ProteinTools (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.seq.ProteinTools

```
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)

Method Summary

Methods
Modifier and Type	Method and Description
`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
  - getAlphabet
```
public static final FiniteAlphabet getAlphabet()
```
    Gets the protein alphabet
  - getTAlphabet
```
public static final FiniteAlphabet getTAlphabet()
```
    Gets the protein alphabet including the translation termination symbols
  - getSymbolPropertyTable
```
public static final SymbolPropertyTable getSymbolPropertyTable(String name)
```
  - 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.
  - 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 PROTEIN
    name - a String to use as the name
    
    Returns:
    a Sequence created form protein
    
    Throws:
    
    IllegalSymbolException - if protein contains any non-PROTEIN characters
  - ala
```
public static AtomicSymbol ala()
```
    Returns the AtomicSymbol for the amino acid Alanine (A)
  - a
```
public static AtomicSymbol a()
```
    Returns the AtomicSymbol for the amino acid Alanine
  - arg
```
public static AtomicSymbol arg()
```
    Returns the AtomicSymbol for the amino acid Arginine (R)
  - r
```
public static AtomicSymbol r()
```
    Returns the AtomicSymbol for the amino acid Arginine
  - asn
```
public static AtomicSymbol asn()
```
    Returns the AtomicSymbol for the amino acid Asparagine (N)
  - n
```
public static AtomicSymbol n()
```
    Returns the AtomicSymbol for the amino acid Asparagine
  - asp
```
public static AtomicSymbol asp()
```
    Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
  - d
```
public static AtomicSymbol d()
```
    Returns the AtomicSymbol for the amino acid Aspartic Acid
  - cys
```
public static AtomicSymbol cys()
```
    Returns the AtomicSymbol for the amino acid Cysteine (C)
  - c
```
public static AtomicSymbol c()
```
    Returns the AtomicSymbol for the amino acid Cysteine
  - gln
```
public static AtomicSymbol gln()
```
    Returns the AtomicSymbol for the amino acid Glutamine (Q)
  - q
```
public static AtomicSymbol q()
```
    Returns the AtomicSymbol for the amino acid Glutamine
  - glu
```
public static AtomicSymbol glu()
```
    Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
  - e
```
public static AtomicSymbol e()
```
    Returns the AtomicSymbol for the amino acid Glutamic Acid
  - gly
```
public static AtomicSymbol gly()
```
    Returns the AtomicSymbol for the amino acid Glycine (G)
  - g
```
public static AtomicSymbol g()
```
    Returns the AtomicSymbol for the amino acid Glycine
  - his
```
public static AtomicSymbol his()
```
    Returns the AtomicSymbol for the amino acid Histidine (H)
  - h
```
public static AtomicSymbol h()
```
    Returns the AtomicSymbol for the amino acid Histidine
  - ile
```
public static AtomicSymbol ile()
```
    Returns the AtomicSymbol for the amino acid Isoleucine (I)
  - i
```
public static AtomicSymbol i()
```
    Returns the AtomicSymbol for the amino acid Isoleucine
  - leu
```
public static AtomicSymbol leu()
```
    Returns the AtomicSymbol for the amino acid Leucine (L)
  - l
```
public static AtomicSymbol l()
```
    Returns the AtomicSymbol for the amino acid Leucine
  - lys
```
public static AtomicSymbol lys()
```
    Returns the AtomicSymbol for the amino acid Lysine (K)
  - k
```
public static AtomicSymbol k()
```
    Returns the AtomicSymbol for the amino acid Lysine
  - met
```
public static AtomicSymbol met()
```
    Returns the AtomicSymbol for the amino acid Methionine (M)
  - m
```
public static AtomicSymbol m()
```
    Returns the AtomicSymbol for the amino acid Methionine
  - phe
```
public static AtomicSymbol phe()
```
    Returns the AtomicSymbol for the amino acid Phenylalanine (F)
  - f
```
public static AtomicSymbol f()
```
    Returns the AtomicSymbol for the amino acid Phenylalanine
  - pro
```
public static AtomicSymbol pro()
```
    Returns the AtomicSymbol for the amino acid Proline (P)
  - p
```
public static AtomicSymbol p()
```
    Returns the AtomicSymbol for the amino acid Proline
  - pyl
```
public static AtomicSymbol pyl()
```
    Returns the AtomicSymbol for the amino acid Pyrrolysine (O)
  - o
```
public static AtomicSymbol o()
```
    Returns the AtomicSymbol for the amino acid Pyrrolysine
  - sec
```
public static AtomicSymbol sec()
```
    Returns the AtomicSymbol for the amino acid Selenocysteine (U)
  - u
```
public static AtomicSymbol u()
```
    Returns the AtomicSymbol for the amino acid Selenocysteine
  - ser
```
public static AtomicSymbol ser()
```
    Returns the AtomicSymbol for the amino acid Serine (S)
  - s
```
public static AtomicSymbol s()
```
    Returns the AtomicSymbol for the amino acid Serine
  - thr
```
public static AtomicSymbol thr()
```
    Returns the AtomicSymbol for the amino acid Threonine (T)
  - t
```
public static AtomicSymbol t()
```
    Returns the AtomicSymbol for the amino acid Threonine
  - trp
```
public static AtomicSymbol trp()
```
    Returns the AtomicSymbol for the amino acid Tryptophan (W)
  - w
```
public static AtomicSymbol w()
```
    Returns the AtomicSymbol for the amino acid Tryptophan
  - tyr
```
public static AtomicSymbol tyr()
```
    Returns the AtomicSymbol for the amino acid Tyrosine (Y)
  - y
```
public static AtomicSymbol y()
```
    Returns the AtomicSymbol for the amino acid Tyrosine
  - val
```
public static AtomicSymbol val()
```
    Returns the AtomicSymbol for the amino acid Valine (V)
  - v
```
public static AtomicSymbol v()
```
    Returns the AtomicSymbol for the amino acid Valine
  - ter
```
public static AtomicSymbol ter()
```
    Returns the AtomicSymbol for the termination (*) placeholder

Class ProteinTools

Method Summary

Methods inherited from class java.lang.Object

Method Detail

getAlphabet

getTAlphabet

getSymbolPropertyTable

createProtein

createGappedProteinSequence

createProteinSequence

ala

a

arg

r

asn

n

asp

d

cys

c

gln

q

glu

e

gly

g

his

h

ile

i

leu

l

lys

k

met

m

phe

f

pro

p

pyl

o

sec

u

ser

s

thr

t

trp

w

tyr

y

val

v

ter