SubstitutionMatrix (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.alignment.SubstitutionMatrix

All Implemented Interfaces:

Serializable
```
public class SubstitutionMatrix
extends Object
implements Serializable
```
This object is able to read a substitution matrix file and constructs a short matrix in memory. Every single element of the matrix can be accessed by the method getValueAt with the parameters being two BioJava symbols. This is why it is not necessary to access the matrix directly. If there is no value for the two specified Symbols an Exception is thrown.

Substitution matrix files, are available at the NCBI FTP directory.

Author:

Andreas Dräger

See Also:
Serialized Form

Constructor Summary

Constructors
Constructor and Description
`SubstitutionMatrix(File file)` This constructor can be used to guess the alphabet of this substitution matrix.
`SubstitutionMatrix(FiniteAlphabet alpha, File matrixFile)` This constructs a `SubstitutionMatrix` object that contains two `Map` data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.
`SubstitutionMatrix(FiniteAlphabet alpha, short match, short replace)` Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.
`SubstitutionMatrix(FiniteAlphabet alpha, String matrixString, String name)` With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.

Method Summary

Methods
Modifier and Type	Method and Description
`FiniteAlphabet`	`getAlphabet()` Gives the alphabet used by this matrix.
`static SubstitutionMatrix`	`getBlosum100_50()` Return the `BLOSUM100.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum100()` Return the `BLOSUM100` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum30_50()` Return the `BLOSUM30.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum30()` Return the `BLOSUM30` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum35_50()` Return the `BLOSUM35.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum35()` Return the `BLOSUM35` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum40_50()` Return the `BLOSUM40.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum40()` Return the `BLOSUM40` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum45_50()` Return the `BLOSUM45.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum45()` Return the `BLOSUM45` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum50_50()` Return the `BLOSUM50.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum50()` Return the `BLOSUM50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum55_50()` Return the `BLOSUM55.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum55()` Return the `BLOSUM55` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum60_50()` Return the `BLOSUM60.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum60()` Return the `BLOSUM60` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum62_50()` Return the `BLOSUM62.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum62()` Return the `BLOSUM62` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum65_50()` Return the `BLOSUM65.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum65()` Return the `BLOSUM65` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum70_50()` Return the `BLOSUM70.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum70()` Return the `BLOSUM70` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum75_50()` Return the `BLOSUM75.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum75()` Return the `BLOSUM75` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum80_50()` Return the `BLOSUM80.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum80()` Return the `BLOSUM80` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum85_50()` Return the `BLOSUM85.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum85()` Return the `BLOSUM85` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum90_50()` Return the `BLOSUM90.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosum90()` Return the `BLOSUM90` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosumn_50()` Return the `BLOSUMN.50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getBlosumn()` Return the `BLOSUMN` amino acid substitution matrix.
`static SubstitutionMatrix`	`getDayhoff()` Return the `DAYHOFF` amino acid substitution matrix.
`String`	`getDescription()` This gives you the description of this matrix if there is one.
`static SubstitutionMatrix`	`getGonnet()` Return the `GONNET` amino acid substitution matrix.
`static SubstitutionMatrix`	`getIdentity()` Return the `IDENTITY` amino acid substitution matrix.
`static SubstitutionMatrix`	`getMatch()` Return the `MATCH` amino acid substitution matrix.
`short`	`getMax()` The maximum score in this matrix.
`short`	`getMin()` The minimum score of this matrix.
`String`	`getName()` Every substitution matrix has a name like "BLOSUM30" or "PAM160".
`static SubstitutionMatrix`	`getNuc4_2()` Return the `NUC.4.2` nucleotide substitution matrix.
`static SubstitutionMatrix`	`getNuc4_4()` Return the `NUC.4.4` nucleotide substitution matrix.
