java.io.Serializable
public class SubstitutionMatrixHelper
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Method | Description |
---|---|---|
static SubstitutionMatrix<AminoAcidCompound> |
getAminoAcidSubstitutionMatrix(java.lang.String name) |
Returns a substitution matrix for
amino acids given by the name name . |
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum100() |
Returns Blosum 100 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum30() |
Returns Blosum 30 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum35() |
Returns Blosum 35 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum40() |
Returns Blosum 40 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum45() |
Returns Blosum 45 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum50() |
Returns Blosum 50 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum55() |
Returns Blosum 55 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum60() |
Returns Blosum 60 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum62() |
Returns Blosum 62 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum65() |
Returns Blosum 65 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum70() |
Returns Blosum 70 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum75() |
Returns Blosum 75 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum80() |
Returns Blosum 80 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum85() |
Returns Blosum 85 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getBlosum90() |
Returns Blosum 90 matrix by Henikoff & Henikoff
|
static SubstitutionMatrix<AminoAcidCompound> |
getGonnet250() |
Returns PAM 250 matrix by Gonnet, Cohen & Benner
|
static SubstitutionMatrix<AminoAcidCompound> |
getIdentity() |
|
static SubstitutionMatrix<AminoAcidCompound> |
getMatrixFromAAINDEX(java.lang.String matrixName) |
Returns any matrix from the AAINDEX database file
|
static SubstitutionMatrix<NucleotideCompound> |
getNuc4_2() |
Returns Nuc 4.2 matrix by Lowe
Only the first nucleotide sequence to align can contain ambiguous nucleotides
|
static SubstitutionMatrix<NucleotideCompound> |
getNuc4_4() |
Returns Nuc 4.4 matrix by Lowe
Both of the nucleotide sequences to align can contain ambiguous nucleotides
|
static SubstitutionMatrix<AminoAcidCompound> |
getPAM250() |
Returns PAM 250 matrix by Dayhoff
|
public static SubstitutionMatrix<AminoAcidCompound> getMatrixFromAAINDEX(java.lang.String matrixName)
matrixName
- SubstitutionMatrix
public static SubstitutionMatrix<AminoAcidCompound> getIdentity()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum100()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum30()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum35()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum40()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum45()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum50()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum55()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum60()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum62()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum65()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum70()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum75()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum80()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum85()
public static SubstitutionMatrix<AminoAcidCompound> getBlosum90()
public static SubstitutionMatrix<AminoAcidCompound> getGonnet250()
public static SubstitutionMatrix<NucleotideCompound> getNuc4_2()
public static SubstitutionMatrix<NucleotideCompound> getNuc4_4()
public static SubstitutionMatrix<AminoAcidCompound> getPAM250()
public static SubstitutionMatrix<AminoAcidCompound> getAminoAcidSubstitutionMatrix(java.lang.String name)
amino acids
given by the name name
.
Searches first in the default AAINDEX file (see @link getMatrixFromAAINDEX(String)
), then in the classpath.
If the required matrix does not exist, null is returned.
Example names:
name
- Either a common name or an AAINDEX name