Uses of Class
com.compomics.util.experiment.biology.aminoacids.AminoAcid

Packages that use AminoAcid

Package	Description
com.compomics.util.experiment.biology.aminoacids	The amino acid classes.
com.compomics.util.experiment.biology.aminoacids.impl	The amino acid implementations.
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.ions.impl	Ion implementations.

Uses of AminoAcid in com.compomics.util.experiment.biology.aminoacids

Fields in com.compomics.util.experiment.biology.aminoacids declared as AminoAcid

Modifier and Type	Field	Description
static final AminoAcid	AminoAcid.A
static final AminoAcid	AminoAcid.B
static final AminoAcid	AminoAcid.C
static final AminoAcid	AminoAcid.D
static final AminoAcid	AminoAcid.E
static final AminoAcid	AminoAcid.F
static final AminoAcid	AminoAcid.G
static final AminoAcid	AminoAcid.H
static final AminoAcid	AminoAcid.I
static final AminoAcid	AminoAcid.J
static final AminoAcid	AminoAcid.K
static final AminoAcid	AminoAcid.L
static final AminoAcid	AminoAcid.M
static final AminoAcid	AminoAcid.N
static final AminoAcid	AminoAcid.O
static final AminoAcid	AminoAcid.P
static final AminoAcid	AminoAcid.Q
static final AminoAcid	AminoAcid.R
static final AminoAcid	AminoAcid.S
static final AminoAcid	AminoAcid.T
static final AminoAcid	AminoAcid.U
static final AminoAcid	AminoAcid.V
static final AminoAcid	AminoAcid.W
static final AminoAcid	AminoAcid.X
static final AminoAcid	AminoAcid.Y
static final AminoAcid	AminoAcid.Z

Methods in com.compomics.util.experiment.biology.aminoacids that return AminoAcid

Modifier and Type	Method	Description
static AminoAcid	AminoAcid.getAminoAcid(char aa)	Returns the amino acid corresponding to the single letter code given.
static AminoAcid	AminoAcid.getAminoAcid(String aa)	Returns the amino acid corresponding to the letter given.
static AminoAcid	AminoAcid.getAminoAcidFromGeneticCode(String geneticCode)	Returns the amino acid from the standard genetic code.

Uses of AminoAcid in com.compomics.util.experiment.biology.aminoacids.impl

Subclasses of AminoAcid in com.compomics.util.experiment.biology.aminoacids.impl

Modifier and Type	Class	Description
class	Alanine	Alanine.
class	Arginine	Arginine.
class	Asparagine	Asparagine.
class	AsparticAcid	Aspartic Acid.
class	B	Asn or Asp: Asx (Mascot).
class	Cysteine	Cysteine.
class	GlutamicAcid	Glutamic Acid.
class	Glutamine	Glutamine.
class	Glycine	Glycine.
class	Histidine	Histidine.
class	Isoleucine	Isoleucine.
class	J	Isoleucine or Leucine.
class	Leucine	Leucine.
class	Lysine	Lysine.
class	Methionine	Methionine.
class	Phenylalanine	Phenylalanine.
class	Proline	Proline.
class	Pyrrolysine	Pyrrolysine.
class	Selenocysteine	SeC (U) (Mascot)-
class	Serine	Serine.
class	Threonine	Threonine.
class	Tryptophan	Tryptophan.
class	Tyrosine	Tyrosine.
class	Valine	Valine.
class	X	Unknown amino acid (Mascot).
class	Z	Glu or Gln: Glx (Mascot).

Uses of AminoAcid in com.compomics.util.experiment.biology.aminoacids.sequence

Methods in com.compomics.util.experiment.biology.aminoacids.sequence that return AminoAcid

Modifier and Type	Method	Description
AminoAcid	AminoAcidSequence.getAminoAcidAt(int aa)	Returns the amino acid at the given index on the sequence.

Uses of AminoAcid in com.compomics.util.experiment.biology.ions.impl

Methods in com.compomics.util.experiment.biology.ions.impl with parameters of type AminoAcid

Modifier and Type	Method	Description
static ArrayList<RelatedIon>	RelatedIon.getRelatedIons(AminoAcid aminoAcidTarget)	Returns the list of related ions for the given amino acid.

Constructors in com.compomics.util.experiment.biology.ions.impl with parameters of type AminoAcid

Modifier	Constructor	Description
	RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType)	Constructor for a related ion.
	RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType, boolean save)	Constructor for a related ion.