com.compomics.util.experiment.biology
Class AminoAcid

java.lang.Object
  extended by com.compomics.util.experiment.biology.AminoAcid
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
Alanine, Arginine, Asparagine, AsparticAcid, B, Cysteine, GlutamicAcid, Glutamine, Glycine, Histidine, Isoleucine, J, Leucine, Lysine, Methionine, Phenylalanine, Proline, Pyrrolysine, Selenocysteine, Serine, Threonine, Tryptophan, Tyrosine, Valine, X, Z

public abstract class AminoAcid
extends Object
implements Serializable

Class representing amino acids.

Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form

Field Summary
static AminoAcid A
           
 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
           
 double monoisotopicMass
          Monoisotopic mass of the amino acid.
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.
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 Summary
AminoAcid()
           
 
Method Summary
abstract  char[] getActualAminoAcids()
          In case of a combination of amino acids, returns the actual amino acids represented by their single letter code.
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 char[] getAminoAcids()
          Convenience method returning an array of all implemented amino-acids represented by their singe letter code.
static ArrayList<String> getAminoAcidsList()
          Convenience method returning an arrayList of all implemented amino-acids.
abstract  char[] getCombinations()
          Returns the amino acids combinations which might represent this amino acid.
 ArrayList<Character> getIndistinguishibleAminoAcids(Double massTolerance)
          Returns the amino acids which cannot be distinguished from this amino acid given a mass tolerance.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

A

public static final AminoAcid A

C

public static final AminoAcid C

D

public static final AminoAcid D

E

public static final AminoAcid E

F

public static final AminoAcid F

G

public static final AminoAcid G

H

public static final AminoAcid H

I

public static final AminoAcid I

K

public static final AminoAcid K

L

public static final AminoAcid L

M

public static final AminoAcid M

N

public static final AminoAcid N

P

public static final AminoAcid P

Q

public static final AminoAcid Q

R

public static final AminoAcid R

S

public static final AminoAcid S

T

public static final AminoAcid T

V

public static final AminoAcid V

W

public static final AminoAcid W

Y

public static final AminoAcid Y

B

public static final AminoAcid B

Z

public static final AminoAcid Z

X

public static final AminoAcid X

U

public static final AminoAcid U

J

public static final AminoAcid J

O

public static final AminoAcid O

singleLetterCode

public String singleLetterCode
Single letter code of the amino acid.


threeLetterCode

public String threeLetterCode
Three letter code of the amino acid.


name

public String name
Name of the amino acid.


averageMass

public double averageMass
Average mass of the amino acid.


monoisotopicMass

public double monoisotopicMass
Monoisotopic mass of the amino acid.

Constructor Detail

AminoAcid

public AminoAcid()
Method Detail

getAminoAcids

public static char[] getAminoAcids()
Convenience method returning an array of all implemented amino-acids represented by their singe letter code.

Returns:
an array of all implemented amino-acids

getAminoAcidsList

public static ArrayList<String> getAminoAcidsList()
Convenience method returning an arrayList of all implemented amino-acids.

Returns:
an arrayList of all implemented amino-acids represented by their character

getAminoAcid

public static AminoAcid getAminoAcid(String aa)
Returns the amino acid corresponding to the letter given, null if not implemented. If more than one letter is given only the first one will be accounted for.

Parameters:
aa - the amino acid single letter code as a String
Returns:
the corresponding amino acid.

getAminoAcid

public static AminoAcid getAminoAcid(char letter)
Returns the amino acid corresponding to the letter given, null if not implemented.

Parameters:
letter - the letter given
Returns:
the corresponding amino acid.

getActualAminoAcids

public abstract char[] getActualAminoAcids()
In case of a combination of amino acids, returns the actual amino acids represented by their single letter code. Example: Z -> {G, Q}.

Returns:
the actual amino acids

getCombinations

public abstract char[] getCombinations()
Returns the amino acids combinations which might represent this amino acid. Example: g -> {Z, X}.

Returns:
the amino acids combinations which might represent this amino acid

getIndistinguishibleAminoAcids

public ArrayList<Character> getIndistinguishibleAminoAcids(Double massTolerance)
Returns the amino acids which cannot be distinguished from this amino acid given a mass tolerance. Note that these amino acids may contain the getActualAminoAcids() and getCombinations() amino acids, not comprehensively though, and the amino acid itself.

Parameters:
massTolerance - the mass tolerance
Returns:
the amino acids which cannot be distinguished using their single character code


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