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

Packages that use AminoAcid
com.compomics.util.experiment.biology This package contains experiement classes related to biological entities. 
com.compomics.util.experiment.biology.aminoacids   
 

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

Fields in com.compomics.util.experiment.biology declared as AminoAcid
static AminoAcid AminoAcid.A
           
static AminoAcid AminoAcid.B
           
static AminoAcid AminoAcid.C
           
static AminoAcid AminoAcid.D
           
static AminoAcid AminoAcid.E
           
static AminoAcid AminoAcid.F
           
static AminoAcid AminoAcid.G
           
static AminoAcid AminoAcid.H
           
static AminoAcid AminoAcid.I
           
static AminoAcid AminoAcid.J
           
static AminoAcid AminoAcid.K
           
static AminoAcid AminoAcid.L
           
static AminoAcid AminoAcid.M
           
static AminoAcid AminoAcid.N
           
static AminoAcid AminoAcid.O
           
static AminoAcid AminoAcid.P
           
static AminoAcid AminoAcid.Q
           
static AminoAcid AminoAcid.R
           
static AminoAcid AminoAcid.S
           
static AminoAcid AminoAcid.T
           
static AminoAcid AminoAcid.U
           
static AminoAcid AminoAcid.V
           
static AminoAcid AminoAcid.W
           
static AminoAcid AminoAcid.X
           
static AminoAcid AminoAcid.Y
           
static AminoAcid AminoAcid.Z
           
 

Methods in com.compomics.util.experiment.biology that return AminoAcid
static AminoAcid AminoAcid.getAminoAcid(char letter)
          Returns the amino acid corresponding to the letter given, null if not implemented.
static AminoAcid AminoAcid.getAminoAcid(String aa)
          Returns the amino acid corresponding to the letter given, null if not implemented.
 AminoAcid Mutation.getOrigin()
          Returns the origin amino acid.
 AminoAcid Mutation.getTarget()
          Returns the target amino acid.
 

Methods in com.compomics.util.experiment.biology that return types with arguments of type AminoAcid
 ArrayList<AminoAcid> AminoAcidPattern.getAminoAcidsAtTarget()
          Returns the targeted amino acids at position "target".
 ArrayList<AminoAcid> AminoAcidPattern.getExcludedAA(int index)
          Returns the excluded amino acids at a given index in the pattern.
 ArrayList<AminoAcid> AminoAcidPattern.getTargetedAA(int index)
          Returns the targeted amino acids at a given index in the pattern.
 

Method parameters in com.compomics.util.experiment.biology with type arguments of type AminoAcid
 void AminoAcidPattern.setExcluded(int index, ArrayList<AminoAcid> exclusions)
          Sets the amino acids excluded at a given index.
 void AminoAcidPattern.setTargeted(int index, ArrayList<AminoAcid> targets)
          Sets the amino acids targeted at a given index.
 

Constructors in com.compomics.util.experiment.biology with parameters of type AminoAcid
Mutation(AminoAcid origin, AminoAcid target)
          Constructs a mutation from one amino acid (origin) to another (target).
 

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

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



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