org.biojava.bio.symbol
Class SimpleSymbol

java.lang.Object
  |
  +--org.biojava.bio.symbol.SimpleSymbol

public class SimpleSymbol
extends java.lang.Object
implements Symbol, java.io.Serializable

A no-frills implementation of a symbol.

Author:
Matthew Pocock
See Also:
Serialized Form

Constructor Summary
SimpleSymbol(char token, java.lang.String name, Alphabet matches, Annotation annotation)
          Create a new SimpleSymbol.
 
Method Summary
 Annotation getAnnotation()
          Should return the associated annotation object.
 Alphabet getMatches()
          The alphabet containing the symbols matched by this ambiguity symbol.
 java.lang.String getName()
          The long name for the symbol.
 char getToken()
          The token for the symbol.
 void setName(java.lang.String name)
          Assign a name to the symbol
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SimpleSymbol

public SimpleSymbol(char token,
                    java.lang.String name,
                    Alphabet matches,
                    Annotation annotation)
Create a new SimpleSymbol.
Parameters:
token - the char to represent this symbol when sequences are stringified
name - the long name
matches - the Alphabet of symbols that this symbol can match
annotation - the annotation
Method Detail

getAnnotation

public Annotation getAnnotation()
Description copied from interface: Annotatable
Should return the associated annotation object.
Tags copied from interface: Annotatable
Returns:
an Annotation object, never null

getToken

public char getToken()
Description copied from interface: Symbol
The token for the symbol.
Specified by:
getToken in interface Symbol
Tags copied from interface: Symbol
Returns:
the token

getName

public java.lang.String getName()
Description copied from interface: Symbol
The long name for the symbol.
Specified by:
getName in interface Symbol
Tags copied from interface: Symbol
Returns:
the long name

setName

public void setName(java.lang.String name)
Assign a name to the symbol
Parameters:
name - the name you wish to give this symbol

getMatches

public Alphabet getMatches()
Description copied from interface: Symbol
The alphabet containing the symbols matched by this ambiguity symbol.

This alphabet contains all of, and only, the symbols matched by this symbol. For example, the symbol representing the DNA ambiguity code for W would contain the symbol for A and T from the DNA alphabet.

Specified by:
getMatches in interface Symbol
Tags copied from interface: Symbol
Returns:
the Alphabet of symbols matched by this symbol

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object