org.biojava.bio.seq.io

Class ParseException

java.lang.Object

java.lang.Throwable

java.lang.Exception

org.biojava.bio.BioException

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

Constructors

Constructor and Description
ParseException()
ParseException(String message)
ParseException(Throwable nested)
ParseException(Throwable nested, String message)

Method Summary

Modifier and Type	Method and Description
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

addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, 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