Package org.biojava.nbio.core.alignment.template

Interface SubstitutionMatrix<C extends Compound>

Type Parameters:

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

All Known Implementing Classes:

ScaledSubstitutionMatrix, SimpleSubstitutionMatrix

public interface SubstitutionMatrix<C extends Compound>

Defines 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, Paolo Pavan

Method Summary

Modifier and Type	Method	Description
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 getMaxValue() - getMinValue() = scale.
void	setDescription(String description)	Sets the description of this matrix.
void	setName(String name)	Sets the name (short description) of this matrix.

Method Detail

getCompoundSet

CompoundSet<C> getCompoundSet()

Returns the CompoundSet on which the matrix is defined.

Returns:

the CompoundSet on which the matrix is defined

getDescription

String getDescription()

Returns the description of this matrix.

Returns:

description

getMatrix

short[][] getMatrix()

Returns entire matrix.

Returns:

matrix

getMatrixAsString

String getMatrixAsString()

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

Returns:

this matrix as a formatted String

getMaxValue

short getMaxValue()

Returns the maximum value in this matrix.

Returns:

the maximum value in this matrix

getMinValue

short getMinValue()

Returns the minimum value in this matrix.

Returns:

the minimum value in this matrix

getName

String getName()

Returns the name (short description) of this matrix.

Returns:

name

getValue

short getValue(C from,
               C to)

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 getMinValue().

Parameters:

from - original Compound

to - replacement Compound

Returns:

value in matrix for conversion from first Compound to the second

Throws:

IllegalArgumentException - possibly, if an argument does not belong to the CompoundSet

normalizeMatrix

SubstitutionMatrix<C> normalizeMatrix(short scale)

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

Parameters:

scale - new normalization scale of this matrix

Throws:

IllegalArgumentException - if scale < 1

setDescription

void setDescription(String description)

Sets the description of this matrix.

Parameters:

description - new description

setName

void setName(String name)

Sets the name (short description) of this matrix.

Parameters:

name - new name

getRow

Map<C,Short> getRow(C row)

getColumn

Map<C,Short> getColumn(C column)