pal.alignment
Class Genotype

java.lang.Object
  pal.alignment.Genotype

public class Genotype
extends java.lang.Object

This class provides from genotype to be constructed from separate but paired alignments. This is just a very basic implementation. Other suggested approaches would be welcome.

Version:

$Id:

Author:

Ed Buckler

Constructor Summary

Genotype(Alignment a1, Alignment a2)

Method Summary

Alignment	getAlignment(int i)
char	getData(int seq, int site, int allele) sequence alignment at (sequence, site, allele)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Genotype

public Genotype(Alignment a1,
                Alignment a2)

Method Detail

getAlignment

public Alignment getAlignment(int i)

getData

public char getData(int seq,
                    int site,
                    int allele)

sequence alignment at (sequence, site, allele)