Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.biology.aminoacids |
Modifier and Type | Field and Description |
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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 |
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<AminoAcid>> |
AminoAcidPattern.getAaExcluded()
Returns the map of excluded amino acids.
|
HashMap<Integer,ArrayList<AminoAcid>> |
AminoAcidPattern.getAaTargeted()
Returns the map of targeted amino acids.
|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Constructor and Description |
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Mutation(AminoAcid origin,
AminoAcid target)
Constructs a mutation from one amino acid (origin) to another (target).
|
Modifier and Type | Class and 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).
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