Package 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

  • Field Details

    • 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:

    • SUBJECT_LABEL

      static final String SUBJECT_LABEL
      Constant SUBJECT_LABEL is the alignment label used for all subject sequences.
      See Also:

    • 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 Details