`static SubstitutionMatrix`	`getPam10()` Return the `PAM10` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam100()` Return the `PAM100` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam110()` Return the `PAM110` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam120()` Return the `PAM120` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam130()` Return the `PAM130` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam140()` Return the `PAM140` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam150()` Return the `PAM150` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam160()` Return the `PAM160` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam170()` Return the `PAM170` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam180()` Return the `PAM180` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam190()` Return the `PAM190` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam20()` Return the `PAM20` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam200()` Return the `PAM200` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam210()` Return the `PAM210` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam220()` Return the `PAM220` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam230()` Return the `PAM230` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam240()` Return the `PAM240` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam250()` Return the `PAM250` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam260()` Return the `PAM260` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam270()` Return the `PAM270` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam280()` Return the `PAM280` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam290()` Return the `PAM290` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam30()` Return the `PAM30` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam300()` Return the `PAM300` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam310()` Return the `PAM310` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam320()` Return the `PAM320` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam330()` Return the `PAM330` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam340()` Return the `PAM340` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam350()` Return the `PAM350` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam360()` Return the `PAM360` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam370()` Return the `PAM370` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam380()` Return the `PAM380` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam390()` Return the `PAM390` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam40()` Return the `PAM40` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam400()` Return the `PAM400` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam410()` Return the `PAM410` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam420()` Return the `PAM420` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam430()` Return the `PAM430` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam440()` Return the `PAM440` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam450()` Return the `PAM450` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam460()` Return the `PAM460` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam470()` Return the `PAM470` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam480()` Return the `PAM480` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam490()` Return the `PAM490` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam50()` Return the `PAM50` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam500()` Return the `PAM500` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam60()` Return the `PAM60` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam70()` Return the `PAM70` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam80()` Return the `PAM80` amino acid substitution matrix.
`static SubstitutionMatrix`	`getPam90()` Return the `PAM90` amino acid substitution matrix.
`static SubstitutionMatrix`	`getSubstitutionMatrix(BufferedReader reader)` This constructor can be used to guess the alphabet of this substitution matrix.
`static SubstitutionMatrix`	`getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader)` Return a new substitution matrix with the specified alphabet.
`static SubstitutionMatrix`	`getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader, String name)` Return a new substitution matrix with the specified alphabet and name.
`short`	`getValueAt(Symbol row, Symbol col)` There are some substitution matrices containing more columns than lines.
`SubstitutionMatrix`	`normalizeMatrix()` With this method you can get a “normalized” `SubstitutionMatrix` object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten.
`void`	`printMatrix()` Just to perform some test.
`void`	`setDescription(String desc)` Sets the description to the given value.
`String`	`stringnifyDescription()` Converts the description of the matrix to a String.
`String`	`stringnifyMatrix()` Creates a `String` representation of this matrix.
`String`	`toString()` Overrides the inherited method.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - SubstitutionMatrix
```
public SubstitutionMatrix(FiniteAlphabet alpha,
                  File matrixFile)
                   throws BioException,
                          NumberFormatException,
                          IOException
```
    This constructs a SubstitutionMatrix object that contains two Map data structures having BioJava symbols as keys and the value being the index of the matrix containing the substitution score.
    
    Parameters:
    alpha - the alphabet of the matrix (e.g., DNA, RNA or PROTEIN, or PROTEIN-TERM)
    matrixFile - the file containing the substitution matrix. Lines starting with '#' are comments. The line starting with a white space, is the table head. Every line has to start with the one letter representation of the Symbol and then the values for the exchange.
    
    Throws:
    
    IOException
    
    BioException
    
    NumberFormatException
  - SubstitutionMatrix
```
public SubstitutionMatrix(FiniteAlphabet alpha,
                  String matrixString,
                  String name)
                   throws BioException,
                          NumberFormatException,
                          IOException
```
    With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file. The given String contains a number of lines separated by System.getProperty("line.separator"). Everything else is the same than for the constructor above.
    
    Parameters:
    alpha - The FiniteAlphabet to use
    matrixString -
    name - of the matrix.
    
    Throws:
    
    BioException
    
    IOException
    
    NumberFormatException
  - SubstitutionMatrix
```
public SubstitutionMatrix(FiniteAlphabet alpha,
                  short match,
                  short replace)
```
    Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters. Ambiguous symbols are not considered because there might be to many of them (for proteins).
    
    Parameters:
    alpha -
    match -
    replace -
  - SubstitutionMatrix
```
public SubstitutionMatrix(File file)
                   throws NumberFormatException,
                          NoSuchElementException,
                          BioException,
                          IOException
```
    This constructor can be used to guess the alphabet of this substitution matrix. However, it is recommended to apply another constructor if the alphabet is known.
    
    Parameters:
    file - A file containing a substitution matrix.
    
    Throws:
    
    NumberFormatException
    
    NoSuchElementException
    
    BioException
    
    IOException
- Method Detail
  - getSubstitutionMatrix
```
public static SubstitutionMatrix getSubstitutionMatrix(BufferedReader reader)
                                                throws NumberFormatException,
                                                       BioException,
                                                       IOException
```
    This constructor can be used to guess the alphabet of this substitution matrix. However, it is recommended to apply another constructor if the alphabet is known.
    
    Parameters:
    reader -
    
    Throws:
    
    NumberFormatException
    
    BioException
    
    IOException
  - getSubstitutionMatrix
```
public static SubstitutionMatrix getSubstitutionMatrix(FiniteAlphabet alphabet,
                                       BufferedReader reader)
                                                throws BioException,
                                                       IOException
```
    Return a new substitution matrix with the specified alphabet.
    
    Parameters:
    alphabet - alphabet, must not be null
    reader - reader, must not be null
    
    Returns:
    a new substitution matrix with the specified alphabet
    
    Throws:
    
    BioException - if an error occurs
    
    IOException - if an I/O error occurs
  - getSubstitutionMatrix
```
public static SubstitutionMatrix getSubstitutionMatrix(FiniteAlphabet alphabet,
                                       BufferedReader reader,
                                       String name)
                                                throws BioException,
                                                       IOException
```
    Return a new substitution matrix with the specified alphabet and name.
    
    Parameters:
    alphabet - alphabet, must not be null
    reader - reader, must not be null
    name - name, must not be null
    
    Returns:
    a new substitution matrix with the specified alphabet and name
    
    Throws:
    
    BioException - if an error occurs
    
    IOException - if an I/O error occurs
  - getBlosum100
```
public static SubstitutionMatrix getBlosum100()
```
    Return the BLOSUM100 amino acid substitution matrix.
    
    Returns:
    the BLOSUM100 amino acid substitution matrix
  - getBlosum100_50
```
public static SubstitutionMatrix getBlosum100_50()
```
    Return the BLOSUM100.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM100.50 amino acid substitution matrix
  - getBlosum30
```
public static SubstitutionMatrix getBlosum30()
```
    Return the BLOSUM30 amino acid substitution matrix.
    
    Returns:
    the BLOSUM30 amino acid substitution matrix
  - getBlosum30_50
```
public static SubstitutionMatrix getBlosum30_50()
```
    Return the BLOSUM30.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM30.50 amino acid substitution matrix
  - getBlosum35
```
public static SubstitutionMatrix getBlosum35()
```
    Return the BLOSUM35 amino acid substitution matrix.
    
    Returns:
    the BLOSUM35 amino acid substitution matrix
  - getBlosum35_50
```
public static SubstitutionMatrix getBlosum35_50()
```
    Return the BLOSUM35.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM35.50 amino acid substitution matrix
  - getBlosum40
```
public static SubstitutionMatrix getBlosum40()
```
    Return the BLOSUM40 amino acid substitution matrix.
    
    Returns:
    the BLOSUM40 amino acid substitution matrix
  - getBlosum40_50
```
public static SubstitutionMatrix getBlosum40_50()
```
    Return the BLOSUM40.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM40.50 amino acid substitution matrix
  - getBlosum45
```
public static SubstitutionMatrix getBlosum45()
```
    Return the BLOSUM45 amino acid substitution matrix.
    
    Returns:
    the BLOSUM45 amino acid substitution matrix
  - getBlosum45_50
```
public static SubstitutionMatrix getBlosum45_50()
```
    Return the BLOSUM45.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM45.50 amino acid substitution matrix
  - getBlosum50
```
public static SubstitutionMatrix getBlosum50()
```
    Return the BLOSUM50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM50 amino acid substitution matrix
  - getBlosum50_50
```
public static SubstitutionMatrix getBlosum50_50()
```
    Return the BLOSUM50.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM50.50 amino acid substitution matrix
  - getBlosum55
```
public static SubstitutionMatrix getBlosum55()
```
    Return the BLOSUM55 amino acid substitution matrix.
    
    Returns:
    the BLOSUM55 amino acid substitution matrix
  - getBlosum55_50
```
public static SubstitutionMatrix getBlosum55_50()
```
    Return the BLOSUM55.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM55.50 amino acid substitution matrix
  - getBlosum60
```
public static SubstitutionMatrix getBlosum60()
```
    Return the BLOSUM60 amino acid substitution matrix.
    
    Returns:
    the BLOSUM60 amino acid substitution matrix
  - getBlosum60_50
```
public static SubstitutionMatrix getBlosum60_50()
```
    Return the BLOSUM60.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM60.50 amino acid substitution matrix
  - getBlosum62
```
public static SubstitutionMatrix getBlosum62()
```
    Return the BLOSUM62 amino acid substitution matrix.
    
    Returns:
    the BLOSUM62 amino acid substitution matrix
  - getBlosum62_50
```
public static SubstitutionMatrix getBlosum62_50()
```
    Return the BLOSUM62.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM62.50 amino acid substitution matrix
  - getBlosum65
```
public static SubstitutionMatrix getBlosum65()
```
    Return the BLOSUM65 amino acid substitution matrix.
    
    Returns:
    the BLOSUM65 amino acid substitution matrix
  - getBlosum65_50
```
public static SubstitutionMatrix getBlosum65_50()
```
    Return the BLOSUM65.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM65.50 amino acid substitution matrix
  - getBlosum70
```
public static SubstitutionMatrix getBlosum70()
```
    Return the BLOSUM70 amino acid substitution matrix.
    
    Returns:
    the BLOSUM70 amino acid substitution matrix
  - getBlosum70_50
```
public static SubstitutionMatrix getBlosum70_50()
```
    Return the BLOSUM70.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM70.50 amino acid substitution matrix
  - getBlosum75
```
public static SubstitutionMatrix getBlosum75()
```
    Return the BLOSUM75 amino acid substitution matrix.
    
    Returns:
    the BLOSUM75 amino acid substitution matrix
  - getBlosum75_50
```
public static SubstitutionMatrix getBlosum75_50()
```
    Return the BLOSUM75.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM75.50 amino acid substitution matrix
  - getBlosum80
```
public static SubstitutionMatrix getBlosum80()
```
    Return the BLOSUM80 amino acid substitution matrix.
    
    Returns:
    the BLOSUM80 amino acid substitution matrix
  - getBlosum80_50
```
public static SubstitutionMatrix getBlosum80_50()
```
    Return the BLOSUM80.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM80.50 amino acid substitution matrix
  - getBlosum85
```
public static SubstitutionMatrix getBlosum85()
```
    Return the BLOSUM85 amino acid substitution matrix.
    
    Returns:
    the BLOSUM85 amino acid substitution matrix
  - getBlosum85_50
```
public static SubstitutionMatrix getBlosum85_50()
```
    Return the BLOSUM85.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM85.50 amino acid substitution matrix
  - getBlosum90
```
public static SubstitutionMatrix getBlosum90()
```
    Return the BLOSUM90 amino acid substitution matrix.
    
    Returns:
    the BLOSUM90 amino acid substitution matrix
  - getBlosum90_50
```
public static SubstitutionMatrix getBlosum90_50()
```
    Return the BLOSUM90.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUM90.50 amino acid substitution matrix
  - getBlosumn
```
public static SubstitutionMatrix getBlosumn()
```
    Return the BLOSUMN amino acid substitution matrix.
    
    Returns:
    the BLOSUMN amino acid substitution matrix
  - getBlosumn_50
```
public static SubstitutionMatrix getBlosumn_50()
```
    Return the BLOSUMN.50 amino acid substitution matrix.
    
    Returns:
    the BLOSUMN.50 amino acid substitution matrix
  - getDayhoff
```
public static SubstitutionMatrix getDayhoff()
```
    Return the DAYHOFF amino acid substitution matrix.
    
    Returns:
    the DAYHOFF amino acid substitution matrix
  - getGonnet
```
public static SubstitutionMatrix getGonnet()
```
    Return the GONNET amino acid substitution matrix.
    
    Returns:
    the GONNET amino acid substitution matrix
  - getIdentity
```
public static SubstitutionMatrix getIdentity()
```
    Return the IDENTITY amino acid substitution matrix.
    
    Returns:
    the IDENTITY amino acid substitution matrix
  - getMatch
```
public static SubstitutionMatrix getMatch()
```
    Return the MATCH amino acid substitution matrix.
    
    Returns:
    the MATCH amino acid substitution matrix
  - getNuc4_2
```
public static SubstitutionMatrix getNuc4_2()
```
    Return the NUC.4.2 nucleotide substitution matrix.
    
    Returns:
    the NUC.4.2 nucleotide substitution matrix
  - getNuc4_4
```
public static SubstitutionMatrix getNuc4_4()
```
    Return the NUC.4.4 nucleotide substitution matrix.
    
    Returns:
    the NUC.4.4 nucleotide substitution matrix
  - getPam10
```
public static SubstitutionMatrix getPam10()
```
    Return the PAM10 amino acid substitution matrix.
    
    Returns:
    the PAM10 amino acid substitution matrix
  - getPam100
```
public static SubstitutionMatrix getPam100()
```
    Return the PAM100 amino acid substitution matrix.
    
    Returns:
    the PAM100 amino acid substitution matrix
  - getPam110
```
public static SubstitutionMatrix getPam110()
```
    Return the PAM110 amino acid substitution matrix.
    
    Returns:
    the PAM110 amino acid substitution matrix
  - getPam120
```
public static SubstitutionMatrix getPam120()
```
    Return the PAM120 amino acid substitution matrix.
    
    Returns:
    the PAM120 amino acid substitution matrix
  - getPam130
```
public static SubstitutionMatrix getPam130()
```
    Return the PAM130 amino acid substitution matrix.
    
    Returns:
    the PAM130 amino acid substitution matrix
  - getPam140
```
public static SubstitutionMatrix getPam140()
```
    Return the PAM140 amino acid substitution matrix.
    
    Returns:
    the PAM140 amino acid substitution matrix
  - getPam150
```
public static SubstitutionMatrix getPam150()
```
    Return the PAM150 amino acid substitution matrix.
    
    Returns:
    the PAM150 amino acid substitution matrix
  - getPam160
```
public static SubstitutionMatrix getPam160()
```
    Return the PAM160 amino acid substitution matrix.
    
    Returns:
    the PAM160 amino acid substitution matrix
  - getPam170
```
public static SubstitutionMatrix getPam170()
```
    Return the PAM170 amino acid substitution matrix.
    
    Returns:
    the PAM170 amino acid substitution matrix
  - getPam180
```
public static SubstitutionMatrix getPam180()
```
    Return the PAM180 amino acid substitution matrix.
    
    Returns:
    the PAM180 amino acid substitution matrix
  - getPam190
```
public static SubstitutionMatrix getPam190()
```
    Return the PAM190 amino acid substitution matrix.
    
    Returns:
    the PAM190 amino acid substitution matrix
  - getPam20
```
public static SubstitutionMatrix getPam20()
```
    Return the PAM20 amino acid substitution matrix.
    
    Returns:
    the PAM20 amino acid substitution matrix
  - getPam200
```
public static SubstitutionMatrix getPam200()
```
    Return the PAM200 amino acid substitution matrix.
    
    Returns:
    the PAM200 amino acid substitution matrix
  - getPam210
```
public static SubstitutionMatrix getPam210()
```
    Return the PAM210 amino acid substitution matrix.
    
    Returns:
    the PAM210 amino acid substitution matrix
  - getPam220
```
public static SubstitutionMatrix getPam220()
```
    Return the PAM220 amino acid substitution matrix.
    
    Returns:
    the PAM220 amino acid substitution matrix
  - getPam230
```
public static SubstitutionMatrix getPam230()
```
    Return the PAM230 amino acid substitution matrix.
    
    Returns:
    the PAM230 amino acid substitution matrix
  - getPam240
```
public static SubstitutionMatrix getPam240()
```
    Return the PAM240 amino acid substitution matrix.
    
    Returns:
    the PAM240 amino acid substitution matrix
  - getPam250
```
public static SubstitutionMatrix getPam250()
```
    Return the PAM250 amino acid substitution matrix.
    
    Returns:
    the PAM250 amino acid substitution matrix
  - getPam260
```
public static SubstitutionMatrix getPam260()
```
    Return the PAM260 amino acid substitution matrix.
    
    Returns:
    the PAM260 amino acid substitution matrix
  - getPam270
```
public static SubstitutionMatrix getPam270()
```
    Return the PAM270 amino acid substitution matrix.
    
    Returns:
    the PAM270 amino acid substitution matrix
  - getPam280
```
public static SubstitutionMatrix getPam280()
```
    Return the PAM280 amino acid substitution matrix.
    
    Returns:
    the PAM280 amino acid substitution matrix
  - getPam290
```
public static SubstitutionMatrix getPam290()
```
    Return the PAM290 amino acid substitution matrix.
    
    Returns:
    the PAM290 amino acid substitution matrix
  - getPam30
```
public static SubstitutionMatrix getPam30()
```
    Return the PAM30 amino acid substitution matrix.
    
    Returns:
    the PAM30 amino acid substitution matrix
  - getPam300
```
public static SubstitutionMatrix getPam300()
```
    Return the PAM300 amino acid substitution matrix.
    
    Returns:
    the PAM300 amino acid substitution matrix
  - getPam310
```
public static SubstitutionMatrix getPam310()
```
    Return the PAM310 amino acid substitution matrix.
    
    Returns:
    the PAM310 amino acid substitution matrix
  - getPam320
```
public static SubstitutionMatrix getPam320()
```
    Return the PAM320 amino acid substitution matrix.
    
    Returns:
    the PAM320 amino acid substitution matrix
  - getPam330
```
public static SubstitutionMatrix getPam330()
```
    Return the PAM330 amino acid substitution matrix.
    
    Returns:
    the PAM330 amino acid substitution matrix
  - getPam340
```
public static SubstitutionMatrix getPam340()
```
    Return the PAM340 amino acid substitution matrix.
    
    Returns:
    the PAM340 amino acid substitution matrix
  - getPam350
```
public static SubstitutionMatrix getPam350()
```
    Return the PAM350 amino acid substitution matrix.
    
    Returns:
    the PAM350 amino acid substitution matrix
  - getPam360
```
public static SubstitutionMatrix getPam360()
```
    Return the PAM360 amino acid substitution matrix.
    
    Returns:
    the PAM360 amino acid substitution matrix
  - getPam370
```
public static SubstitutionMatrix getPam370()
```
    Return the PAM370 amino acid substitution matrix.
    
