All Methods Static Methods Instance Methods Concrete Methods  Modifier and Type Method Description FiniteAlphabet getAlphabet()

Gives the alphabet used by this matrix.

static SubstitutionMatrix getBlosum100()

Return the BLOSUM100 amino acid substitution matrix.

static SubstitutionMatrix getBlosum100_50()

Return the BLOSUM100.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum30()

Return the BLOSUM30 amino acid substitution matrix.

static SubstitutionMatrix getBlosum30_50()

Return the BLOSUM30.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum35()

Return the BLOSUM35 amino acid substitution matrix.

static SubstitutionMatrix getBlosum35_50()

Return the BLOSUM35.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum40()

Return the BLOSUM40 amino acid substitution matrix.

static SubstitutionMatrix getBlosum40_50()

Return the BLOSUM40.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum45()

Return the BLOSUM45 amino acid substitution matrix.

static SubstitutionMatrix getBlosum45_50()

Return the BLOSUM45.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum50()

Return the BLOSUM50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum50_50()

Return the BLOSUM50.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum55()

Return the BLOSUM55 amino acid substitution matrix.

static SubstitutionMatrix getBlosum55_50()

Return the BLOSUM55.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum60()

Return the BLOSUM60 amino acid substitution matrix.

static SubstitutionMatrix getBlosum60_50()

Return the BLOSUM60.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum62()

Return the BLOSUM62 amino acid substitution matrix.

static SubstitutionMatrix getBlosum62_50()

Return the BLOSUM62.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum65()

Return the BLOSUM65 amino acid substitution matrix.

static SubstitutionMatrix getBlosum65_50()

Return the BLOSUM65.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum70()

Return the BLOSUM70 amino acid substitution matrix.

static SubstitutionMatrix getBlosum70_50()

Return the BLOSUM70.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum75()

Return the BLOSUM75 amino acid substitution matrix.

static SubstitutionMatrix getBlosum75_50()

Return the BLOSUM75.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum80()

Return the BLOSUM80 amino acid substitution matrix.

static SubstitutionMatrix getBlosum80_50()

Return the BLOSUM80.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum85()

Return the BLOSUM85 amino acid substitution matrix.

static SubstitutionMatrix getBlosum85_50()

Return the BLOSUM85.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosum90()

Return the BLOSUM90 amino acid substitution matrix.

static SubstitutionMatrix getBlosum90_50()

Return the BLOSUM90.50 amino acid substitution matrix.

static SubstitutionMatrix getBlosumn()

Return the BLOSUMN amino acid substitution matrix.

static SubstitutionMatrix getBlosumn_50()

Return the BLOSUMN.50 amino acid substitution matrix.

static SubstitutionMatrix getDayhoff()

Return the DAYHOFF amino acid substitution matrix.

String getDescription()

This gives you the description of this matrix if there is one.

static SubstitutionMatrix getGonnet()

Return the GONNET amino acid substitution matrix.

static SubstitutionMatrix getIdentity()

Return the IDENTITY amino acid substitution matrix.

static SubstitutionMatrix getMatch()

Return the MATCH amino acid substitution matrix.

short getMax()

The maximum score in this matrix.

short getMin()

The minimum score of this matrix.

String getName()

Every substitution matrix has a name like "BLOSUM30" or "PAM160".

static SubstitutionMatrix getNuc4_2()

Return the NUC.4.2 nucleotide substitution matrix.

static SubstitutionMatrix getNuc4_4()

Return the NUC.4.4 nucleotide substitution matrix.

static SubstitutionMatrix getPam10()

Return the PAM10 amino acid substitution matrix.

static SubstitutionMatrix getPam100()

Return the PAM100 amino acid substitution matrix.

static SubstitutionMatrix getPam110()

Return the PAM110 amino acid substitution matrix.

static SubstitutionMatrix getPam120()

Return the PAM120 amino acid substitution matrix.

static SubstitutionMatrix getPam130()

Return the PAM130 amino acid substitution matrix.

static SubstitutionMatrix getPam140()

Return the PAM140 amino acid substitution matrix.

static SubstitutionMatrix getPam150()

Return the PAM150 amino acid substitution matrix.

static SubstitutionMatrix getPam160()

Return the PAM160 amino acid substitution matrix.

static SubstitutionMatrix getPam170()

Return the PAM170 amino acid substitution matrix.

static SubstitutionMatrix getPam180()

Return the PAM180 amino acid substitution matrix.

static SubstitutionMatrix getPam190()

Return the PAM190 amino acid substitution matrix.

