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java.lang.Objectorg.biojava3.alignment.SubstitutionMatrixHelper
public class SubstitutionMatrixHelper
Static utility to access substitution matrices that come bundled with BioJava. All matrices were downloaded from ftp://ftp.ncbi.nih.gov/blast/matrices/
Method Summary | |
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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> |
getMatrixFromAAINDEX(String matrixName)
Returns any matrix from the AAINDEX database file |
static SubstitutionMatrix<NucleotideCompound> |
getNuc4_2()
Returns Nuc 4.2 matrix by Lowe |
static SubstitutionMatrix<NucleotideCompound> |
getNuc4_4()
Returns Nuc 4.4 matrix by Lowe |
static SubstitutionMatrix<AminoAcidCompound> |
getPAM250()
Returns PAM 250 matrix by Dayhoff |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static SubstitutionMatrix<AminoAcidCompound> getMatrixFromAAINDEX(String matrixName)
matrixName
-
SubstitutionMatrix
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()
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