Interface ComponentFeature

  • All Superinterfaces:
    Annotatable, Changeable, Feature, FeatureHolder, StrandedFeature

    public interface ComponentFeature
    extends StrandedFeature
    Feature which represents a component in an assembly (contig). This implies that a portion (possibly all) of the associated componentSequence is included in this feature's parent sequence.

    There are important invariants which apply to all ComponentFeatures. The Location returned by getLocation() must contain the same number of unique point locations as that returned by getComponentLocation().

    In BioJava 1.2, two extra properties were added to ComponentFeature to support the use of these features in environments were it it necessary to represent an assembly built from sequences which are not currently available. Widespread use of such sequences is not encouraged, but it is recognized that they are useful as intermediate objects for data integration applications.

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    • Method Detail

      • getComponentSequence

        Sequence getComponentSequence()
        Get the sequence object which provides a component of this feature's parent sequence.
        A sequence.
      • getComponentLocation

        Location getComponentLocation()
        Return a location which identifies a portion of the component sequence which is to be included in the assembly.
        A location within the component sequence.
      • getComponentSequenceName

        String getComponentSequenceName()
        Get the name of the component sequence. In general, this should be equivalent to getComponentSequence().getName(). However, it may still be defined for un-resolveable components.
      • isComponentResolvable

        boolean isComponentResolvable()
        Determine if the sequence references by this ComponentFeature is available in this context. If not, calls to getComponentSequence will fail, and getSymbols will return a non-informative SymbolList (in a DNA context, a list of Ns).