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:

• Throw a ParserException. This need only contain a detail message, the parser will fill in other fields. parsing will be aborted.
• Throw an IgnoreRecordException. This line of the GFF file will be ignored, but parsing will not be aborted
• Return a value for the field.

Author:

Thomas Down, Matthew Pocock

Nested 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.

Returns:

A parsed value, if this is possible

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.

Returns:

A parsed value, if this is possible

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.

Returns:

A parsed value, if this is possible

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.

Returns:

A parsed value, if this is possible

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.

Returns:

A parsed value, if this is possible

Throws:

ParserException - If parsing should be aborted

IgnoreRecordException - If this record should be silently skipped.