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.

          example
             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)

    Author:
    David Waring
    • Method Detail

      • locInAlignment

        Location locInAlignment​(java.lang.Object label)
        The location of an individual SymbolList relative to overall Alignment
      • labelsAt

        java.util.List<java.lang.String> labelsAt​(int column)
        Returns a list labels, of all seqs that cover that column
      • labelsInRange

        java.util.List<java.lang.String> labelsInRange​(Location loc)
        Returns list of all the labels that intersect that range