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java.lang.Objectorg.biojava.bio.seq.ProteinTools
public class ProteinTools
The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
Method Summary | |
---|---|
static AtomicSymbol |
a()
Returns the AtomicSymbol for the amino acid
Alanine |
static AtomicSymbol |
ala()
Returns the AtomicSymbol for the amino acid Alanine
(A) |
static AtomicSymbol |
arg()
Returns the AtomicSymbol for the amino acid
Arginine (R) |
static AtomicSymbol |
asn()
Returns the AtomicSymbol for the amino acid
Asparagine (N) |
static AtomicSymbol |
asp()
Returns the AtomicSymbol for the amino acid
Aspartic Acid (D) |
static AtomicSymbol |
c()
Returns the AtomicSymbol for the amino acid
Cysteine |
static GappedSequence |
createGappedProteinSequence(String theProtein,
String name)
Get a new protein as a GappedSequence |
static SymbolList |
createProtein(String theProtein)
Return a new Protein SymbolList for protein. |
static Sequence |
createProteinSequence(String protein,
String name)
Return a new PROTEIN Sequence for protein. |
static AtomicSymbol |
cys()
Returns the AtomicSymbol for the amino acid
Cysteine (C) |
static AtomicSymbol |
d()
Returns the AtomicSymbol for the amino acid
Aspartic Acid |
static AtomicSymbol |
e()
Returns the AtomicSymbol for the amino acid
Glutamic Acid |
static AtomicSymbol |
f()
Returns the AtomicSymbol for the amino acid
Phenylalanine |
static AtomicSymbol |
g()
Returns the AtomicSymbol for the amino acid
Glycine |
static FiniteAlphabet |
getAlphabet()
Gets the protein alphabet |
static SymbolPropertyTable |
getSymbolPropertyTable(String name)
|
static FiniteAlphabet |
getTAlphabet()
Gets the protein alphabet including the translation termination symbols |
static AtomicSymbol |
gln()
Returns the AtomicSymbol for the amino acid
Glutamine (Q) |
static AtomicSymbol |
glu()
Returns the AtomicSymbol for the amino acid
Glutamic Acid (E) |
static AtomicSymbol |
gly()
Returns the AtomicSymbol for the amino acid
Glycine (G) |
static AtomicSymbol |
h()
Returns the AtomicSymbol for the amino acid
Histidine |
static AtomicSymbol |
his()
Returns the AtomicSymbol for the amino acid
Histidine (H) |
static AtomicSymbol |
i()
Returns the AtomicSymbol for the amino acid
Isoleucine |
static AtomicSymbol |
ile()
Returns the AtomicSymbol for the amino acid
Isoleucine (I) |
static AtomicSymbol |
k()
Returns the AtomicSymbol for the amino acid
Lysine |
static AtomicSymbol |
l()
Returns the AtomicSymbol for the amino acid
Leucine |
static AtomicSymbol |
leu()
Returns the AtomicSymbol for the amino acid
Leucine (L) |
static AtomicSymbol |
lys()
Returns the AtomicSymbol for the amino acid
Lysine (K) |
static AtomicSymbol |
m()
Returns the AtomicSymbol for the amino acid
Methionine |
static AtomicSymbol |
met()
Returns the AtomicSymbol for the amino acid
Methionine (M) |
static AtomicSymbol |
n()
Returns the AtomicSymbol for the amino acid
Asparagine |
static AtomicSymbol |
o()
Returns the AtomicSymbol for the amino acid
Pyrrolysine |
static AtomicSymbol |
p()
Returns the AtomicSymbol for the amino acid
Proline |
static AtomicSymbol |
phe()
Returns the AtomicSymbol for the amino acid
Phenylalanine (F) |
static AtomicSymbol |
pro()
Returns the AtomicSymbol for the amino acid
Proline (P) |
static AtomicSymbol |
pyl()
Returns the AtomicSymbol for the amino acid
Pyrrolysine (O) |
static AtomicSymbol |
q()
Returns the AtomicSymbol for the amino acid
Glutamine |
static AtomicSymbol |
r()
Returns the AtomicSymbol for the amino acid
Arginine |
static AtomicSymbol |
s()
Returns the AtomicSymbol for the amino acid
Serine |
static AtomicSymbol |
sec()
Returns the AtomicSymbol for the amino acid
Selenocysteine (U) |
static AtomicSymbol |
ser()
Returns the AtomicSymbol for the amino acid
Serine (S) |
static AtomicSymbol |
t()
Returns the AtomicSymbol for the amino acid
Threonine |
static AtomicSymbol |
ter()
Returns the AtomicSymbol for the termination (*)
placeholder |
static AtomicSymbol |
thr()
Returns the AtomicSymbol for the amino acid
Threonine (T) |
static AtomicSymbol |
trp()
Returns the AtomicSymbol for the amino acid
Tryptophan (W) |
static AtomicSymbol |
tyr()
Returns the AtomicSymbol for the amino acid
Tyrosine (Y) |
static AtomicSymbol |
u()
Returns the AtomicSymbol for the amino acid
Selenocysteine |
static AtomicSymbol |
v()
Returns the AtomicSymbol for the amino acid
Valine |
static AtomicSymbol |
val()
Returns the AtomicSymbol for the amino acid Valine (V) |
