org.biojava.bio.seq
Class ProteinTools

java.lang.Object
  extended byorg.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

Throws:
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