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

    Fields
    Modifier and Type
    Field
    Description
    static final ChangeType
    Signals that the alignment describing the homologous sequences has changed.
  • Method Summary

    Modifier and Type
    Method
    Description
    Retrieve the Alignment that specifies how the homologous regions are aligned.
    Retrieve the set of features that mark homologous regions.
  • Field Details

    • ALIGNMENT

      static final ChangeType ALIGNMENT
      Signals that the alignment describing the homologous sequences has changed. For implementations which implement Changeable.
  • 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