Package org.biojavax.bio.seq

Interface RichSequence

All Superinterfaces:
Annotatable, BioEntry, Changeable, Comparable, FeatureHolder, RankedCrossRefable, RichAnnotatable, Sequence, SymbolList
All Known Implementing Classes:
SimpleRichSequence, ThinRichSequence
public interface RichSequence extends BioEntry, Sequence
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence. It inherits and merges the methods of both. The RichSequence is based on the BioSQL model and provides a richer array of methods to access information than Sequence does. Whenever possible RichSequence should be used in preference to Sequence.
Since:
1.5
Author:
Mark Schreiber, Richard Holland, George Waldon

  • Field Details

  • Method Details

    • getSeqVersion

      Double getSeqVersion()
      The version of the associated symbol list. Note the use of an object for the value means that it can be nulled.
      Returns:
      the version

    • setSeqVersion

      void setSeqVersion(Double seqVersion) throws ChangeVetoException
      Sets the version of the associated symbol list. Note the use of an object for the value means that it can be nulled.
      Parameters:
      seqVersion - the version to set.
      Throws:
      ChangeVetoException - if it doesn't want to change.

    • getFeatureSet

      Set<Feature> getFeatureSet()
      The features for this sequence.
      Returns:
      a set of RichFeature objects.

    • setFeatureSet

      void setFeatureSet(Set<Feature> features) throws ChangeVetoException
      Sets the features of this sequence. Note that it is not checked to see if the features actually belong to this sequence, you'd best check that yourself and make changes using feature.setParent() if necessary.
      Parameters:
      features - the features to assign to this sequence, replacing all others. Must be a set of RichFeature objects.
      Throws:
      ChangeVetoException - if they could not be assigned.

    • setCircular

      void setCircular(boolean circular) throws ChangeVetoException
      Circularises the Sequence. The circular length can then be said to be the length of the sequence itself.
      Parameters:
      circular - set to true if you want it to be circular
      Throws:
      ChangeVetoException - if the change is blocked. Some implementations may choose not to support circularisation and should throw an exception here. Some implementations may only support this method for certain Alphabets.

    • getCircular

      boolean getCircular()
      Is the sequence circular? Circularity has implications for work with locations and any coordinate work eg symbolAt(int i). Classes that allow it should test this method when working with coordinates or locations / features.
      Returns:
      true if the this is circular else false.

    • getInternalSymbolList

      SymbolList getInternalSymbolList()
      A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.
      Returns:
      the internal SymbolList of the RichSequence, NOT the RichSequence object itself.