Package pal.alignment

Class GapBalancedAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.GapBalancedAlignment
All Implemented Interfaces:
Serializable, Alignment, IdGroup, Report

public class GapBalancedAlignment extends AbstractAlignment implements 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:
  • Constructor Details

    • 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)
  • Method Details