABEL
is the alignment label used for all subject sequences.- See Also:
-
EMPTY_PAIRWISE
ConstantEMPTY_PAIRWISE
is an empty alignment for situations where there is no available alignment data or the implementation does not want to create one.
-
-
Method Details
-
getSibling
getSibling
returns the siblingFeature
, query for subject and vice versa.- Returns:
- a
Feature
.
-
setSibling
setSibling
sets the sibling feature of the pair. This is used to set the reciprocalSimilarityPairFeature
as both cannot be set using theTemplate
.- Throws:
ChangeVetoException
-
getAlignment
getAlignment
returns theAlignment
of two similar features.- Returns:
- an
Alignment
value.
-
getScore
double getScore()getScore
returns the alignment score.- Returns:
- a
double
.
-