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org.biojava.nbio.structure.align.util

Class AlignmentTools

Parameters:
alignment - The input function, as a map (see alignmentAsMap(AFPChain))
identity - An identity-like function providing the isomorphism between the codomain of alignment (of type ) and the domain (type ).
Returns:
  • fromConciseAlignmentString

    public static java.util.Map<java.lang.Integer,java.lang.Integer> fromConciseAlignmentString(java.lang.String string)
    See Also:
    toConciseAlignmentString(Map, Map)
  • calculateBlockGap

    public static int[] calculateBlockGap(int[][][] optAln)
    Method that calculates the number of gaps in each subunit block of an optimal AFP alignment. INPUT: an optimal alignment in the format int[][][]. OUTPUT: an int[] array of length containing the gaps in each block as int[block].