Package | Description |
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org.biojava.bio.alignment |
Classes to generate and describe sequence alignments.
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org.biojava.bio.structure.io |
Input and Output of Structures
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Modifier and Type | Field and Description |
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protected SubstitutionMatrix |
NeedlemanWunsch.subMatrix
A matrix with the size length(alphabet) times length(alphabet)
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Modifier and Type | Method and Description |
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static SubstitutionMatrix |
SubstitutionMatrix.getSubstitutionMatrix(java.io.BufferedReader reader)
This constructor can be used to guess the alphabet of this substitution
matrix.
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SubstitutionMatrix |
SubstitutionMatrix.normalizeMatrix()
With this method you can get a “normalized”
SubstitutionMatrix object; however, since this
implementation uses an short matrix, the normalized matrix will be scaled
by ten. |
Modifier and Type | Method and Description |
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void |
NeedlemanWunsch.setSubstitutionMatrix(SubstitutionMatrix matrix)
Sets the substitution matrix to be used to the specified one.
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Constructor and Description |
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NeedlemanWunsch(short match,
short replace,
short insert,
short delete,
short 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(short match,
short replace,
short insert,
short delete,
short gapExtend,
SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object.
|
Modifier and Type | Method and Description |
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static SubstitutionMatrix |
SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet) |