org.biojava.bio.seq
Class ProteinTools

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

public class ProteinTools

extends java.lang.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

Constructor Summary

ProteinTools()

Method Summary

static GappedSequence	createGappedProteinSequence(java.lang.String theProtein, java.lang.String name) Get a new protein as a GappedSequence
static SymbolList	createProtein(java.lang.String theProtein) Return a new Protein SymbolList for protein.
static Sequence	createProteinSequence(java.lang.String protein, java.lang.String name) Return a new PROTEIN Sequence for protein.
static FiniteAlphabet	getAlphabet() Gets the protein alphabet
static SymbolPropertyTable	getSymbolPropertyTable(java.lang.String name)
static FiniteAlphabet	getTAlphabet() Gets the protein alphabet including the translation termination symbols

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProteinTools

public ProteinTools()

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(java.lang.String name)

createProtein

public static SymbolList createProtein(java.lang.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(java.lang.String theProtein,
                                                         java.lang.String name)
                                                  throws IllegalSymbolException

Get a new protein as a GappedSequence

IllegalSymbolException

createProteinSequence

public static Sequence createProteinSequence(java.lang.String protein,
                                             java.lang.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