public abstract class AminoAcid extends Object implements Serializable
Modifier and Type | Field and Description |
---|---|
static AminoAcid |
A |
protected char[] |
aminoAcidCombinations
The amino acid combinations.
|
static String[] |
aminoAcidStrings
The amino acid one letter codes as string array.
|
double |
averageMass
Average mass of the amino acid.
|
static AminoAcid |
B |
static AminoAcid |
C |
static AminoAcid |
D |
static AminoAcid |
E |
static AminoAcid |
F |
static AminoAcid |
G |
static AminoAcid |
H |
static AminoAcid |
I |
static AminoAcid |
J |
static AminoAcid |
K |
static AminoAcid |
L |
static AminoAcid |
M |
protected AtomChain |
monoisotopicAtomChain
The monoisotopic atom chain.
|
protected Double |
monoisotopicMass
Deprecated.
use the atomchain
|
static AminoAcid |
N |
String |
name
Name of the amino acid.
|
static AminoAcid |
O |
static AminoAcid |
P |
static AminoAcid |
Q |
static AminoAcid |
R |
static AminoAcid |
S |
String |
singleLetterCode
Single letter code of the amino acid.
|
protected String[] |
standardGeneticCode
The standard genetic code.
|
protected char[] |
subAminoAcidsWithCombination
The sub amino acids.
|
protected char[] |
subAminoAcidsWithoutCombination
The sub amino acids.
|
static AminoAcid |
T |
String |
threeLetterCode
Three letter code of the amino acid.
|
static AminoAcid |
U |
static AminoAcid |
V |
static AminoAcid |
W |
static AminoAcid |
X |
static AminoAcid |
Y |
static AminoAcid |
Z |
Constructor and Description |
---|
AminoAcid() |
Modifier and Type | Method and Description |
---|---|
boolean |
equals(Object obj) |
static AminoAcid |
getAminoAcid(char letter)
Returns the amino acid corresponding to the letter given, null if not
implemented.
|
static AminoAcid |
getAminoAcid(String aa)
Returns the amino acid corresponding to the letter given, null if not
implemented.
|
static AminoAcid |
getAminoAcidFromGeneticCode(String geneticCode)
Returns the amino acid from the standard genetic code.
|
static char[] |
getAminoAcids()
Convenience method returning an array of all implemented amino acids
represented by their singe letter code.
|
static List<String> |
getAminoAcidsList()
Convenience method returning an arrayList of all implemented amino acids.
|
char[] |
getCombinations()
Returns the amino acids combinations which might represent this amino
acid.
|
static String |
getMatchingAminoAcid(String aminoAcid,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a matching amino acid using the given preferences.
|
static String |
getMatchingSequence(String sequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the matching sequence of a given sequence.
|
AtomChain |
getMonoisotopicAtomChain()
Returns the monoisotopic atom chain representing this amino acid.
|
Double |
getMonoisotopicMass()
Returns the mass of the amino acid.
|
char |
getSingleLetterCodeAsChar()
Returns the single letter code as character.
|
String[] |
getStandardGeneticCode()
Returns the standard genetic triplets associated to this amino acid.
|
protected String[] |
getStandardGeneticCodeForCombination()
Returns the genetic code as combination of the sub amino acid genetic
codes.
|
char[] |
getSubAminoAcids()
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code
including sub combinations.
|
char[] |
getSubAminoAcids(boolean includeCombinations)
In case of a combination of amino acids, returns the comprised amino
acids or amino acid groups represented by their single letter code.
|
static char[] |
getUniqueAminoAcids()
Returns a char array of the one letter code of amino acids without
combinations of amino acids.
|
abstract boolean |
iscombination()
Indicates whether the amino acid object refers to a combination of amino
acids like B, J, Z or X.
|
public static final AminoAcid A
public static final AminoAcid C
public static final AminoAcid D
public static final AminoAcid E
public static final AminoAcid F
public static final AminoAcid G
public static final AminoAcid H
public static final AminoAcid I
public static final AminoAcid K
public static final AminoAcid L
public static final AminoAcid M
public static final AminoAcid N
public static final AminoAcid P
public static final AminoAcid Q
public static final AminoAcid R
public static final AminoAcid S
public static final AminoAcid T
public static final AminoAcid V
public static final AminoAcid W
public static final AminoAcid Y
public static final AminoAcid U
public static final AminoAcid O
public static final AminoAcid B
public static final AminoAcid J
public static final AminoAcid Z
public static final AminoAcid X
public String singleLetterCode
public String threeLetterCode
public String name
public double averageMass
protected Double monoisotopicMass
protected AtomChain monoisotopicAtomChain
protected char[] subAminoAcidsWithoutCombination
protected char[] subAminoAcidsWithCombination
protected char[] aminoAcidCombinations
protected String[] standardGeneticCode
public static final String[] aminoAcidStrings
public static char[] getAminoAcids()
public char getSingleLetterCodeAsChar()
public static List<String> getAminoAcidsList()
public static char[] getUniqueAminoAcids()
public static AminoAcid getAminoAcid(String aa)
aa
- the amino acid single letter code as a Stringpublic static AminoAcid getAminoAcid(char letter)
letter
- the letter givenpublic abstract boolean iscombination()
public char[] getSubAminoAcids()
public char[] getSubAminoAcids(boolean includeCombinations)
includeCombinations
- if true, sub-amino acids which are amino acids
combinations like Z will also be includedpublic char[] getCombinations()
public static String getMatchingAminoAcid(String aminoAcid, SequenceMatchingPreferences sequenceMatchingPreferences)
aminoAcid
- the single letter code of the amino acid of interestsequenceMatchingPreferences
- the sequence matching preferencespublic static String getMatchingSequence(String sequence, SequenceMatchingPreferences sequenceMatchingPreferences)
sequence
- the sequence of interestsequenceMatchingPreferences
- the sequence matching preferencespublic String[] getStandardGeneticCode()
public static AminoAcid getAminoAcidFromGeneticCode(String geneticCode)
geneticCode
- the three letter genetic code of the desired amino
acidprotected String[] getStandardGeneticCodeForCombination()
public AtomChain getMonoisotopicAtomChain()
public Double getMonoisotopicMass()
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