Uses of Class
com.milaboratory.core.sequence.Wildcard

Packages that use Wildcard

Package	Description
com.milaboratory.core.sequence

Uses of Wildcard in com.milaboratory.core.sequence

Fields in com.milaboratory.core.sequence declared as Wildcard

Modifier and Type	Field and Description
static Wildcard	NucleotideAlphabet.A_WILDCARD Adenine byte representation
static Wildcard	AminoAcidAlphabet.A_WILDCARD Alanine wildcard
static Wildcard	NucleotideAlphabet.B_WILDCARD not A (B comes after A)
static Wildcard	AminoAcidAlphabet.B_WILDCARD Aspartic acid or Asparagine (N or D) wildcard
static Wildcard	NucleotideAlphabet.C_WILDCARD Cytosine byte representation
static Wildcard	AminoAcidAlphabet.C_WILDCARD Cysteine wildcard
static Wildcard	NucleotideAlphabet.D_WILDCARD not C (D comes after C)
static Wildcard	AminoAcidAlphabet.D_WILDCARD Aspartic Acid wildcard
static Wildcard	AminoAcidAlphabet.E_WILDCARD Glutamic Acid wildcard
static Wildcard	AminoAcidAlphabet.F_WILDCARD Phenylalanine wildcard
static Wildcard	NucleotideAlphabet.G_WILDCARD Guanine byte representation
static Wildcard	AminoAcidAlphabet.G_WILDCARD Glycine wildcard
static Wildcard	NucleotideAlphabet.H_WILDCARD not G (H comes after G)
static Wildcard	AminoAcidAlphabet.H_WILDCARD Histidine wildcard
static Wildcard	AminoAcidAlphabet.I_WILDCARD Isoleucine wildcard
static Wildcard	AminoAcidAlphabet.INCOMPLETE_CODON_WILDCARD Incomplete codon wildcard
static Wildcard	AminoAcidAlphabet.J_WILDCARD Leucine or Isoleucine (I or L) wildcard
static Wildcard	NucleotideAlphabet.K_WILDCARD Keto
static Wildcard	AminoAcidAlphabet.K_WILDCARD Lysine wildcard
static Wildcard	AminoAcidAlphabet.L_WILDCARD Leucine wildcard
static Wildcard	NucleotideAlphabet.M_WILDCARD aMino
static Wildcard	AminoAcidAlphabet.M_WILDCARD Methionine wildcard
static Wildcard	NucleotideAlphabet.N_WILDCARD any Nucleotide
static Wildcard	AminoAcidAlphabet.N_WILDCARD Asparagine wildcard
static Wildcard	AminoAcidAlphabet.P_WILDCARD Proline wildcard
static Wildcard	AminoAcidAlphabet.Q_WILDCARD Glutamine wildcard
static Wildcard	NucleotideAlphabet.R_WILDCARD puRine
static Wildcard	AminoAcidAlphabet.R_WILDCARD Arginine wildcard
static Wildcard	NucleotideAlphabet.S_WILDCARD Strong
static Wildcard	AminoAcidAlphabet.S_WILDCARD Serine wildcard
static Wildcard	AminoAcidAlphabet.STOP_WILDCARD Stop codon wildcard
static Wildcard	NucleotideAlphabet.T_WILDCARD Thymine byte representation
static Wildcard	AminoAcidAlphabet.T_WILDCARD Threonine wildcard
static Wildcard	NucleotideAlphabet.V_WILDCARD not T (V comes after T and U)
static Wildcard	AminoAcidAlphabet.V_WILDCARD Valine wildcard
static Wildcard	NucleotideAlphabet.W_WILDCARD Weak
static Wildcard	AminoAcidAlphabet.W_WILDCARD Tryptophan wildcard
static Wildcard	AminoAcidAlphabet.X_WILDCARD Any amino acid wildcard
static Wildcard	NucleotideAlphabet.Y_WILDCARD pYrimidine
static Wildcard	AminoAcidAlphabet.Y_WILDCARD Tyrosine wildcard
static Wildcard	AminoAcidAlphabet.Z_WILDCARD Glutamine or Glutamic acid (E or Q) wildcard

Methods in com.milaboratory.core.sequence that return Wildcard

Modifier and Type	Method and Description
Wildcard	Alphabet.codeToWildcard(byte code) Returns wildcard defined by specified code (letter).
static Wildcard	NucleotideAlphabet.complementWildcard(byte code) Returns a complementary wildcard object
static Wildcard	NucleotideAlphabet.complementWildcard(Wildcard wildcard) Returns a complementary wildcard object
Wildcard	Alphabet.getWildcardForAnyLetter() Returns wildcard for any letter (e.g.
Wildcard	Alphabet.maskToWildcard(long basicMask) Converts wildcard basicMask to Wildcard object.
Wildcard	Alphabet.symbolToWildcard(char symbol) Returns a wildcard object for specified letter.

Methods in com.milaboratory.core.sequence that return types with arguments of type Wildcard

Modifier and Type	Method and Description
List<Wildcard>	Alphabet.getAllWildcards() Returns a collection of all wildcards defined for this.

Methods in com.milaboratory.core.sequence with parameters of type Wildcard

Modifier and Type	Method and Description
static byte	NucleotideAlphabet.complementCode(Wildcard wildcard) Returns a complementary nucleotide code.
static Wildcard	NucleotideAlphabet.complementWildcard(Wildcard wildcard) Returns a complementary wildcard object
boolean	Wildcard.intersectsWith(Wildcard otherWildcard) Returns true if set of symbols represented by this wildcard intersects with set of symbols represented by otherWildcard.