pal.alignment
Class AlignmentTool

java.lang.Object
  pal.alignment.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 Summary

AlignmentTool()

Method Summary

static Alignment	convertToUniversalAminoAcids(Alignment base, int startingIndex) Convert an alignment to one of amino acids (using Universal Translation)
static Alignment	createBootstrapReplicate(Alignment base) A simple approach to creating a bootstrap replicate
static Alignment	createGapBalanced(Alignment base, int startingIndex) Create a gap balanced alignment.
static Alignment	readAlignment(java.io.Reader r, DataType dt) Attempt to read a file from a reader object

Methods inherited from class java.lang.Object

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

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