org.biojava3.alignment
Class SubstitutionMatrixHelper

java.lang.Object
  extended by org.biojava3.alignment.SubstitutionMatrixHelper

public class SubstitutionMatrixHelper
extends Object

Static utility to access substitution matrices that come bundled with BioJava. All matrices were downloaded from ftp://ftp.ncbi.nih.gov/blast/matrices/

Author:
Mark Chapman

Method Summary
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

getMatrixFromAAINDEX

public static SubstitutionMatrix<AminoAcidCompound> getMatrixFromAAINDEX(String matrixName)
Returns any matrix from the AAINDEX database file

Parameters:
matrixName -
Returns:
a SubstitutionMatrix

getBlosum100

public static SubstitutionMatrix<AminoAcidCompound> getBlosum100()
Returns Blosum 100 matrix by Henikoff & Henikoff

Returns:
Blosum 100 matrix

getBlosum30

public static SubstitutionMatrix<AminoAcidCompound> getBlosum30()
Returns Blosum 30 matrix by Henikoff & Henikoff

Returns:
Blosum 30 matrix

getBlosum35

public static SubstitutionMatrix<AminoAcidCompound> getBlosum35()
Returns Blosum 35 matrix by Henikoff & Henikoff

Returns:
Blosum 35 matrix

getBlosum40

public static SubstitutionMatrix<AminoAcidCompound> getBlosum40()
Returns Blosum 40 matrix by Henikoff & Henikoff

Returns:
Blosum 40 matrix

getBlosum45

public static SubstitutionMatrix<AminoAcidCompound> getBlosum45()
Returns Blosum 45 matrix by Henikoff & Henikoff

Returns:
Blosum 45 matrix

getBlosum50

public static SubstitutionMatrix<AminoAcidCompound> getBlosum50()
Returns Blosum 50 matrix by Henikoff & Henikoff

Returns:
Blosum 50 matrix

getBlosum55

public static SubstitutionMatrix<AminoAcidCompound> getBlosum55()
Returns Blosum 55 matrix by Henikoff & Henikoff

Returns:
Blosum 55 matrix

getBlosum60

public static SubstitutionMatrix<AminoAcidCompound> getBlosum60()
Returns Blosum 60 matrix by Henikoff & Henikoff

Returns:
Blosum 60 matrix

getBlosum62

public static SubstitutionMatrix<AminoAcidCompound> getBlosum62()
Returns Blosum 62 matrix by Henikoff & Henikoff

Returns:
Blosum 62 matrix

getBlosum65

public static SubstitutionMatrix<AminoAcidCompound> getBlosum65()
Returns Blosum 65 matrix by Henikoff & Henikoff

Returns:
Blosum 65 matrix

getBlosum70

public static SubstitutionMatrix<AminoAcidCompound> getBlosum70()
Returns Blosum 70 matrix by Henikoff & Henikoff

Returns:
Blosum 70 matrix

getBlosum75

public static SubstitutionMatrix<AminoAcidCompound> getBlosum75()
Returns Blosum 75 matrix by Henikoff & Henikoff

Returns:
Blosum 75 matrix

getBlosum80

public static SubstitutionMatrix<AminoAcidCompound> getBlosum80()
Returns Blosum 80 matrix by Henikoff & Henikoff

Returns:
Blosum 80 matrix

getBlosum85

public static SubstitutionMatrix<AminoAcidCompound> getBlosum85()
Returns Blosum 85 matrix by Henikoff & Henikoff

Returns:
Blosum 85 matrix

getBlosum90

public static SubstitutionMatrix<AminoAcidCompound> getBlosum90()
Returns Blosum 90 matrix by Henikoff & Henikoff

Returns:
Blosum 90 matrix

getGonnet250

public static SubstitutionMatrix<AminoAcidCompound> getGonnet250()
Returns PAM 250 matrix by Gonnet, Cohen & Benner

Returns:
Gonnet 250 matrix

getNuc4_2

public static SubstitutionMatrix<NucleotideCompound> getNuc4_2()
Returns Nuc 4.2 matrix by Lowe

Returns:
Nuc 4.2 matrix

getNuc4_4

public static SubstitutionMatrix<NucleotideCompound> getNuc4_4()
Returns Nuc 4.4 matrix by Lowe

Returns:
Nuc 4.4 matrix

getPAM250

public static SubstitutionMatrix<AminoAcidCompound> getPAM250()
Returns PAM 250 matrix by Dayhoff

Returns:
PAM 250 matrix