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.

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.getBlosum100()	Return the BLOSUM100 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum100_50()	Return the BLOSUM100.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum30()	Return the BLOSUM30 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum30_50()	Return the BLOSUM30.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum35()	Return the BLOSUM35 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum35_50()	Return the BLOSUM35.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum40()	Return the BLOSUM40 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum40_50()	Return the BLOSUM40.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum45()	Return the BLOSUM45 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum45_50()	Return the BLOSUM45.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum50()	Return the BLOSUM50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum50_50()	Return the BLOSUM50.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum55()	Return the BLOSUM55 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum55_50()	Return the BLOSUM55.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum60()	Return the BLOSUM60 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum60_50()	Return the BLOSUM60.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum62()	Return the BLOSUM62 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum62_50()	Return the BLOSUM62.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum65()	Return the BLOSUM65 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum65_50()	Return the BLOSUM65.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum70()	Return the BLOSUM70 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum70_50()	Return the BLOSUM70.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum75()	Return the BLOSUM75 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum75_50()	Return the BLOSUM75.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum80()	Return the BLOSUM80 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum80_50()	Return the BLOSUM80.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum85()	Return the BLOSUM85 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum85_50()	Return the BLOSUM85.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum90()	Return the BLOSUM90 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosum90_50()	Return the BLOSUM90.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosumn()	Return the BLOSUMN amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getBlosumn_50()	Return the BLOSUMN.50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getDayhoff()	Return the DAYHOFF amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getGonnet()	Return the GONNET amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getIdentity()	Return the IDENTITY amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getMatch()	Return the MATCH amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getNuc4_2()	Return the NUC.4.2 nucleotide substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getNuc4_4()	Return the NUC.4.4 nucleotide substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam10()	Return the PAM10 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam100()	Return the PAM100 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam110()	Return the PAM110 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam120()	Return the PAM120 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam130()	Return the PAM130 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam140()	Return the PAM140 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam150()	Return the PAM150 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam160()	Return the PAM160 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam170()	Return the PAM170 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam180()	Return the PAM180 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam190()	Return the PAM190 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam20()	Return the PAM20 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam200()	Return the PAM200 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam210()	Return the PAM210 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam220()	Return the PAM220 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam230()	Return the PAM230 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam240()	Return the PAM240 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam250()	Return the PAM250 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam260()	Return the PAM260 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam270()	Return the PAM270 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam280()	Return the PAM280 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam290()	Return the PAM290 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam30()	Return the PAM30 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam300()	Return the PAM300 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam310()	Return the PAM310 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam320()	Return the PAM320 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam330()	Return the PAM330 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam340()	Return the PAM340 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam350()	Return the PAM350 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam360()	Return the PAM360 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam370()	Return the PAM370 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam380()	Return the PAM380 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam390()	Return the PAM390 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam40()	Return the PAM40 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam400()	Return the PAM400 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam410()	Return the PAM410 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam420()	Return the PAM420 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam430()	Return the PAM430 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam440()	Return the PAM440 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam450()	Return the PAM450 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam460()	Return the PAM460 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam470()	Return the PAM470 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam480()	Return the PAM480 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam490()	Return the PAM490 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam50()	Return the PAM50 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam500()	Return the PAM500 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam60()	Return the PAM60 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam70()	Return the PAM70 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam80()	Return the PAM80 amino acid substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getPam90()	Return the PAM90 amino acid substitution matrix.
SubstitutionMatrix	SmithWaterman.getSubMatrix()
SubstitutionMatrix	AlignmentPair.getSubstitutionMatrix()
static SubstitutionMatrix	SubstitutionMatrix.getSubstitutionMatrix(BufferedReader reader)	This constructor can be used to guess the alphabet of this substitution matrix.
static SubstitutionMatrix	SubstitutionMatrix.getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader)	Return a new substitution matrix with the specified alphabet.
static SubstitutionMatrix	SubstitutionMatrix.getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader, String name)	Return a new substitution matrix with the specified alphabet and name.
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	SmithWaterman.setSubMatrix(SubstitutionMatrix subMatrix)
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
AlignmentPair(Sequence query, Sequence subject, int queryStart, int queryEnd, int subjectStart, int subjectEnd, SubstitutionMatrix subMatrix)
AlignmentPair(Sequence query, Sequence subject, SubstitutionMatrix subMatrix)
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.