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java.lang.Objectpal.alignment.AlignmentTool
public final class AlignmentTool
Simple access for alignment functions. The purpose of this class is to provide a set interface for doing basic alignment operations. History
Constructor Summary | |
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AlignmentTool()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AlignmentTool()
Method Detail |
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public static final Alignment createBootstrapReplicate(Alignment base)
base
- The original alignment
public 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 alignment
java.io.IOException
- if there is a problem reading the alignment
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