Package 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
FieldsModifier and TypeFieldDescriptionstatic final ChangeType
Signals that the alignment describing the homologous sequences has changed. -
Method Summary
Modifier and TypeMethodDescriptionRetrieve the Alignment that specifies how the homologous regions are aligned.Retrieve the set of features that mark homologous regions.
-
Field Details
-
ALIGNMENT
Signals that the alignment describing the homologous sequences has changed. For implementations which implementChangeable
.
-
-
Method Details
-
getFeatures
Retrieve the set of features that mark homologous regions.- Returns:
- the FeatureHolder containing each homologous region
-
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
-