Class AlignerHelper.Subproblem

  • Enclosing class:
    AlignerHelper

    public static class AlignerHelper.Subproblem
    extends Object
    Alignment subproblem. The bounds of the subproblem are the indicies representing the inclusive bounds of the dynamic programming alignment problem.
    Author:
    Daniel Cameron
    • Constructor Detail

      • Subproblem

        public Subproblem​(int queryStartIndex,
                          int targetStartIndex,
                          int queryEndIndex,
                          int targetEndIndex)
      • Subproblem

        public Subproblem​(int queryStartIndex,
                          int targetStartIndex,
                          int queryEndIndex,
                          int targetEndIndex,
                          boolean isAnchored)
    • Method Detail

      • isStartAnchored

        public boolean isStartAnchored()
        Indicates whether the start query and start target index compounds are anchored to each other
        Returns:
        true if the compounds are anchored in the alignment, false otherwise
      • getSubproblems

        public static List<AlignerHelper.SubproblemgetSubproblems​(List<AlignerHelper.Anchor> anchors,
                                                                    int querySequenceLength,
                                                                    int targetSequenceLength)
        Convert a list of anchors into a subproblem list.
        Parameters:
        anchors - anchored read pairs
        querySequenceLength - length of query sequence
        targetSequenceLength - length of target sequence
        Returns:
        list alignment subproblems