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Packages that use SubstitutionMatrix | |
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org.biojava.bio.alignment | Classes to generate and describe sequence alignments. |
org.biojava.bio.structure.io | Input and Output of Structures |
Uses of SubstitutionMatrix in org.biojava.bio.alignment |
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Fields in org.biojava.bio.alignment declared as SubstitutionMatrix | |
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protected SubstitutionMatrix |
NeedlemanWunsch.subMatrix
A matrix with the size length(alphabet) times length(alphabet) |
Methods in org.biojava.bio.alignment that return SubstitutionMatrix | |
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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. |
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. |
Methods in org.biojava.bio.alignment with parameters of type SubstitutionMatrix | |
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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 | |
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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. |
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SmithWaterman(short match,
short replace,
short insert,
short delete,
short gapExtend,
SubstitutionMatrix matrix)
Constructs the new SmithWaterman alignment object. |
Uses of SubstitutionMatrix in org.biojava.bio.structure.io |
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Methods in org.biojava.bio.structure.io that return SubstitutionMatrix | |
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static SubstitutionMatrix |
SeqRes2AtomAligner.getSubstitutionMatrix(FiniteAlphabet alphabet)
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