org.biojava.bio.symbol
Class IllegalSymbolException

java.lang.Object
  extended byjava.lang.Throwable
      extended byjava.lang.Exception
          extended byorg.biojava.utils.NestedException
              extended byorg.biojava.bio.BioException
                  extended byorg.biojava.bio.symbol.IllegalSymbolException
All Implemented Interfaces:
java.io.Serializable

public class IllegalSymbolException
extends BioException

The exception to indicate that a symbol is not valid within a context.

The usual reason for throwing an IllegalSymbolException is that you are trying to add a symbol to a sequence with an alpabet that does not contain the symbol. This is the sequence/alphabet equivalent of a ClassCastException for objects.

Frequently, these excepions are actualy generated from Alphabet.validate.

Author:
Matthew Pocock
See Also:
Serialized Form

Constructor Summary
IllegalSymbolException(java.lang.String message)
          Make the exception with a message.
IllegalSymbolException(Symbol sym, java.lang.String message)
          Make the exception with a message and a symbol.
IllegalSymbolException(java.lang.Throwable cause, java.lang.String message)
           
IllegalSymbolException(java.lang.Throwable cause, Symbol sym, java.lang.String message)
           
 
Method Summary
 Symbol getSymbol()
          Retrieve the symbol that caused this exception, or null.
 
Methods inherited from class org.biojava.utils.NestedException
printStackTrace, printStackTrace, printStackTrace
 
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, setStackTrace, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

IllegalSymbolException

public IllegalSymbolException(java.lang.String message)
Make the exception with a message.


IllegalSymbolException

public IllegalSymbolException(Symbol sym,
                              java.lang.String message)
Make the exception with a message and a symbol.


IllegalSymbolException

public IllegalSymbolException(java.lang.Throwable cause,
                              java.lang.String message)

IllegalSymbolException

public IllegalSymbolException(java.lang.Throwable cause,
                              Symbol sym,
                              java.lang.String message)
Method Detail

getSymbol

public Symbol getSymbol()
Retrieve the symbol that caused this exception, or null.