static AtomicSymbol |
w()
Returns the AtomicSymbol for the amino acid
Tryptophan |
static AtomicSymbol |
y()
Returns the AtomicSymbol for the amino acid
Tyrosine |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
---|
public static final FiniteAlphabet getAlphabet()
public static final FiniteAlphabet getTAlphabet()
public static final SymbolPropertyTable getSymbolPropertyTable(String name)
public static SymbolList createProtein(String theProtein) throws IllegalSymbolException
theProtein
- a String to parse into Protein
IllegalSymbolException
- if dna contains
any non-Amino Acid characters.public static GappedSequence createGappedProteinSequence(String theProtein, String name) throws IllegalSymbolException
IllegalSymbolException
public static Sequence createProteinSequence(String protein, String name) throws IllegalSymbolException
protein
- a String to parse into PROTEINname
- a String to use as the name
IllegalSymbolException
- if protein contains
any non-PROTEIN characterspublic static AtomicSymbol ala()
AtomicSymbol
for the amino acid Alanine
(A)
public static AtomicSymbol a()
AtomicSymbol
for the amino acid
Alanine
public static AtomicSymbol arg()
AtomicSymbol
for the amino acid
Arginine (R)
public static AtomicSymbol r()
AtomicSymbol
for the amino acid
Arginine
public static AtomicSymbol asn()
AtomicSymbol
for the amino acid
Asparagine (N)
public static AtomicSymbol n()
AtomicSymbol
for the amino acid
Asparagine
public static AtomicSymbol asp()
AtomicSymbol
for the amino acid
Aspartic Acid (D)
public static AtomicSymbol d()
AtomicSymbol
for the amino acid
Aspartic Acid
public static AtomicSymbol cys()
AtomicSymbol
for the amino acid
Cysteine (C)
public static AtomicSymbol c()
AtomicSymbol
for the amino acid
Cysteine
public static AtomicSymbol gln()
AtomicSymbol
for the amino acid
Glutamine (Q)
public static AtomicSymbol q()
AtomicSymbol
for the amino acid
Glutamine
public static AtomicSymbol glu()
AtomicSymbol
for the amino acid
Glutamic Acid (E)
public static AtomicSymbol e()
AtomicSymbol
for the amino acid
Glutamic Acid
public static AtomicSymbol gly()
AtomicSymbol
for the amino acid
Glycine (G)
public static AtomicSymbol g()
AtomicSymbol
for the amino acid
Glycine
public static AtomicSymbol his()
AtomicSymbol
for the amino acid
Histidine (H)
public static AtomicSymbol h()
AtomicSymbol
for the amino acid
Histidine
public static AtomicSymbol ile()
AtomicSymbol
for the amino acid
Isoleucine (I)
public static AtomicSymbol i()
AtomicSymbol
for the amino acid
Isoleucine
public static AtomicSymbol leu()
AtomicSymbol
for the amino acid
Leucine (L)
public static AtomicSymbol l()
AtomicSymbol
for the amino acid
Leucine
public static AtomicSymbol lys()
AtomicSymbol
for the amino acid
Lysine (K)
public static AtomicSymbol k()
AtomicSymbol
for the amino acid
Lysine
public static AtomicSymbol met()
AtomicSymbol
for the amino acid
Methionine (M)
public static AtomicSymbol m()
AtomicSymbol
for the amino acid
Methionine
public static AtomicSymbol phe()
AtomicSymbol
for the amino acid
Phenylalanine (F)
public static AtomicSymbol f()
AtomicSymbol
for the amino acid
Phenylalanine
public static AtomicSymbol pro()
AtomicSymbol
for the amino acid
Proline (P)
public static AtomicSymbol p()
AtomicSymbol
for the amino acid
Proline
public static AtomicSymbol pyl()
AtomicSymbol
for the amino acid
Pyrrolysine (O)
public static AtomicSymbol o()
AtomicSymbol
for the amino acid
Pyrrolysine
public static AtomicSymbol sec()
AtomicSymbol
for the amino acid
Selenocysteine (U)
public static AtomicSymbol u()
AtomicSymbol
for the amino acid
Selenocysteine
public static AtomicSymbol ser()
AtomicSymbol
for the amino acid
Serine (S)
public static AtomicSymbol s()
AtomicSymbol
for the amino acid
Serine
public static AtomicSymbol thr()
AtomicSymbol
for the amino acid
Threonine (T)
public static AtomicSymbol t()
AtomicSymbol
for the amino acid
Threonine
public static AtomicSymbol trp()
AtomicSymbol
for the amino acid
Tryptophan (W)
public static AtomicSymbol w()
AtomicSymbol
for the amino acid
Tryptophan
public static AtomicSymbol tyr()
AtomicSymbol
for the amino acid
Tyrosine (Y)
public static AtomicSymbol y()
AtomicSymbol
for the amino acid
Tyrosine
public static AtomicSymbol val()
AtomicSymbol
for the amino acid Valine (V)
public static AtomicSymbol v()
AtomicSymbol
for the amino acid
Valine
public static AtomicSymbol ter()
AtomicSymbol
for the termination (*)
placeholder
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