Uses of Class
org.biojava.bio.alignment.SubstitutionMatrix
-
Packages that use SubstitutionMatrix Package Description 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
Fields in org.biojava.bio.alignment declared as SubstitutionMatrix Modifier and Type Field Description protected SubstitutionMatrix
NeedlemanWunsch. subMatrix
A matrix with the size length(alphabet) times length(alphabet)Methods in org.biojava.bio.alignment that return SubstitutionMatrix Modifier and Type Method Description 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 Modifier and Type Method Description 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 Constructor Description 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. -
Uses of SubstitutionMatrix in org.biojava.bio.structure.io
Methods in org.biojava.bio.structure.io that return SubstitutionMatrix Modifier and Type Method Description static SubstitutionMatrix
SeqRes2AtomAligner. getSubstitutionMatrix(FiniteAlphabet alphabet)
-