org.biojava.bio
Class BioRuntimeException

java.lang.Object
  java.lang.Throwable
      java.lang.Exception
          java.lang.RuntimeException
              org.biojava.bio.BioRuntimeException

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

IllegalAlignmentEditException

public class BioRuntimeException
extends RuntimeException

A nestable biological exception.

In BioJava, checked exceptions are generally preferred to RuntimeExceptions, but RuntimeExceptions can be used as a fall-back if you are implementing an interface which doesn't support checked exceptions. If you do this, please document this clearly in the implementing class.

Since:

1.0

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

For advanced users:

Occasionaly methods will document that the object they return may emit BioRuntimeExceptions. If you know what you are doing, you can catch these and do something sensible with them. An example would be an iterator() method that returns an Iterator where next() could fail due to a database connection flaking out. This could raise a BioRuntimeException wrapping the real cause. It would then not be unreasonable for the code calling next() to catch this BioRuntimeException and extract the cause.

For developers:

Occasionaly it is necisary to abuse the exception system by throwing BioError to get arround limitations in APIs that you do not control. For example, when implementing Iterator.next(), you may need to call a method that can fail. Catch the failure and throw it as a BioError. If you want people to handle this gracefully in their scripts, then document this behavior and hope they catch the error.

Constructor Summary

BioRuntimeException()
Create a new BioRuntimeException.

BioRuntimeException(String message)
Create a new BioRuntimeException with a message.

BioRuntimeException(String message, Throwable ex)
Create a new BioRuntimeException with a cause and a message.

BioRuntimeException(Throwable ex)
Create a new BioRuntimeException with a cause.

BioRuntimeException(Throwable ex, String message)
Deprecated. use new BioRuntimeException(message, ex) instead

Method Summary

Methods inherited from class java.lang.Throwable

fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BioRuntimeException

public BioRuntimeException(String message)

Create a new BioRuntimeException with a message.

Parameters:

message - the message

BioRuntimeException

public BioRuntimeException(Throwable ex)

Create a new BioRuntimeException with a cause.

Parameters:

ex - the Throwable that caused this BioRuntimeException

BioRuntimeException

public BioRuntimeException(Throwable ex,
                           String message)

Deprecated. use new BioRuntimeException(message, ex) instead

Create a new BioRuntimeException with a cause and a message.

Parameters:

ex - the Throwable that caused this BioRuntimeException

message - the message

BioRuntimeException

public BioRuntimeException(String message,
                           Throwable ex)

Create a new BioRuntimeException with a cause and a message.

Parameters:

message - the message

ex - the Throwable that caused this BioRuntimeException

BioRuntimeException

public BioRuntimeException()

Create a new BioRuntimeException.