Alignments
Class AlignmentException

java.lang.Object
  extended by java.lang.Throwable
      extended by java.lang.Exception
          extended by Exceptions.GeneralException
              extended by Alignments.AlignmentException
All Implemented Interfaces:
java.io.Serializable

public class AlignmentException
extends GeneralException

Exception related to an alignment (currently only input errors)

Version:
1.0
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class Exceptions.GeneralException
GeneralException.Debug
 
Constructor Summary
AlignmentException(java.lang.String msg)
          Constructor for when there is a problem unrelated to an input file
AlignmentException(java.lang.String location, java.lang.String text, java.lang.String reason, java.lang.Throwable cause)
          Constructor for when there is a problem in the input file
 
Method Summary
 
Methods inherited from class Exceptions.GeneralException
setDebug, toString
 
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

AlignmentException

public AlignmentException(java.lang.String msg)
Constructor for when there is a problem unrelated to an input file

Parameters:
msg - The cause of the problem

AlignmentException

public AlignmentException(java.lang.String location,
                          java.lang.String text,
                          java.lang.String reason,
                          java.lang.Throwable cause)
Constructor for when there is a problem in the input file

Parameters:
location - Information on the location in the file
text - The text that caused the problem
reason - Why the text was problematic
cause - The Throwable that caused the problem (if applicable)