Uses of Class
org.biojava.bio.alignment.SubstitutionMatrix
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Uses of SubstitutionMatrix in org.biojava.bio.alignment
Fields in org.biojava.bio.alignment declared as SubstitutionMatrixModifier and TypeFieldDescriptionprotected SubstitutionMatrixNeedlemanWunsch.subMatrixA matrix with the size length(alphabet) times length(alphabet)Methods in org.biojava.bio.alignment that return SubstitutionMatrixModifier and TypeMethodDescriptionstatic SubstitutionMatrixSubstitutionMatrix.getBlosum100()Return theBLOSUM100amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum100_50()Return theBLOSUM100.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum30()Return theBLOSUM30amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum30_50()Return theBLOSUM30.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum35()Return theBLOSUM35amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum35_50()Return theBLOSUM35.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum40()Return theBLOSUM40amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum40_50()Return theBLOSUM40.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum45()Return theBLOSUM45amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum45_50()Return theBLOSUM45.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum50()Return theBLOSUM50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum50_50()Return theBLOSUM50.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum55()Return theBLOSUM55amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum55_50()Return theBLOSUM55.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum60()Return theBLOSUM60amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum60_50()Return theBLOSUM60.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum62()Return theBLOSUM62amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum62_50()Return theBLOSUM62.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum65()Return theBLOSUM65amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum65_50()Return theBLOSUM65.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum70()Return theBLOSUM70amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum70_50()Return theBLOSUM70.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum75()Return theBLOSUM75amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum75_50()Return theBLOSUM75.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum80()Return theBLOSUM80amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum80_50()Return theBLOSUM80.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum85()Return theBLOSUM85amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum85_50()Return theBLOSUM85.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum90()Return theBLOSUM90amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosum90_50()Return theBLOSUM90.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosumn()Return theBLOSUMNamino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getBlosumn_50()Return theBLOSUMN.50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getDayhoff()Return theDAYHOFFamino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getGonnet()Return theGONNETamino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getIdentity()Return theIDENTITYamino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getMatch()Return theMATCHamino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getNuc4_2()Return theNUC.4.2nucleotide substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getNuc4_4()Return theNUC.4.4nucleotide substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam10()Return thePAM10amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam100()Return thePAM100amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam110()Return thePAM110amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam120()Return thePAM120amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam130()Return thePAM130amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam140()Return thePAM140amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam150()Return thePAM150amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam160()Return thePAM160amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam170()Return thePAM170amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam180()Return thePAM180amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam190()Return thePAM190amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam20()Return thePAM20amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam200()Return thePAM200amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam210()Return thePAM210amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam220()Return thePAM220amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam230()Return thePAM230amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam240()Return thePAM240amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam250()Return thePAM250amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam260()Return thePAM260amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam270()Return thePAM270amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam280()Return thePAM280amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam290()Return thePAM290amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam30()Return thePAM30amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam300()Return thePAM300amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam310()Return thePAM310amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam320()Return thePAM320amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam330()Return thePAM330amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam340()Return thePAM340amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam350()Return thePAM350amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam360()Return thePAM360amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam370()Return thePAM370amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam380()Return thePAM380amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam390()Return thePAM390amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam40()Return thePAM40amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam400()Return thePAM400amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam410()Return thePAM410amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam420()Return thePAM420amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam430()Return thePAM430amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam440()Return thePAM440amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam450()Return thePAM450amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam460()Return thePAM460amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam470()Return thePAM470amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam480()Return thePAM480amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam490()Return thePAM490amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam50()Return thePAM50amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam500()Return thePAM500amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam60()Return thePAM60amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam70()Return thePAM70amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam80()Return thePAM80amino acid substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getPam90()Return thePAM90amino acid substitution matrix.SmithWaterman.getSubMatrix()AlignmentPair.getSubstitutionMatrix()static SubstitutionMatrixSubstitutionMatrix.getSubstitutionMatrix(BufferedReader reader) This constructor can be used to guess the alphabet of this substitution matrix.static SubstitutionMatrixSubstitutionMatrix.getSubstitutionMatrix(FiniteAlphabet alphabet, BufferedReader reader) Return a new substitution matrix with the specified alphabet.static SubstitutionMatrixSubstitutionMatrix.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”SubstitutionMatrixobject; 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 TypeMethodDescriptionvoidSmithWaterman.setSubMatrix(SubstitutionMatrix subMatrix) voidNeedlemanWunsch.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.