pal.alignment
public final class AlignmentTool extends java.lang.Object
Constructor and Description |
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AlignmentTool() |
Modifier and Type | Method and Description |
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static Alignment |
convertToUniversalAminoAcids(Alignment base,
int startingIndex)
Convert an alignment to one of amino acids (using Universal Translation)
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static Alignment |
createBootstrapReplicate(Alignment base)
A simple approach to creating a bootstrap replicate
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static Alignment |
createGapBalanced(Alignment base,
int startingIndex)
Create a gap balanced alignment.
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static Alignment |
readAlignment(java.io.Reader r,
DataType dt)
Attempt to read a file from a reader object
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public static final Alignment createBootstrapReplicate(Alignment base)
base
- The original alignmentpublic static final Alignment createGapBalanced(Alignment base, int startingIndex)
base
- The original alignmentstartingIndex
- The nucleotide position at which to start the translating (counting from zero)public static final Alignment convertToUniversalAminoAcids(Alignment base, int startingIndex)
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)public static final Alignment readAlignment(java.io.Reader r, DataType dt) throws java.io.IOException
r
- A reader objectdt
- The datatype of the resulting alignmentjava.io.IOException
- if there is a problem reading the alignment