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