Interface StrandedFeature

All Superinterfaces:
Annotatable, Changeable, Feature, FeatureHolder
All Known Subinterfaces:
ComponentFeature, FramedFeature, HomologyFeature, RemoteFeature, RestrictionSite, RichFeature, SimilarityPairFeature
All Known Implementing Classes:
SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleSimilarityPairFeature, SimpleStrandedFeature

public interface StrandedFeature extends Feature
Adds the concept of 'strand' to features.

Strandedness only applies to some types of sequence, such as DNA. Any implementation should blow chunks to avoid being added to a sequence for which strand is a foreign concept. Strand is intrinsicly part of all RichFeatures We strongly recommend using this interface.

Author:
Matthew Pocock
See Also:
  • Field Details

  • Method Details

    • getStrand

      Retrieve the strand that this feature lies upon.

      This will be one of StrandedFeature.POSITIVE or NEGATIVE.

      Returns:
      one of the Strand constants
    • setStrand

      Set the strand that this feature lies upon.

      This will be one of StrandedFeature.POSITIVE or NEGATIVE.

      Parameters:
      strand - a Strand.
      Throws:
      ChangeVetoException - if the strand may not be changed.
    • getSymbols

      Return a list of symbols that are contained in this feature.

      The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

      The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

      If the feature is on the negative strand then the SymbolList will be reverse-complemented as appropriate.

      Specified by:
      getSymbols in interface Feature
      Returns:
      a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent