org.biojava.bio.alignment
Class SubstitutionMatrix

java.lang.Object
  extended by org.biojava.bio.alignment.SubstitutionMatrix

public class SubstitutionMatrix
extends Object

This object is able to read a substitution matrix file and constructs an int matrix to store the matrix. Every single element of the matrix can be accessed by the method getValueAt with the parameters being tow 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

Field Summary
protected  FiniteAlphabet alphabet
           
protected  Map colSymbols
           
protected  String description
           
protected  int[][] matrix
           
protected  int max
           
protected  int min
           
protected  String name
           
protected  Map rowSymbols
           
 
Constructor Summary
SubstitutionMatrix(FiniteAlphabet alpha, File matrixFile)
          This constructs a SubstitutionMatrix-object that contains two Map data structures having biojava symbols as key and the value being the index of the matrix containing the substitution score.
SubstitutionMatrix(FiniteAlphabet alpha, int match, int 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
 FiniteAlphabet getAlphabet()
          Gives the alphabet used by this matrix.
 String getDescription()
          This gives you the description of this matrix if there is one.
 int getMax()
          The maximum score in this matrix.
 int getMin()
          The minimum score of this matrix.
 String getName()
          Every substitution matrix has a name like "BLOSUM30" or "PAM160".
 int 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 int matrix, the normalized matrix will be scaled by ten.
protected  int[][] parseMatrix(String matString)
          Reads a String representing the contents of a substitution matrix file.
 void printMatrix()
          Just to perform some test.
 void setDescription(String desc)
          Sets the description to the given value.
 String stringnifyDescription()
          Stringnifies the description of the matrix.
 String stringnifyMatrix()
          Creates a String representation of this matrix.
 String toString()
          Overides the inherited method.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

rowSymbols

protected Map rowSymbols

colSymbols

protected Map colSymbols

matrix

protected int[][] matrix

min

protected int min

max

protected int max

alphabet

protected FiniteAlphabet alphabet

description

protected String description

name

protected String name
Constructor Detail

SubstitutionMatrix

public SubstitutionMatrix(FiniteAlphabet alpha,
                          File matrixFile)
                   throws IOException,
                          BioException
This constructs a SubstitutionMatrix-object that contains two Map data structures having biojava symbols as key and the value being the index of the matrix containing the substitution score.

Parameters:
alpha - the alphabet of the matrix (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

SubstitutionMatrix

public SubstitutionMatrix(FiniteAlphabet alpha,
                          String matrixString,
                          String name)
                   throws BioException
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 \n. Everything else is the same than for the constructor above.

Parameters:
alpha - The FiniteAlphabet to use
matrixString -
name - of the matrix.
Throws:
BioException

SubstitutionMatrix

public SubstitutionMatrix(FiniteAlphabet alpha,
                          int match,
                          int replace)
Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters. Ambigious symbols are not considered because there might be to many of them (for proteins).

Parameters:
alpha -
match -
replace -
Method Detail

parseMatrix

protected int[][] parseMatrix(String matString)
                       throws BioException
Reads a String representing the contents of a substitution matrix file.

Parameters:
matString -
Returns:
matrix
Throws:
BioException

getValueAt

public int getValueAt(Symbol row,
                      Symbol col)
               throws BioException
There are some substitution matrices containing more columns than lines. This has to do with the ambigious 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 ambigious 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 col.
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 int getMin()
The minimum score of this matrix.

Returns:
minimum of the matrix.

getMax

public int 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()
Stringnifies the description of the matrix.

Returns:
Gives a description with approximately 60 letters on every line separated by \n. Every line starts with #.

toString

public String toString()
Overides 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()
With this method you can get a "normalized" SubstitutionMatrix object; however, since this implementation uses an int matrix, the normalized matrix will be scaled by ten. If you need values between zero and one, you have to devide every value returnd by getValueAt by ten.

Returns:
a new and normalized SubstitutionMatrix object given by this substitution matrix. Because this uses an int matrix, all values are skaled by 10.