Package pal.alignment

Class GapBalancedAlignment

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, IdGroup, Report

    public class GapBalancedAlignment
    extends AbstractAlignment
    implements java.io.Serializable
    Creates a "Gap-Balanced" alignment.
    Version:
    $Id: GapBalancedAlignment.java,v 1.14 2003/04/10 05:53:47 matt Exp $
    Author:
    Matthew Goode
    See Also:
    Serialized Form
    • Constructor Detail

      • GapBalancedAlignment

        public GapBalancedAlignment​(Alignment base,
                                    int startingCodonPosition,
                                    boolean alignGap)
        The standard GapBalanced constructor
        Parameters:
        Alignment - on which to based this gap balanced alignment
        the - estimated startingCodonPosition of the alignment
      • GapBalancedAlignment

        public GapBalancedAlignment​(Alignment base,
                                    int startingCodonPosition,
                                    int codonLength)
        GapBalanced power user constructor
        Parameters:
        Alignment - on which to based this gap balanced alignment
        startingCodonPosition - the starting codon position of the alignment
        codonLength - the length of a codon (to make things general, - the author is a Computer Scientist)
      • GapBalancedAlignment

        public GapBalancedAlignment​(Alignment base,
                                    int startingCodonPosition,
                                    boolean alignGap,
                                    int codonLength)
        GapBalanced power user constructor
        Parameters:
        Alignment - on which to based this gap balanced alignment
        startingCodonPosition - the starting codon position of the alignment
        alignGap - sometimes a large cap may occur in the middle of a sequence's codon. If this is true than no columns can match up in this area (it's hard to explain - for safety choose true!)
        codonLength - the length of a codon (to make things general, - the author is a Computer Scientist)