Package pal.alignment

Class AlignmentTool

  • public final class AlignmentTool
extends java.lang.Object
    Simple access for alignment functions. The purpose of this class is to provide a set interface for doing basic alignment operations. History
    • 15/09/2003 - Created
    Version:
    $Id: AlignmentTool.java,v 1.2 2004/01/13 22:04:49 matt Exp $
    Author:
    Matthew Goode

    • Constructor Detail

      • AlignmentTool

        public AlignmentTool()

    • Method Detail

      • createBootstrapReplicate

        public static final Alignment createBootstrapReplicate​(Alignment base)
        A simple approach to creating a bootstrap replicate
        Parameters:
        base - The original alignment
        Returns:
        A bootstrap replicate of the input alignment

      • createGapBalanced

        public static final Alignment createGapBalanced​(Alignment base,
                                                int startingIndex)
        Create a gap balanced alignment. That is one that removes sites where sequences are out of frame from other sequences in the site.
        Parameters:
        base - The original alignment
        startingIndex - The nucleotide position at which to start the translating (counting from zero)
        Returns:
        The gap balanced version

      • convertToUniversalAminoAcids

        public static final Alignment convertToUniversalAminoAcids​(Alignment base,
                                                           int startingIndex)
        Convert an alignment to one of amino acids (using Universal Translation)
        Parameters:
        base - The base alignment (in any datatype, but for best results a Nucleotide alignment)
        startingIndex - The nucleotide position at which to start the translating (counting from zero)
        Returns:
        The converted alignment

      • readAlignment

        public static final Alignment readAlignment​(java.io.Reader r,
                                            DataType dt)
                                     throws java.io.IOException
        Attempt to read a file from a reader object
        Parameters:
        r - A reader object
        dt - The datatype of the resulting alignment
        Returns:
        A loaded alignment
        Throws:
        java.io.IOException - if there is a problem reading the alignment