org.biojava.bio.seq
Class ProteinTools

java.lang.Object
  extended by 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
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