    Returns:
    the PAM370 amino acid substitution matrix
  - getPam380
```
public static SubstitutionMatrix getPam380()
```
    Return the PAM380 amino acid substitution matrix.
    
    Returns:
    the PAM380 amino acid substitution matrix
  - getPam390
```
public static SubstitutionMatrix getPam390()
```
    Return the PAM390 amino acid substitution matrix.
    
    Returns:
    the PAM390 amino acid substitution matrix
  - getPam40
```
public static SubstitutionMatrix getPam40()
```
    Return the PAM40 amino acid substitution matrix.
    
    Returns:
    the PAM40 amino acid substitution matrix
  - getPam400
```
public static SubstitutionMatrix getPam400()
```
    Return the PAM400 amino acid substitution matrix.
    
    Returns:
    the PAM400 amino acid substitution matrix
  - getPam410
```
public static SubstitutionMatrix getPam410()
```
    Return the PAM410 amino acid substitution matrix.
    
    Returns:
    the PAM410 amino acid substitution matrix
  - getPam420
```
public static SubstitutionMatrix getPam420()
```
    Return the PAM420 amino acid substitution matrix.
    
    Returns:
    the PAM420 amino acid substitution matrix
  - getPam430
```
public static SubstitutionMatrix getPam430()
```
    Return the PAM430 amino acid substitution matrix.
    
    Returns:
    the PAM430 amino acid substitution matrix
  - getPam440
```
public static SubstitutionMatrix getPam440()
```
    Return the PAM440 amino acid substitution matrix.
    
    Returns:
    the PAM440 amino acid substitution matrix
  - getPam450
```
public static SubstitutionMatrix getPam450()
```
    Return the PAM450 amino acid substitution matrix.
    
    Returns:
    the PAM450 amino acid substitution matrix
  - getPam460
```
public static SubstitutionMatrix getPam460()
```
    Return the PAM460 amino acid substitution matrix.
    
    Returns:
    the PAM460 amino acid substitution matrix
  - getPam470
```
public static SubstitutionMatrix getPam470()
```
    Return the PAM470 amino acid substitution matrix.
    
    Returns:
    the PAM470 amino acid substitution matrix
  - getPam480
```
public static SubstitutionMatrix getPam480()
```
    Return the PAM480 amino acid substitution matrix.
    
    Returns:
    the PAM480 amino acid substitution matrix
  - getPam490
```
public static SubstitutionMatrix getPam490()
```
    Return the PAM490 amino acid substitution matrix.
    
    Returns:
    the PAM490 amino acid substitution matrix
  - getPam50
```
public static SubstitutionMatrix getPam50()
```
    Return the PAM50 amino acid substitution matrix.
    
    Returns:
    the PAM50 amino acid substitution matrix
  - getPam500
```
public static SubstitutionMatrix getPam500()
```
    Return the PAM500 amino acid substitution matrix.
    
    Returns:
    the PAM500 amino acid substitution matrix
  - getPam60
```
public static SubstitutionMatrix getPam60()
```
    Return the PAM60 amino acid substitution matrix.
    
    Returns:
    the PAM60 amino acid substitution matrix
  - getPam70
```
public static SubstitutionMatrix getPam70()
```
    Return the PAM70 amino acid substitution matrix.
    
    Returns:
    the PAM70 amino acid substitution matrix
  - getPam80
```
public static SubstitutionMatrix getPam80()
```
    Return the PAM80 amino acid substitution matrix.
    
    Returns:
    the PAM80 amino acid substitution matrix
  - getPam90
```
public static SubstitutionMatrix getPam90()
```
    Return the PAM90 amino acid substitution matrix.
    
    Returns:
    the PAM90 amino acid substitution matrix
  - getValueAt
```
public short getValueAt(Symbol row,
               Symbol col)
                 throws BioException
```
    There are some substitution matrices containing more columns than lines. This has to do with the ambiguous symbols. Lines are always good, columns might not contain the whole information. The matrix is supposed to be symmetric anyway, so you can always set the ambiguous symbol to be the first argument.
    
