Skip navigation links

Class AlignmentTools

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 ).
  • 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].
  • alignmentToSIF

    public static void alignmentToSIF(Writer out,
                                      AFPChain afpChain,
                                      Atom[] ca1,
                                      Atom[] ca2,
                                      String backboneInteraction,
                                      String alignmentInteraction)
                               throws IOException
    Creates a simple interaction format (SIF) file for an alignment. The SIF file can be read by network software (eg Cytoscape) to analyze alignments as graphs. This function creates a graph with residues as nodes and two types of edges: 1. backbone edges, which connect adjacent residues in the aligned protein 2. alignment edges, which connect aligned residues
    out - Stream to write to
    afpChain - alignment to write
    ca1 - First protein, used to generate node names
    ca2 - Second protein, used to generate node names
    backboneInteraction - Two-letter string used to identify backbone edges
    alignmentInteraction - Two-letter string used to identify alignment edges

Copyright © 2000–2016 BioJava. All rights reserved.