Package org.biojava.bio.seq
Class ProteinTools
java.lang.Object
org.biojava.bio.seq.ProteinTools
The central port-of-call for all information and functionality specific to
SymbolLists over the protein alphabet.
- Author:
- Matthew Pocock, Greg Cox, Thomas Down, MarkSchreiber, Jonathan Warren, gwaldon (pyrrolysine, pKs)
-
Method Summary
Modifier and TypeMethodDescriptionstatic AtomicSymbol
a()
Returns theAtomicSymbol
for the amino acid Alaninestatic AtomicSymbol
ala()
Returns theAtomicSymbol
for the amino acid Alanine (A)static AtomicSymbol
arg()
Returns theAtomicSymbol
for the amino acid Arginine (R)static AtomicSymbol
asn()
Returns theAtomicSymbol
for the amino acid Asparagine (N)static AtomicSymbol
asp()
Returns theAtomicSymbol
for the amino acid Aspartic Acid (D)static AtomicSymbol
c()
Returns theAtomicSymbol
for the amino acid Cysteinestatic GappedSequence
createGappedProteinSequence
(String theProtein, String name) Get a new protein as a GappedSequencestatic 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 theAtomicSymbol
for the amino acid Cysteine (C)static AtomicSymbol
d()
Returns theAtomicSymbol
for the amino acid Aspartic Acidstatic AtomicSymbol
e()
Returns theAtomicSymbol
for the amino acid Glutamic Acidstatic AtomicSymbol
f()
Returns theAtomicSymbol
for the amino acid Phenylalaninestatic AtomicSymbol
g()
Returns theAtomicSymbol
for the amino acid Glycinestatic final FiniteAlphabet
Gets the protein alphabetstatic final SymbolPropertyTable
getSymbolPropertyTable
(String name) static final FiniteAlphabet
Gets the protein alphabet including the translation termination symbolsstatic AtomicSymbol
gln()
Returns theAtomicSymbol
for the amino acid Glutamine (Q)static AtomicSymbol
glu()
Returns theAtomicSymbol
for the amino acid Glutamic Acid (E)static AtomicSymbol
gly()
Returns theAtomicSymbol
for the amino acid Glycine (G)static AtomicSymbol
h()
Returns theAtomicSymbol
for the amino acid Histidinestatic AtomicSymbol
his()
Returns theAtomicSymbol
for the amino acid Histidine (H)static AtomicSymbol
i()
Returns theAtomicSymbol
for the amino acid Isoleucinestatic AtomicSymbol
ile()
Returns theAtomicSymbol
for the amino acid Isoleucine (I)static AtomicSymbol
k()
Returns theAtomicSymbol
for the amino acid Lysinestatic AtomicSymbol
l()
Returns theAtomicSymbol
for the amino acid Leucinestatic AtomicSymbol
leu()
Returns theAtomicSymbol
for the amino acid Leucine (L)static AtomicSymbol
lys()
Returns theAtomicSymbol
for the amino acid Lysine (K)static AtomicSymbol
m()
Returns theAtomicSymbol
for the amino acid Methioninestatic AtomicSymbol
met()
Returns theAtomicSymbol
for the amino acid Methionine (M)static AtomicSymbol
n()
Returns theAtomicSymbol
for the amino acid Asparaginestatic AtomicSymbol
o()
Returns theAtomicSymbol
for the amino acid Pyrrolysinestatic AtomicSymbol
p()
Returns theAtomicSymbol
for the amino acid Prolinestatic AtomicSymbol
phe()
Returns theAtomicSymbol
for the amino acid Phenylalanine (F)static AtomicSymbol
pro()
Returns theAtomicSymbol
for the amino acid Proline (P)static AtomicSymbol
pyl()
Returns theAtomicSymbol
for the amino acid Pyrrolysine (O)static AtomicSymbol
q()
Returns theAtomicSymbol
for the amino acid Glutaminestatic AtomicSymbol
r()
Returns theAtomicSymbol
for the amino acid Argininestatic AtomicSymbol
s()
Returns theAtomicSymbol
for the amino acid Serinestatic AtomicSymbol
sec()
Returns theAtomicSymbol
for the amino acid Selenocysteine (U)static AtomicSymbol
ser()
Returns theAtomicSymbol
for the amino acid Serine (S)static AtomicSymbol
t()
Returns theAtomicSymbol
for the amino acid Threoninestatic AtomicSymbol
ter()
Returns theAtomicSymbol
for the termination (*) placeholderstatic AtomicSymbol
thr()
Returns theAtomicSymbol
for the amino acid Threonine (T)static AtomicSymbol
trp()
Returns theAtomicSymbol
for the amino acid Tryptophan (W)static AtomicSymbol
tyr()
Returns theAtomicSymbol
for the amino acid Tyrosine (Y)static AtomicSymbol
u()
Returns theAtomicSymbol
for the amino acid Selenocysteinestatic AtomicSymbol
v()
Returns theAtomicSymbol
for the amino acid Valinestatic AtomicSymbol
val()
Returns theAtomicSymbol
for the amino acid Valine (V)static AtomicSymbol
w()
Returns theAtomicSymbol
for the amino acid Tryptophanstatic AtomicSymbol
y()
Returns theAtomicSymbol
for the amino acid Tyrosine
-
Method Details
-
getAlphabet
Gets the protein alphabet -
getTAlphabet
Gets the protein alphabet including the translation termination symbols -
getSymbolPropertyTable
-
createProtein
Return a new Protein SymbolList for protein.- Parameters:
theProtein
- a String to parse into Protein- Returns:
- a SymbolList created form Protein
- Throws:
IllegalSymbolException
- if dna contains any non-Amino Acid characters.
