org.biojava.bio.seq.io
Class ParseException

java.lang.Object
  extended by java.lang.Throwable
      extended by java.lang.Exception
          extended by org.biojava.bio.BioException
              extended by org.biojava.bio.seq.io.ParseException
All Implemented Interfaces:
Serializable

public class ParseException
extends BioException

ParseException should be thrown to indicate that there was a problem with parsing sequence information.

Author:
Matthew Pocock
See Also:
Serialized Form

Constructor Summary
ParseException()
           
ParseException(String message)
           
ParseException(Throwable nested)
           
ParseException(Throwable nested, String message)
           
 
Method Summary
static String newMessage(Class format, String accession, String identifier, String comments, String parseBlock)
          Make a new error message.
 
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

ParseException

public ParseException()

ParseException

public ParseException(String message)

ParseException

public ParseException(Throwable nested)

ParseException

public ParseException(Throwable nested,
                      String message)
Method Detail

newMessage

public static String newMessage(Class format,
                                String accession,
                                String identifier,
                                String comments,
                                String parseBlock)
Make a new error message.

Parameters:
format - the format object that was doing the parsing
accession - the accession number of the record that failed
identifier - the identifier of the sequence that failed (eg the GI number for genbank)
comments - any additional information
parseBlock - the chunk of the file the parser was trying to parse when the error occured
Returns:
the formatted error message


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