Interface UnequalLengthAlignment

  • All Superinterfaces:
    Alignment, Changeable, SymbolList
    All Known Implementing Classes:
    AbstractULAlignment, AbstractULAlignment.SubULAlignment, FlexibleAlignment

    public interface UnequalLengthAlignment
    extends Alignment

    UnequalLengthAlignment has the following behavior. Two or more SymbolLists may align in such a way that their ends do not overlap.

             1         aaaaaatttcttt
             2               tttgtttggggggc

    length returns ??
    symbolAt(1,1) returns 20
    symbolAt(2,1) returns null -- NOT an exception
    symbolAt(2,99) throws NoSuchElementException
    leftMost returns 1
    rightMost returns 2
    locInAlignment (1) returns (1,13)
    locInAlignment (2) returns (7,20)
    alignmentRange() returns (7,13)

    David Waring