org.biojava.bio.alignment

Class SubstitutionMatrix

java.lang.Object

org.biojava.bio.alignment.SubstitutionMatrix

public class SubstitutionMatrix
extends java.lang.Object

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

Field Summary

Fields

Modifier and Type	Field and Description
protected FiniteAlphabet	alphabet
protected java.util.Map<Symbol,java.lang.Integer>	colSymbols
protected java.lang.String	description
protected short[][]	matrix
protected short	max
protected short	min
protected java.lang.String	name
protected java.util.Map<Symbol,java.lang.Integer>	rowSymbols

Constructor Summary

Constructors

Constructor and Description
SubstitutionMatrix(java.io.File file) This constructor can be used to guess the alphabet of this substitution matrix.
SubstitutionMatrix(FiniteAlphabet alpha, java.io.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, java.lang.String matrixString, java.lang.String name) With this constructor it is possible to construct a SubstitutionMatrix object from a substitution matrix file.

Method Summary

Modifier and Type	Method and Description
FiniteAlphabet	getAlphabet() Gives the alphabet used by this matrix.
java.lang.String	getDescription() This gives you the description of this matrix if there is one.
short	getMax() The maximum score in this matrix.
short	getMin() The minimum score of this matrix.
java.lang.String	getName() Every substitution matrix has a name like "BLOSUM30" or "PAM160".
static SubstitutionMatrix	getSubstitutionMatrix(java.io.BufferedReader reader) This constructor can be used to guess the alphabet of this substitution matrix.
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(java.lang.String desc) Sets the description to the given value.
java.lang.String	stringnifyDescription() Converts the description of the matrix to a String.
java.lang.String	stringnifyMatrix() Creates a String representation of this matrix.
java.lang.String	toString() Overrides the inherited method.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

rowSymbols

protected java.util.Map<Symbol,java.lang.Integer> rowSymbols

colSymbols

protected java.util.Map<Symbol,java.lang.Integer> colSymbols

matrix

protected short[][] matrix

min

protected short min

max

protected short max

alphabet

protected FiniteAlphabet alphabet

description

protected java.lang.String description

name

protected java.lang.String name

Constructor Detail

SubstitutionMatrix

public SubstitutionMatrix(FiniteAlphabet alpha,
                          java.io.File matrixFile)
                   throws BioException,
                          java.lang.NumberFormatException,
                          java.io.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:

java.io.IOException

BioException

java.lang.NumberFormatException

SubstitutionMatrix

public SubstitutionMatrix(FiniteAlphabet alpha,
                          java.lang.String matrixString,
                          java.lang.String name)
                   throws BioException,
                          java.lang.NumberFormatException,
                          java.io.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

java.io.IOException

java.lang.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(java.io.File file)
                   throws java.lang.NumberFormatException,
                          java.util.NoSuchElementException,
                          BioException,
                          java.io.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:

java.lang.NumberFormatException

java.util.NoSuchElementException

BioException

java.io.IOException

Method Detail

getSubstitutionMatrix

public static SubstitutionMatrix getSubstitutionMatrix(java.io.BufferedReader reader)
                                                throws java.lang.NumberFormatException,
                                                       BioException,
                                                       java.io.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:

java.lang.NumberFormatException

BioException

java.io.IOException

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 java.lang.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 java.lang.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(java.lang.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 java.lang.String stringnifyMatrix()

Creates a String representation of this matrix.

Returns:

a string representation of this matrix without the description.

stringnifyDescription

public java.lang.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 java.lang.String toString()

Overrides the inherited method.

Overrides:

toString in class java.lang.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,
                                          java.lang.NumberFormatException,
                                          java.io.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

java.io.IOException

java.lang.NumberFormatException