| Package | Description |
|---|---|
| com.milaboratory.core.sequence |
| 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
|
| 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.
|
| Modifier and Type | Method and Description |
|---|---|
List<Wildcard> |
Alphabet.getAllWildcards()
Returns a collection of all wildcards defined for this.
|
| 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. |
Copyright © 2018. All rights reserved.