All Methods Static Methods Concrete Methods  Modifier and Type Method Description static AtomicSymbol a()

Returns the AtomicSymbol for the amino acid Alanine

static AtomicSymbol ala()

Returns the AtomicSymbol for the amino acid Alanine (A)

static AtomicSymbol arg()

Returns the AtomicSymbol for the amino acid Arginine (R)

static AtomicSymbol asn()

Returns the AtomicSymbol for the amino acid Asparagine (N)

static AtomicSymbol asp()

Returns the AtomicSymbol for the amino acid Aspartic Acid (D)

static AtomicSymbol c()

Returns the AtomicSymbol for the amino acid Cysteine

static GappedSequence createGappedProteinSequence​(String theProtein, String name)

Get a new protein as a GappedSequence

static SymbolList createProtein​(String theProtein)

Return a new Protein SymbolList for protein.

static Sequence createProteinSequence​(String protein, String name)

Return a new PROTEIN Sequence for protein.

static AtomicSymbol cys()

Returns the AtomicSymbol for the amino acid Cysteine (C)

static AtomicSymbol d()

Returns the AtomicSymbol for the amino acid Aspartic Acid

static AtomicSymbol e()

Returns the AtomicSymbol for the amino acid Glutamic Acid

static AtomicSymbol f()

Returns the AtomicSymbol for the amino acid Phenylalanine

static AtomicSymbol g()

Returns the AtomicSymbol for the amino acid Glycine

static FiniteAlphabet getAlphabet()

Gets the protein alphabet

static SymbolPropertyTable getSymbolPropertyTable​(String name)   static FiniteAlphabet getTAlphabet()

Gets the protein alphabet including the translation termination symbols

static AtomicSymbol gln()

Returns the AtomicSymbol for the amino acid Glutamine (Q)

static AtomicSymbol glu()

Returns the AtomicSymbol for the amino acid Glutamic Acid (E)

static AtomicSymbol gly()

Returns the AtomicSymbol for the amino acid Glycine (G)

static AtomicSymbol h()

Returns the AtomicSymbol for the amino acid Histidine

static AtomicSymbol his()

Returns the AtomicSymbol for the amino acid Histidine (H)

static AtomicSymbol i()

Returns the AtomicSymbol for the amino acid Isoleucine

static AtomicSymbol ile()

Returns the AtomicSymbol for the amino acid Isoleucine (I)

static AtomicSymbol k()

Returns the AtomicSymbol for the amino acid Lysine

static AtomicSymbol l()

Returns the AtomicSymbol for the amino acid Leucine

static AtomicSymbol leu()

Returns the AtomicSymbol for the amino acid Leucine (L)

static AtomicSymbol lys()

Returns the AtomicSymbol for the amino acid Lysine (K)

static AtomicSymbol m()

Returns the AtomicSymbol for the amino acid Methionine

static AtomicSymbol met()

Returns the AtomicSymbol for the amino acid Methionine (M)

static AtomicSymbol n()

Returns the AtomicSymbol for the amino acid Asparagine

static AtomicSymbol o()

Returns the AtomicSymbol for the amino acid Pyrrolysine

static AtomicSymbol p()

Returns the AtomicSymbol for the amino acid Proline

static AtomicSymbol phe()

Returns the AtomicSymbol for the amino acid Phenylalanine (F)

static AtomicSymbol pro()

Returns the AtomicSymbol for the amino acid Proline (P)

static AtomicSymbol pyl()

Returns the AtomicSymbol for the amino acid Pyrrolysine (O)

static AtomicSymbol q()

Returns the AtomicSymbol for the amino acid Glutamine

static AtomicSymbol r()

Returns the AtomicSymbol for the amino acid Arginine

static AtomicSymbol s()

Returns the AtomicSymbol for the amino acid Serine

static AtomicSymbol sec()

Returns the AtomicSymbol for the amino acid Selenocysteine (U)

static AtomicSymbol ser()

Returns the AtomicSymbol for the amino acid Serine (S)

static AtomicSymbol t()

Returns the AtomicSymbol for the amino acid Threonine

static AtomicSymbol ter()

Returns the AtomicSymbol for the termination (*) placeholder

static AtomicSymbol thr()

Returns the AtomicSymbol for the amino acid Threonine (T)

static AtomicSymbol trp()

Returns the AtomicSymbol for the amino acid Tryptophan (W)

static AtomicSymbol tyr()

Returns the AtomicSymbol for the amino acid Tyrosine (Y)

static AtomicSymbol u()

Returns the AtomicSymbol for the amino acid Selenocysteine

static AtomicSymbol v()

Returns the AtomicSymbol for the amino acid Valine

static AtomicSymbol val()

Returns the AtomicSymbol for the amino acid Valine (V)

static AtomicSymbol w()

Returns the AtomicSymbol for the amino acid Tryptophan

static AtomicSymbol y()

Returns the AtomicSymbol for the amino acid Tyrosine