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C
- each element of the matrix corresponds to a pair of Compound
s of type Cpublic 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.
Method Summary | |
---|---|
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. |
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 |
---|
CompoundSet<C> getCompoundSet()
CompoundSet
on which the matrix is defined.
CompoundSet
on which the matrix is definedString getDescription()
short[][] getMatrix()
String getMatrixAsString()
Compound
labels along the axes.
short getMaxValue()
short getMinValue()
String getName()
short getValue(C from, C to)
Compound
to the second. If an argument does not
belong to the CompoundSet
, this could either throw an IllegalArgumentException
or it could
return getMinValue()
.
from
- original Compound
to
- replacement Compound
Compound
to the second
IllegalArgumentException
- possibly, if an argument does not belong to the CompoundSet
SubstitutionMatrix<C> normalizeMatrix(short scale)
getMaxValue()
- getMinValue()
= scale.
scale
- new normalization scale of this matrix
IllegalArgumentException
- if scale < 1void setDescription(String description)
description
- new descriptionvoid setName(String name)
name
- new name
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