Package pal.alignment
Class AlignmentTool
java.lang.Object
pal.alignment.AlignmentTool
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final Alignment
convertToUniversalAminoAcids
(Alignment base, int startingIndex) Convert an alignment to one of amino acids (using Universal Translation)static final Alignment
A simple approach to creating a bootstrap replicatestatic final Alignment
createGapBalanced
(Alignment base, int startingIndex) Create a gap balanced alignment.static final Alignment
readAlignment
(Reader r, DataType dt) Attempt to read a file from a reader object
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Constructor Details
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AlignmentTool
public AlignmentTool()
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Method Details
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createBootstrapReplicate
A simple approach to creating a bootstrap replicate- Parameters:
base
- The original alignment- Returns:
- A bootstrap replicate of the input alignment
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createGapBalanced
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 alignmentstartingIndex
- The nucleotide position at which to start the translating (counting from zero)- Returns:
- The gap balanced version
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convertToUniversalAminoAcids
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
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readAlignment
Attempt to read a file from a reader object- Parameters:
r
- A reader objectdt
- The datatype of the resulting alignment- Returns:
- A loaded alignment
- Throws:
IOException
- if there is a problem reading the alignment
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