Class Edit.Substitute<C extends Compound>

  • 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 Detail

      • Substitute

        public Substitute​(java.lang.String sequence,
                          int position)
      • Substitute

        public Substitute​(Sequence<C> sequence,
                          int position)
    • Method Detail

      • 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.