Package org.biojava.nbio.phylo
Class Comparison
- java.lang.Object
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- org.biojava.nbio.phylo.Comparison
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public class Comparison extends Object
This class provides static methods for the calculation of the percentage of identity between two aligned sequences.Since 4.1.1 the methods for distance inference in forester are also used in BioJava, so this implementation of percentage of identity is not needed anymore. However, the code is maintained as the own BioJava implementation.
- Author:
- Scooter Willis
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Constructor Summary
Constructors Constructor Description Comparison()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static boolean
isGap(char c)
Method that determines if a character means a gap in the alignment.static float
PID(String seq1, String seq2)
this is a gapped PID calculationstatic float
PID(String seq1, String seq2, int start, int end)
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Constructor Detail
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Comparison
public Comparison()
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Method Detail
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PID
public static final float PID(String seq1, String seq2)
this is a gapped PID calculation- Parameters:
s1
- SequenceIs2
- SequenceI- Returns:
- float
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isGap
public static final boolean isGap(char c)
Method that determines if a character means a gap in the alignment.- Parameters:
c
- gap character is one of the symbols in {' ','-','.'}- Returns:
- true if it is a gap, false otherwise
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