|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use SubstitutionMatrix | |
---|---|
org.biojava.bio.alignment | Classes to generate and describe sequence alignments. |
Uses of SubstitutionMatrix in org.biojava.bio.alignment |
---|
Fields in org.biojava.bio.alignment declared as SubstitutionMatrix | |
---|---|
protected SubstitutionMatrix |
NeedlemanWunsch.subMatrix
|
Methods in org.biojava.bio.alignment that return SubstitutionMatrix | |
---|---|
SubstitutionMatrix |
SubstitutionMatrix.normalizeMatrix()
With this method you can get a "normalized" SubstitutionMatrix object;
however, since this implementation uses an int matrix, the normalized matrix will
be scaled by ten. |
Methods in org.biojava.bio.alignment with parameters of type SubstitutionMatrix | |
---|---|
void |
NeedlemanWunsch.setSubstitutionMatrix(SubstitutionMatrix matrix)
Sets the substitution matrix to be used to the specified one. |
Constructors in org.biojava.bio.alignment with parameters of type SubstitutionMatrix | |
---|---|
NeedlemanWunsch(double match,
double replace,
double insert,
double delete,
double gapExtend,
SubstitutionMatrix subMat)
Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix. |
|
SmithWaterman(double match,
double replace,
double insert,
double delete,
double gapExtend,
SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |