org.biojava.bio.program.gff
Interface GFFErrorHandler

All Known Implementing Classes:
GFFErrorHandler.AbortErrorHandler, GFFErrorHandler.SkipRecordErrorHandler

public interface GFFErrorHandler

Interface which captures any errors which occur when parsing a GFF stream. Providing a custom implementation of this interface allows intelligent recovery from errors when parsing GFF.

Each of these methods has three options:

Author:
Thomas Down, Matthew Pocock

Inner Class Summary
static class GFFErrorHandler.AbortErrorHandler
           
static class GFFErrorHandler.SkipRecordErrorHandler
           
 
Field Summary
static GFFErrorHandler ABORT_PARSING
           
static GFFErrorHandler SKIP_RECORD
           
 
Method Summary
 int invalidEnd(java.lang.String token)
          The `end' field of the GFF entry was not a valid value.
 int invalidFrame(java.lang.String token)
          The `frame' field of the GFF entry was not a valid value.
 double invalidScore(java.lang.String token)
          The `score' field of the GFF entry was not a valid value.
 int invalidStart(java.lang.String token)
          The `start' field of the GFF entry was not a valid value.
 StrandedFeature.Strand invalidStrand(java.lang.String token)
          The `strand' field of the GFF entry was not a valid value.
 

Field Detail

ABORT_PARSING

public static final GFFErrorHandler ABORT_PARSING

SKIP_RECORD

public static final GFFErrorHandler SKIP_RECORD
Method Detail

invalidStart

public int invalidStart(java.lang.String token)
                 throws ParserException,
                        IgnoreRecordException
The `start' field of the GFF entry was not a valid value.
Parameters:
token - The start token found.
Throws:
ParserException - If parsing should be aborted
IgnoreRecordException - If this record should be silently skipped.

invalidEnd

public int invalidEnd(java.lang.String token)
               throws ParserException,
                      IgnoreRecordException
The `end' field of the GFF entry was not a valid value.
Parameters:
token - The end token found.
Throws:
ParserException - If parsing should be aborted
IgnoreRecordException - If this record should be silently skipped.

invalidScore

public double invalidScore(java.lang.String token)
                    throws ParserException,
                           IgnoreRecordException
The `score' field of the GFF entry was not a valid value.
Parameters:
token - The score token found.
Throws:
ParserException - If parsing should be aborted
IgnoreRecordException - If this record should be silently skipped.

invalidFrame

public int invalidFrame(java.lang.String token)
                 throws ParserException,
                        IgnoreRecordException
The `frame' field of the GFF entry was not a valid value.
Parameters:
token - The frame token found.
Throws:
ParserException - If parsing should be aborted
IgnoreRecordException - If this record should be silently skipped.

invalidStrand

public StrandedFeature.Strand invalidStrand(java.lang.String token)
                                     throws ParserException,
                                            IgnoreRecordException
The `strand' field of the GFF entry was not a valid value.
Parameters:
token - The strand token found.
Throws:
ParserException - If parsing should be aborted
IgnoreRecordException - If this record should be silently skipped.