Uses of Class
org.biojava.bio.alignment.SubstitutionMatrix
Packages that use SubstitutionMatrix
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Uses of SubstitutionMatrix in org.biojava.bio.alignment
Fields in org.biojava.bio.alignment declared as SubstitutionMatrixModifier and TypeFieldDescriptionprotected SubstitutionMatrix
NeedlemanWunsch.subMatrix
A matrix with the size length(alphabet) times length(alphabet)Methods in org.biojava.bio.alignment that return SubstitutionMatrixModifier and TypeMethodDescriptionstatic SubstitutionMatrix
SubstitutionMatrix.getBlosum100()
Return theBLOSUM100
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum100_50()
Return theBLOSUM100.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum30()
Return theBLOSUM30
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum30_50()
Return theBLOSUM30.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum35()
Return theBLOSUM35
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum35_50()
Return theBLOSUM35.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum40()
Return theBLOSUM40
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum40_50()
Return theBLOSUM40.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum45()
Return theBLOSUM45
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum45_50()
Return theBLOSUM45.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum50()
Return theBLOSUM50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum50_50()
Return theBLOSUM50.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum55()
Return theBLOSUM55
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum55_50()
Return theBLOSUM55.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum60()
Return theBLOSUM60
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum60_50()
Return theBLOSUM60.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum62()
Return theBLOSUM62
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum62_50()
Return theBLOSUM62.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum65()
Return theBLOSUM65
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum65_50()
Return theBLOSUM65.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum70()
Return theBLOSUM70
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum70_50()
Return theBLOSUM70.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum75()
Return theBLOSUM75
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum75_50()
Return theBLOSUM75.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum80()
Return theBLOSUM80
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum80_50()
Return theBLOSUM80.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum85()
Return theBLOSUM85
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum85_50()
Return theBLOSUM85.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum90()
Return theBLOSUM90
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosum90_50()
Return theBLOSUM90.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosumn()
Return theBLOSUMN
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getBlosumn_50()
Return theBLOSUMN.50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getDayhoff()
Return theDAYHOFF
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getGonnet()
Return theGONNET
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getIdentity()
Return theIDENTITY
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getMatch()
Return theMATCH
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getNuc4_2()
Return theNUC.4.2
nucleotide substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getNuc4_4()
Return theNUC.4.4
nucleotide substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam10()
Return thePAM10
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam100()
Return thePAM100
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam110()
Return thePAM110
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam120()
Return thePAM120
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam130()
Return thePAM130
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam140()
Return thePAM140
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam150()
Return thePAM150
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam160()
Return thePAM160
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam170()
Return thePAM170
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam180()
Return thePAM180
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam190()
Return thePAM190
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam20()
Return thePAM20
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam200()
Return thePAM200
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam210()
Return thePAM210
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam220()
Return thePAM220
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam230()
Return thePAM230
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam240()
Return thePAM240
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam250()
Return thePAM250
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam260()
Return thePAM260
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam270()
Return thePAM270
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam280()
Return thePAM280
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam290()
Return thePAM290
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam30()
Return thePAM30
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam300()
Return thePAM300
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam310()
Return thePAM310
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam320()
Return thePAM320
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam330()
Return thePAM330
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam340()
Return thePAM340
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam350()
Return thePAM350
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam360()
Return thePAM360
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam370()
Return thePAM370
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam380()
Return thePAM380
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam390()
Return thePAM390
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam40()
Return thePAM40
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam400()
Return thePAM400
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam410()
Return thePAM410
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam420()
Return thePAM420
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam430()
Return thePAM430
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam440()
Return thePAM440
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam450()
Return thePAM450
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam460()
Return thePAM460
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam470()
Return thePAM470
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam480()
Return thePAM480
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam490()
Return thePAM490
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam50()
Return thePAM50
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam500()
Return thePAM500
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam60()
Return thePAM60
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam70()
Return thePAM70
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam80()
Return thePAM80
amino acid substitution matrix.static SubstitutionMatrix
SubstitutionMatrix.getPam90()
Return thePAM90
amino acid substitution matrix.SmithWaterman.getSubMatrix()
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.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 SubstitutionMatrixModifier and TypeMethodDescriptionvoid
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 SubstitutionMatrixModifierConstructorDescriptionAlignmentPair
(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.