Package org.biojava.bio.seq
Class ProteinTools
- java.lang.Object
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- org.biojava.bio.seq.ProteinTools
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public class ProteinTools extends Object
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)
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static 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 FiniteAlphabet
getAlphabet()
Gets the protein alphabetstatic SymbolPropertyTable
getSymbolPropertyTable(String name)
static FiniteAlphabet
getTAlphabet()
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
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Method Detail
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getAlphabet
public static final FiniteAlphabet getAlphabet()
Gets the protein alphabet
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getTAlphabet
public static final FiniteAlphabet getTAlphabet()
Gets the protein alphabet including the translation termination symbols
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getSymbolPropertyTable
public static final SymbolPropertyTable getSymbolPropertyTable(String name)
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createProtein
public static SymbolList createProtein(String theProtein) throws IllegalSymbolException
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.
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createGappedProteinSequence
public static GappedSequence createGappedProteinSequence(String theProtein, String name) throws IllegalSymbolException
Get a new protein as a GappedSequence- Throws:
IllegalSymbolException
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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
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ala
public static AtomicSymbol ala()
Returns theAtomicSymbol
for the amino acid Alanine (A)
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a
public static AtomicSymbol a()
Returns theAtomicSymbol
for the amino acid Alanine
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arg
public static AtomicSymbol arg()
Returns theAtomicSymbol
for the amino acid Arginine (R)
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r
public static AtomicSymbol r()
Returns theAtomicSymbol
for the amino acid Arginine
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asn
public static AtomicSymbol asn()
Returns theAtomicSymbol
for the amino acid Asparagine (N)
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n
public static AtomicSymbol n()
Returns theAtomicSymbol
for the amino acid Asparagine
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asp
public static AtomicSymbol asp()
Returns theAtomicSymbol
for the amino acid Aspartic Acid (D)
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d
public static AtomicSymbol d()
Returns theAtomicSymbol
for the amino acid Aspartic Acid
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cys
public static AtomicSymbol cys()
Returns theAtomicSymbol
for the amino acid Cysteine (C)
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c
public static AtomicSymbol c()
Returns theAtomicSymbol
for the amino acid Cysteine
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gln
public static AtomicSymbol gln()
Returns theAtomicSymbol
for the amino acid Glutamine (Q)
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q
public static AtomicSymbol q()
Returns theAtomicSymbol
for the amino acid Glutamine
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glu
public static AtomicSymbol glu()
Returns theAtomicSymbol
for the amino acid Glutamic Acid (E)
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e
public static AtomicSymbol e()
Returns theAtomicSymbol
for the amino acid Glutamic Acid
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gly
public static AtomicSymbol gly()
Returns theAtomicSymbol
for the amino acid Glycine (G)
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g
public static AtomicSymbol g()
Returns theAtomicSymbol
for the amino acid Glycine
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his
public static AtomicSymbol his()
Returns theAtomicSymbol
for the amino acid Histidine (H)
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h
public static AtomicSymbol h()
Returns theAtomicSymbol
for the amino acid Histidine
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ile
public static AtomicSymbol ile()
Returns theAtomicSymbol
for the amino acid Isoleucine (I)
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i
public static AtomicSymbol i()
Returns theAtomicSymbol
for the amino acid Isoleucine
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leu
public static AtomicSymbol leu()
Returns theAtomicSymbol
for the amino acid Leucine (L)
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l
public static AtomicSymbol l()
Returns theAtomicSymbol
for the amino acid Leucine
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lys
public static AtomicSymbol lys()
Returns theAtomicSymbol
for the amino acid Lysine (K)
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k
public static AtomicSymbol k()
Returns theAtomicSymbol
for the amino acid Lysine
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met
public static AtomicSymbol met()
Returns theAtomicSymbol
for the amino acid Methionine (M)
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m
public static AtomicSymbol m()
Returns theAtomicSymbol
for the amino acid Methionine
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phe
public static AtomicSymbol phe()
Returns theAtomicSymbol
for the amino acid Phenylalanine (F)
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f
public static AtomicSymbol f()
Returns theAtomicSymbol
for the amino acid Phenylalanine
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pro
public static AtomicSymbol pro()
Returns theAtomicSymbol
for the amino acid Proline (P)
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p
public static AtomicSymbol p()
Returns theAtomicSymbol
for the amino acid Proline
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pyl
public static AtomicSymbol pyl()
Returns theAtomicSymbol
for the amino acid Pyrrolysine (O)
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o
public static AtomicSymbol o()
Returns theAtomicSymbol
for the amino acid Pyrrolysine
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sec
public static AtomicSymbol sec()
Returns theAtomicSymbol
for the amino acid Selenocysteine (U)
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u
public static AtomicSymbol u()
Returns theAtomicSymbol
for the amino acid Selenocysteine
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ser
public static AtomicSymbol ser()
Returns theAtomicSymbol
for the amino acid Serine (S)
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s
public static AtomicSymbol s()
Returns theAtomicSymbol
for the amino acid Serine
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thr
public static AtomicSymbol thr()
Returns theAtomicSymbol
for the amino acid Threonine (T)
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t
public static AtomicSymbol t()
Returns theAtomicSymbol
for the amino acid Threonine
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trp
public static AtomicSymbol trp()
Returns theAtomicSymbol
for the amino acid Tryptophan (W)
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w
public static AtomicSymbol w()
Returns theAtomicSymbol
for the amino acid Tryptophan
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tyr
public static AtomicSymbol tyr()
Returns theAtomicSymbol
for the amino acid Tyrosine (Y)
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y
public static AtomicSymbol y()
Returns theAtomicSymbol
for the amino acid Tyrosine
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val
public static AtomicSymbol val()
Returns theAtomicSymbol
for the amino acid Valine (V)
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v
public static AtomicSymbol v()
Returns theAtomicSymbol
for the amino acid Valine
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ter
public static AtomicSymbol ter()
Returns theAtomicSymbol
for the termination (*) placeholder
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