Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
com.compomics.util.experiment.biology.aminoacids |
Modifier and Type | Field and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
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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