Package org.biojava.nbio.core.sequence.edits

Class Edit.Substitute<C extends Compound>

java.lang.Object
org.biojava.nbio.core.sequence.edits.Edit.AbstractEdit<C>
org.biojava.nbio.core.sequence.edits.Edit.Substitute<C>
All Implemented Interfaces:
Edit<C>
Enclosing interface:
Edit<C extends Compound>
public static class Edit.Substitute<C extends Compound> extends Edit.AbstractEdit<C>
Allows for the substitution of bases into an existing Sequence. This allows us to do edits like: 
    Sub TT @ position 2
    AAAA -> ATTA
We do not support Edits do not require the length of the insertion but do rely on the presence of a CompoundSet to parse a String (if given) which means the eventual length of a Sequence is a lazy operation.

  • Constructor Details

    • Substitute

      public Substitute(String sequence, int position)

    • Substitute

      public Substitute(Sequence<C> sequence, int position)

  • Method Details

    • getEnd

      public int getEnd(Sequence<C> sequence)
      Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.

    • getFivePrime

      protected Sequence<C> getFivePrime(Sequence<C> editingSequence)
      Description copied from class: Edit.AbstractEdit
      Should return the 5-prime end of the given Sequence according to the edit. An empty Sequence is valid.
      Specified by:
      getFivePrime in class Edit.AbstractEdit<C extends Compound>

    • getThreePrime

      protected Sequence<C> getThreePrime(Sequence<C> editingSequence)
      Description copied from class: Edit.AbstractEdit
      Should return the 3-prime end of the given Sequence according to the edit. An empty Sequence is valid.
      Specified by:
      getThreePrime in class Edit.AbstractEdit<C extends Compound>