org.biojava.bio
Class BioRuntimeException

java.lang.Object
  extended by java.lang.Throwable
      extended by java.lang.Exception
          extended by java.lang.RuntimeException
              extended by org.biojava.bio.BioRuntimeException
All Implemented Interfaces:
java.io.Serializable
Direct Known Subclasses:
IllegalAlignmentEditException

public class BioRuntimeException
extends java.lang.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(java.lang.String message)
          Create a new BioRuntimeException with a message.
BioRuntimeException(java.lang.String message, java.lang.Throwable ex)
          Create a new BioRuntimeException with a cause and a message.
BioRuntimeException(java.lang.Throwable ex)
          Create a new BioRuntimeException with a cause.
BioRuntimeException(java.lang.Throwable ex, java.lang.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(java.lang.String message)
Create a new BioRuntimeException with a message.

Parameters:
message - the message

BioRuntimeException

public BioRuntimeException(java.lang.Throwable ex)
Create a new BioRuntimeException with a cause.

Parameters:
ex - the Throwable that caused this BioRuntimeException

BioRuntimeException

public BioRuntimeException(java.lang.Throwable ex,
                           java.lang.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(java.lang.String message,
                           java.lang.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.