Package org.biojava.nbio.core.alignment.matrices

Class SimpleSubstitutionMatrix<C extends Compound>

java.lang.Object

org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix<C>

Type Parameters:

C - each element of the matrix corresponds to a pair of Compounds of type C

All Implemented Interfaces:

Serializable, SubstitutionMatrix<C>

public class SimpleSubstitutionMatrix<C extends Compound>
extends Object
implements SubstitutionMatrix<C>, Serializable

Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one Compound in a sequence for another.

Author:

Mark Chapman, Daniel Cameron, Paolo Pavan

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, short match, short replace)	Creates an identity substitution matrix from match and replace values.
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, File fileInput)	Creates a substitution matrix by reading in a file.
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, Reader input, String name)	Creates a substitution matrix by parsing some input.
SimpleSubstitutionMatrix(CompoundSet<C> compoundSet, String matrixInput, String name)	Creates a substitution matrix by parsing a String.

Method Summary

Modifier and Type	Method	Description
static SubstitutionMatrix<AminoAcidCompound>	getBlosum62()
Map<C,Short>	getColumn(C column)
CompoundSet<C>	getCompoundSet()	Returns the CompoundSet on which the matrix is defined.
String	getDescription()	Returns the description of this matrix.
short[][]	getMatrix()	Returns entire matrix.
String	getMatrixAsString()	Returns this matrix as a formatted String with Compound labels along the axes.
short	getMaxValue()	Returns the maximum value in this matrix.
short	getMinValue()	Returns the minimum value in this matrix.
String	getName()	Returns the name (short description) of this matrix.
Map<C,Short>	getRow(C row)
short	getValue(C from, C to)	Returns value in matrix for conversion from first Compound to the second.
SubstitutionMatrix<C>	normalizeMatrix(short scale)	Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.
void	setDescription(String description)	Sets the description of this matrix.
void	setName(String name)	Sets the name (short description) of this matrix.
String	toString()	Returns in a format similar to the standard NCBI files.

Methods inherited from class java.lang.Object

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

Constructor Details

SimpleSubstitutionMatrix

public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
 File fileInput)
                         throws FileNotFoundException

Creates a substitution matrix by reading in a file.

Parameters:

compoundSet - the CompoundSet on which the matrix is defined

fileInput - file parsed for a substitution matrix

Throws:

FileNotFoundException - if fileInput parameter cannot be read

SimpleSubstitutionMatrix

public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
 Reader input,
 String name)

Creates a substitution matrix by parsing some input.

Parameters:

compoundSet - the CompoundSet on which the matrix is defined

input - input parsed for a substitution matrix

name - the name (short description) of this matrix

SimpleSubstitutionMatrix

public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
 String matrixInput,
 String name)

Creates a substitution matrix by parsing a String.

Parameters:

compoundSet - the CompoundSet on which the matrix is defined

matrixInput - String parsed for a substitution matrix

name - the name (short description) of this matrix

SimpleSubstitutionMatrix

public SimpleSubstitutionMatrix(CompoundSet<C> compoundSet,
 short match,
 short replace)

Creates an identity substitution matrix from match and replace values.

Parameters:

compoundSet - the CompoundSet on which the matrix is defined

match - matrix value used for equivalent Compounds

replace - matrix value used for differing Compounds

Method Details

getBlosum62

public static SubstitutionMatrix<AminoAcidCompound> getBlosum62()

getCompoundSet

public CompoundSet<C> getCompoundSet()

Description copied from interface: SubstitutionMatrix

Returns the CompoundSet on which the matrix is defined.

Specified by:

getCompoundSet in interface SubstitutionMatrix<C extends Compound>

Returns:

the CompoundSet on which the matrix is defined

getDescription

public String getDescription()

Description copied from interface: SubstitutionMatrix

Returns the description of this matrix.

Specified by:

getDescription in interface SubstitutionMatrix<C extends Compound>

Returns:

description

getMatrix

public short[][] getMatrix()

Description copied from interface: SubstitutionMatrix

Returns entire matrix.

Specified by:

getMatrix in interface SubstitutionMatrix<C extends Compound>

Returns:

matrix

getMatrixAsString

public String getMatrixAsString()

Description copied from interface: SubstitutionMatrix

Returns this matrix as a formatted String with Compound labels along the axes.

Specified by:

getMatrixAsString in interface SubstitutionMatrix<C extends Compound>

Returns:

this matrix as a formatted String

getMaxValue

public short getMaxValue()

Description copied from interface: SubstitutionMatrix

Returns the maximum value in this matrix.

Specified by:

getMaxValue in interface SubstitutionMatrix<C extends Compound>

Returns:

the maximum value in this matrix

getMinValue

public short getMinValue()

Description copied from interface: SubstitutionMatrix

Returns the minimum value in this matrix.

Specified by:

getMinValue in interface SubstitutionMatrix<C extends Compound>

Returns:

the minimum value in this matrix

getName

public String getName()

Description copied from interface: SubstitutionMatrix

Returns the name (short description) of this matrix.

Specified by:

getName in interface SubstitutionMatrix<C extends Compound>

Returns:

name

getValue

public short getValue(C from,
 C to)

Description copied from interface: SubstitutionMatrix

Returns value in matrix for conversion from first Compound to the second. If an argument does not belong to the CompoundSet, this could either throw an IllegalArgumentException or it could return SubstitutionMatrix.getMinValue().

Specified by:

getValue in interface SubstitutionMatrix<C extends Compound>

Parameters:

from - original Compound

to - replacement Compound

Returns:

value in matrix for conversion from first Compound to the second

normalizeMatrix

public SubstitutionMatrix<C> normalizeMatrix(short scale)

Description copied from interface: SubstitutionMatrix

Rescales the matrix so that to SubstitutionMatrix.getMaxValue() - SubstitutionMatrix.getMinValue() = scale.

Specified by:

normalizeMatrix in interface SubstitutionMatrix<C extends Compound>

Parameters:

scale - new normalization scale of this matrix

setDescription

public void setDescription(String description)

Description copied from interface: SubstitutionMatrix

Sets the description of this matrix.

Specified by:

setDescription in interface SubstitutionMatrix<C extends Compound>

Parameters:

description - new description

setName

public void setName(String name)

Description copied from interface: SubstitutionMatrix

Sets the name (short description) of this matrix.

Specified by:

setName in interface SubstitutionMatrix<C extends Compound>

Parameters:

name - new name

toString

public String toString()

Returns in a format similar to the standard NCBI files.

Overrides:

toString in class Object

getRow

public Map<C,Short> getRow(C row)

Specified by:

getRow in interface SubstitutionMatrix<C extends Compound>

getColumn

public Map<C,Short> getColumn(C column)

Specified by:

getColumn in interface SubstitutionMatrix<C extends Compound>