BioJava:Cookbook:Alphabets

From BioJava

How do I get a DNA, RNA or Protein Alphabet?

In BioJava Alphabets are collections of Symbols. Common biological alphabets (DNA, RNA, protein, etc) are registered with the BioJava AlphabetManager at startup and can be accessed by name. The DNA, RNA and protein alphabets can also be accessed using convenient static methods from DNATools, RNATools and ProteinTools respectively.

Both of these approaches are shown in the example below

import org.biojava.bio.symbol.*;
import java.util.*;
import org.biojava.bio.seq.*;
 
public class AlphabetExample {
  public static void main(String[] args) {
    Alphabet dna, rna, prot;
 
    //get the DNA alphabet by name
    dna = AlphabetManager.alphabetForName("DNA");
 
    //get the RNA alphabet by name
    rna = AlphabetManager.alphabetForName("RNA");
 
    //get the Protein alphabet by name
    prot = AlphabetManager.alphabetForName("PROTEIN");
    //get the protein alphabet that includes the * termination Symbol
    prot = AlphabetManager.alphabetForName("PROTEIN-TERM");
 
    //get those same Alphabets from the Tools classes
    dna = DNATools.getDNA();
    rna = RNATools.getRNA();
    prot = ProteinTools.getAlphabet();
    //or the one with the * symbol
    prot = ProteinTools.getTAlphabet();
 
  }
}