-
createGappedProteinSequence
public static GappedSequence createGappedProteinSequence(String theProtein, String name) throws IllegalSymbolException Get a new protein as a GappedSequence- Throws:
IllegalSymbolException
-
createProteinSequence
public static Sequence createProteinSequence(String protein, String name) throws IllegalSymbolException Return a new PROTEIN Sequence for protein.- Parameters:
protein
- a String to parse into PROTEINname
- a String to use as the name- Returns:
- a Sequence created form protein
- Throws:
IllegalSymbolException
- if protein contains any non-PROTEIN characters
-
ala
Returns theAtomicSymbol
for the amino acid Alanine (A) -
a
Returns theAtomicSymbol
for the amino acid Alanine -
arg
Returns theAtomicSymbol
for the amino acid Arginine (R) -
r
Returns theAtomicSymbol
for the amino acid Arginine -
asn
Returns theAtomicSymbol
for the amino acid Asparagine (N) -
n
Returns theAtomicSymbol
for the amino acid Asparagine -
asp
Returns theAtomicSymbol
for the amino acid Aspartic Acid (D) -
d
Returns theAtomicSymbol
for the amino acid Aspartic Acid -
cys
Returns theAtomicSymbol
for the amino acid Cysteine (C) -
c
Returns theAtomicSymbol
for the amino acid Cysteine -
gln
Returns theAtomicSymbol
for the amino acid Glutamine (Q) -
q
Returns theAtomicSymbol
for the amino acid Glutamine -
glu
Returns theAtomicSymbol
for the amino acid Glutamic Acid (E) -
e
Returns theAtomicSymbol
for the amino acid Glutamic Acid -
gly
Returns theAtomicSymbol
for the amino acid Glycine (G) -
g
Returns theAtomicSymbol
for the amino acid Glycine -
his
Returns theAtomicSymbol
for the amino acid Histidine (H) -
h
Returns theAtomicSymbol
for the amino acid Histidine -
ile
Returns theAtomicSymbol
for the amino acid Isoleucine (I) -
i
Returns theAtomicSymbol
for the amino acid Isoleucine -
leu
Returns theAtomicSymbol
for the amino acid Leucine (L) -
l
Returns theAtomicSymbol
for the amino acid Leucine -
lys
Returns theAtomicSymbol
for the amino acid Lysine (K) -
k
Returns theAtomicSymbol
for the amino acid Lysine -
met
Returns theAtomicSymbol
for the amino acid Methionine (M) -
m
Returns theAtomicSymbol
for the amino acid Methionine -
phe
Returns theAtomicSymbol
for the amino acid Phenylalanine (F) -
f
Returns theAtomicSymbol
for the amino acid Phenylalanine -
pro
Returns theAtomicSymbol
for the amino acid Proline (P) -
p
Returns theAtomicSymbol
for the amino acid Proline -
pyl
Returns theAtomicSymbol
for the amino acid Pyrrolysine (O) -
o
Returns theAtomicSymbol
for the amino acid Pyrrolysine -
sec
Returns theAtomicSymbol
for the amino acid Selenocysteine (U) -
u
Returns theAtomicSymbol
for the amino acid Selenocysteine -
ser
Returns theAtomicSymbol
for the amino acid Serine (S) -
s
Returns theAtomicSymbol
for the amino acid Serine -
thr
Returns theAtomicSymbol
for the amino acid Threonine (T) -
t
Returns theAtomicSymbol
for the amino acid Threonine -
trp
Returns theAtomicSymbol
for the amino acid Tryptophan (W) -
w
Returns theAtomicSymbol
for the amino acid Tryptophan -
tyr
Returns theAtomicSymbol
for the amino acid Tyrosine (Y) -
y
Returns theAtomicSymbol
for the amino acid Tyrosine -
val
Returns theAtomicSymbol
for the amino acid Valine (V) -
v
Returns theAtomicSymbol
for the amino acid Valine -
ter
Returns theAtomicSymbol
for the termination (*) placeholder
-