BioJava:Cookbook:Alphabets:Custom

From BioJava

How do I make a custom Alphabet from custom Symbols?

This example demonstrates the creation of a 'binary' alphabet that will have two Symbols, zero and one. The custom made Symbols and Alphabet can then be used to make SymbolList, Sequences, Distributions, etc.

package biojava_in_anger;
 
import org.biojava.bio.symbol.*;
import org.biojava.bio.*;
import java.util.*;
 
public class Binary {
  public static void main(String[] args) {
 
    //make the "zero" Symbol with no annotation
    Symbol zero =
        AlphabetManager.createSymbol("zero", Annotation.EMPTY_ANNOTATION);
 
    //make the "one" Symbol
    Symbol one =
        AlphabetManager.createSymbol("one", Annotation.EMPTY_ANNOTATION);
 
    //collect the Symbols in a Set
    Set symbols = new HashSet();
    symbols.add(zero); symbols.add(one);
 
    //make the Binary Alphabet
    FiniteAlphabet binary = new SimpleAlphabet(symbols, "Binary");
 
    //iterate through the symbols to show everything works
    for (Iterator i = binary.iterator(); i.hasNext(); ) {
      Symbol sym = (Symbol)i.next();
      System.out.println(sym.getName());
    }
 
    //it is usual to register newly created Alphabets with the AlphabetManager
    AlphabetManager.registerAlphabet(binary.getName(), binary);
 
    /*
     * The newly created Alphabet will have been registered with the
     * AlphabetManager under the name "Binary". If you retreive an instance
     * of it using this name it should be canonical with the previous instance
     */
    Alphabet alpha = AlphabetManager.alphabetForName("Binary");
 
    //check canonical status
    System.out.println(alpha == binary);
  }
}