Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.biology.aminoacids |
The amino acid classes.
|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.experiment.biology.mutations |
Experiment classes related to mutations.
|
com.compomics.util.experiment.identification.amino_acid_tags |
Amino Acid Tag classes.
|
com.compomics.util.experiment.identification.amino_acid_tags.matchers |
Tag matching classes.
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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.
|
AminoAcid |
AminoAcidSequence.getAminoAcidAt(int aa)
Returns the amino acid at the given index on the sequence.
|
static AminoAcid |
AminoAcid.getAminoAcidFromGeneticCode(String geneticCode)
Returns the amino acid from the standard genetic code.
|
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).
|
Modifier and Type | Method and Description |
---|---|
static ArrayList<RelatedIon> |
RelatedIon.getRelatedIons(AminoAcid aminoAcidTarget)
Returns the list of related ions for the given amino acid.
|
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
AminoAcid |
Mutation.getOrigin()
Returns the origin amino acid.
|
AminoAcid |
Mutation.getTarget()
Returns the target amino acid.
|
Constructor and Description |
---|
Mutation(AminoAcid origin,
AminoAcid target)
Constructs a mutation from one amino acid (origin) to another (target).
|
Modifier and Type | Method and Description |
---|---|
void |
SequenceSegment.appendTerminus(AminoAcid aminoAcid)
Appends an amino acid to the terminus of sequencing.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SequenceSegment> |
TagMatcher.addSequenceSegmentsToCache(HashMap<Integer,ArrayList<SequenceSegment>> indexCache,
String sequence,
AminoAcid aminoAcid,
Integer currentIndex,
Integer aaIndex,
boolean nTerminus)
Adds the possible new sequence segments generated when appending the
given amino acid to the given cache and returns the list of possible
segments.
|
ArrayList<SequenceSegment> |
TagMatcher.addSequenceSegmentsToCacheSynchronized(HashMap<Integer,ArrayList<SequenceSegment>> indexCache,
String sequence,
AminoAcid aminoAcid,
Integer currentIndex,
Integer aaIndex,
boolean nTerminus)
Adds the possible new sequence segments generated when appending the
given amino acid to the given cache and returns the list of possible
segments.
|
ArrayList<SequenceSegment> |
TagMatcher.getCombinationsForAminoAcid(String sequence,
ArrayList<SequenceSegment> possibleSequences,
AminoAcid aminoAcid,
Integer currentIndex,
Integer aaIndex,
boolean nTerminus)
Adds the possible new sequence segments generated when appending the
given amino acid.
|
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