static SubstitutionMatrix getPam20()

Return the PAM20 amino acid substitution matrix.

static SubstitutionMatrix getPam200()

Return the PAM200 amino acid substitution matrix.

static SubstitutionMatrix getPam210()

Return the PAM210 amino acid substitution matrix.

static SubstitutionMatrix getPam220()

Return the PAM220 amino acid substitution matrix.

static SubstitutionMatrix getPam230()

Return the PAM230 amino acid substitution matrix.

static SubstitutionMatrix getPam240()

Return the PAM240 amino acid substitution matrix.

static SubstitutionMatrix getPam250()

Return the PAM250 amino acid substitution matrix.

static SubstitutionMatrix getPam260()

Return the PAM260 amino acid substitution matrix.

static SubstitutionMatrix getPam270()

Return the PAM270 amino acid substitution matrix.

static SubstitutionMatrix getPam280()

Return the PAM280 amino acid substitution matrix.

static SubstitutionMatrix getPam290()

Return the PAM290 amino acid substitution matrix.

static SubstitutionMatrix getPam30()

Return the PAM30 amino acid substitution matrix.

static SubstitutionMatrix getPam300()

Return the PAM300 amino acid substitution matrix.

static SubstitutionMatrix getPam310()

Return the PAM310 amino acid substitution matrix.

static SubstitutionMatrix getPam320()

Return the PAM320 amino acid substitution matrix.

static SubstitutionMatrix getPam330()

Return the PAM330 amino acid substitution matrix.

static SubstitutionMatrix getPam340()

Return the PAM340 amino acid substitution matrix.

static SubstitutionMatrix getPam350()

Return the PAM350 amino acid substitution matrix.

static SubstitutionMatrix getPam360()

Return the PAM360 amino acid substitution matrix.

static SubstitutionMatrix getPam370()

Return the PAM370 amino acid substitution matrix.

static SubstitutionMatrix getPam380()

Return the PAM380 amino acid substitution matrix.

static SubstitutionMatrix getPam390()

Return the PAM390 amino acid substitution matrix.

static SubstitutionMatrix getPam40()

Return the PAM40 amino acid substitution matrix.

static SubstitutionMatrix getPam400()

Return the PAM400 amino acid substitution matrix.

static SubstitutionMatrix getPam410()

Return the PAM410 amino acid substitution matrix.

static SubstitutionMatrix getPam420()

Return the PAM420 amino acid substitution matrix.

static SubstitutionMatrix getPam430()

Return the PAM430 amino acid substitution matrix.

static SubstitutionMatrix getPam440()

Return the PAM440 amino acid substitution matrix.

static SubstitutionMatrix getPam450()

Return the PAM450 amino acid substitution matrix.

static SubstitutionMatrix getPam460()

Return the PAM460 amino acid substitution matrix.

static SubstitutionMatrix getPam470()

Return the PAM470 amino acid substitution matrix.

static SubstitutionMatrix getPam480()

Return the PAM480 amino acid substitution matrix.

static SubstitutionMatrix getPam490()

Return the PAM490 amino acid substitution matrix.

static SubstitutionMatrix getPam50()

Return the PAM50 amino acid substitution matrix.

static SubstitutionMatrix getPam500()

Return the PAM500 amino acid substitution matrix.

static SubstitutionMatrix getPam60()

Return the PAM60 amino acid substitution matrix.

static SubstitutionMatrix getPam70()

Return the PAM70 amino acid substitution matrix.

static SubstitutionMatrix getPam80()

Return the PAM80 amino acid substitution matrix.

static SubstitutionMatrix getPam90()

Return the PAM90 amino acid substitution matrix.

static SubstitutionMatrix getSubstitutionMatrix​(BufferedReader reader)

This constructor can be used to guess the alphabet of this substitution matrix.

static SubstitutionMatrix getSubstitutionMatrix​(FiniteAlphabet alphabet, BufferedReader reader)

Return a new substitution matrix with the specified alphabet.

static SubstitutionMatrix getSubstitutionMatrix​(FiniteAlphabet alphabet, BufferedReader reader, String name)

Return a new substitution matrix with the specified alphabet and name.

short getValueAt​(Symbol row, Symbol col)

There are some substitution matrices containing more columns than lines.

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.

void printMatrix()

Just to perform some test.

void setDescription​(String desc)

Sets the description to the given value.

String stringnifyDescription()

Converts the description of the matrix to a String.

String stringnifyMatrix()

Creates a String representation of this matrix.

String toString()

Overrides the inherited method.