    Parameters:
    row - Symbol of the line
    col - Symbol of the column
    
    Returns:
    expenses for the exchange of symbol row and symbol column.
    
    Throws:
    
    BioException
  - getDescription
```
public String getDescription()
```
    This gives you the description of this matrix if there is one. Normally substitution matrix files like BLOSUM contain some lines of description.
    
    Returns:
    the comment of the matrix
  - getName
```
public String getName()
```
    Every substitution matrix has a name like "BLOSUM30" or "PAM160". This will be returned by this method.
    
    Returns:
    the name of the matrix.
  - getMin
```
public short getMin()
```
    The minimum score of this matrix.
    
    Returns:
    minimum of the matrix.
  - getMax
```
public short getMax()
```
    The maximum score in this matrix.
    
    Returns:
    maximum of the matrix.
  - setDescription
```
public void setDescription(String desc)
```
    Sets the description to the given value.
    
    Parameters:
    desc - a description. This doesn't have to start with '#'.
  - getAlphabet
```
public FiniteAlphabet getAlphabet()
```
    Gives the alphabet used by this matrix.
    
    Returns:
    the alphabet of this matrix.
  - stringnifyMatrix
```
public String stringnifyMatrix()
```
    Creates a String representation of this matrix.
    
    Returns:
    a string representation of this matrix without the description.
  - stringnifyDescription
```
public String stringnifyDescription()
```
    Converts the description of the matrix to a String.
    
    Returns:
    Gives a description with approximately 60 letters on every line separated by System.getProperty("line.separator"). Every line starts with #.
  - toString
```
public String toString()
```
    Overrides the inherited method.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    Gives a string representation of the SubstitutionMatrix. This is a valid input for the constructor which needs a matrix string. This String also contains the description of the matrix if there is one.
  - printMatrix
```
public void printMatrix()
```
    Just to perform some test. It prints the matrix on the screen.
  - normalizeMatrix
```
public SubstitutionMatrix normalizeMatrix()
                                   throws BioException,
                                          NumberFormatException,
                                          IOException
```
    With this method you can get a “normalized” SubstitutionMatrix object; however, since this implementation uses an short matrix, the normalized matrix will be scaled by ten. If you need values between zero and one, you have to divide every value returned by getValueAt by ten.
    
    Returns:
    a new and normalized SubstitutionMatrix object given by this substitution matrix. Because this uses an short matrix, all values are scaled by 10.
    
    Throws:
    
    BioException
    
    IOException
    
    NumberFormatException

Class SubstitutionMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SubstitutionMatrix

SubstitutionMatrix

SubstitutionMatrix

SubstitutionMatrix

Method Detail

getSubstitutionMatrix

getSubstitutionMatrix

getSubstitutionMatrix

getBlosum100

getBlosum100_50

getBlosum30

getBlosum30_50

getBlosum35

getBlosum35_50

getBlosum40

getBlosum40_50

getBlosum45

getBlosum45_50

getBlosum50

getBlosum50_50

getBlosum55

getBlosum55_50

getBlosum60

getBlosum60_50

getBlosum62

getBlosum62_50

getBlosum65

getBlosum65_50

getBlosum70

getBlosum70_50

getBlosum75

getBlosum75_50

getBlosum80

getBlosum80_50

getBlosum85

getBlosum85_50

getBlosum90

getBlosum90_50

getBlosumn

getBlosumn_50

getDayhoff

getGonnet

getIdentity

getMatch

getNuc4_2

getNuc4_4

getPam10

getPam100

getPam110

getPam120

getPam130

getPam140

getPam150

getPam160

getPam170

getPam180

getPam190

getPam20

getPam200

getPam210

getPam220

getPam230

getPam240

getPam250

getPam260

getPam270

getPam280

getPam290

getPam30

getPam300

getPam310

getPam320

getPam330

getPam340

getPam350