java.lang.Object
- org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper

All Implemented Interfaces:

Serializable
```
public class SubstitutionMatrixHelper
extends Object
implements Serializable
```
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, Paolo Pavan

See Also:

Serialized Form

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static SubstitutionMatrix<AminoAcidCompound>`	`getAminoAcidSubstitutionMatrix(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()`	Gets identity matrix where matches score 1 and mismatches score -10000
`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 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

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
  - getIdentity
```
public static SubstitutionMatrix<AminoAcidCompound> getIdentity()
```
    Gets identity matrix where matches score 1 and mismatches score -10000
    
    Returns:
  - 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 Only the first nucleotide sequence to align can contain ambiguous nucleotides
    
    Returns:
    
    Nuc 4.2 matrix
  - getNuc4_4
```
public static SubstitutionMatrix<NucleotideCompound> getNuc4_4()
```
    Returns Nuc 4.4 matrix by Lowe Both of the nucleotide sequences to align can contain ambiguous nucleotides
    
    Returns:
    
    Nuc 4.4 matrix
  - getPAM250
```
public static SubstitutionMatrix<AminoAcidCompound> getPAM250()
```
    Returns PAM 250 matrix by Dayhoff
    
    Returns:
    
    PAM 250 matrix
  - getAminoAcidSubstitutionMatrix
```
public static SubstitutionMatrix<AminoAcidCompound> getAminoAcidSubstitutionMatrix(String name)
```
    Returns a substitution matrix for amino acids given by the name name. Searches first in the default AAINDEX file (see @link getMatrixFromAAINDEX(String)), then in the classpath in src/main/resources/matrices. Example names:
    
    blosum62
    
    JOND920103
    
    pam250
    
    gonnet250
    Parameters:
    
    name - Either a common name or an AAINDEX name
    
    Returns:
    
    a SubstitutionMatrix or null if no matrix is found

Class SubstitutionMatrixHelper

Method Summary

Methods inherited from class java.lang.Object

Method Detail

getMatrixFromAAINDEX

getIdentity

getBlosum100

getBlosum30

getBlosum35

getBlosum40

getBlosum45

getBlosum50

getBlosum55

getBlosum60

getBlosum62

getBlosum65

getBlosum70

getBlosum75

getBlosum80

getBlosum85

getBlosum90

getGonnet250

getNuc4_2

getNuc4_4

getPAM250

getAminoAcidSubstitutionMatrix