blinAlignment
Class SubstitutionMatrix

java.lang.Object
  blinAlignment.SubstitutionMatrix

public class SubstitutionMatrix
extends java.lang.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

Constructor Summary

SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet alpha, double match, double replace)
Constructs a SubstitutionMatrix with every Match and every Replace having the same expenses given by the parameters.

SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet alpha, java.io.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.

Method Summary

org.biojava.bio.symbol.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.
double	getMax() The maximum score in this matrix.
double	getMin() The minimum score of this matrix.
java.lang.String	getName() Every substitution matrix has a name like "BLOSUM30" or "PAM160".
double	getValueAt(org.biojava.bio.symbol.Symbol row, org.biojava.bio.symbol.Symbol col) There are some substitution matrices containing more columns than lines.
void	printMatrix() Just to perform some test.
void	setDescription(java.lang.String desc) Sets the description to the given value.
java.lang.String	stringnifyDescription() Stringnifies the description of the matrix.
java.lang.String	stringnifyMatrix() Creates a String representation of this matrix.
java.lang.String	toString() Overides the inherited method.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SubstitutionMatrix

public SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet alpha,
                          java.io.File matrixFile)
                   throws java.io.IOException,
                          org.biojava.bio.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:

java.io.IOException

org.biojava.bio.BioException

SubstitutionMatrix

public SubstitutionMatrix(org.biojava.bio.symbol.FiniteAlphabet alpha,
                          double match,
                          double 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

getValueAt

public double getValueAt(org.biojava.bio.symbol.Symbol row,
                         org.biojava.bio.symbol.Symbol col)
                  throws org.biojava.bio.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:

org.biojava.bio.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 double getMin()

The minimum score of this matrix.

Returns:

minimum of the matrix.

getMax

public double 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 org.biojava.bio.symbol.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()

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 java.lang.String toString()

Overides 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.