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

Nested Classes

Modifier and Type	Interface and Description
static class	GFFErrorHandler.AbortErrorHandler
static class	GFFErrorHandler.SkipRecordErrorHandler

Field Summary

Fields

Modifier and Type	Field and Description
static GFFErrorHandler	ABORT_PARSING
static GFFErrorHandler	SKIP_RECORD

Method Summary

Methods

Modifier and Type	Method and Description
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

static final GFFErrorHandler ABORT_PARSING

SKIP_RECORD

static final GFFErrorHandler SKIP_RECORD

Method Detail

invalidStart

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

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

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

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

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.