Package org.biojava.bio.program.gff

Class GFFErrorHandler.SkipRecordErrorHandler

java.lang.Object

org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler

All Implemented Interfaces:

GFFErrorHandler

Enclosing interface:

GFFErrorHandler

public static class GFFErrorHandler.SkipRecordErrorHandler
extends Object
implements GFFErrorHandler

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.program.gff.GFFErrorHandler

GFFErrorHandler.AbortErrorHandler, GFFErrorHandler.SkipRecordErrorHandler

Field Summary

Fields inherited from interface org.biojava.bio.program.gff.GFFErrorHandler

ABORT_PARSING, SKIP_RECORD

Constructor Summary

Constructors

Constructor	Description
SkipRecordErrorHandler()

Method Summary

Modifier and Type	Method	Description
int	invalidEnd(String token)	The `end' field of the GFF entry was not a valid value.
int	invalidFrame(String token)	The `frame' field of the GFF entry was not a valid value.
double	invalidScore(String token)	The `score' field of the GFF entry was not a valid value.
int	invalidStart(String token)	The `start' field of the GFF entry was not a valid value.
StrandedFeature.Strand	invalidStrand(String token)	The `strand' field of the GFF entry was not a valid value.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SkipRecordErrorHandler

public SkipRecordErrorHandler()

Method Detail

invalidStart

public int invalidStart(String token)
                 throws IgnoreRecordException

Description copied from interface: GFFErrorHandler

The `start' field of the GFF entry was not a valid value.

Specified by:

invalidStart in interface GFFErrorHandler

Parameters:

token - The start token found.

Returns:

A parsed value, if this is possible

Throws:

IgnoreRecordException - If this record should be silently skipped.

invalidEnd

public int invalidEnd(String token)
               throws IgnoreRecordException

Description copied from interface: GFFErrorHandler

The `end' field of the GFF entry was not a valid value.

Specified by:

invalidEnd in interface GFFErrorHandler

Parameters:

token - The end token found.

Returns:

A parsed value, if this is possible

Throws:

IgnoreRecordException - If this record should be silently skipped.

invalidScore

public double invalidScore(String token)
                    throws IgnoreRecordException

Description copied from interface: GFFErrorHandler

The `score' field of the GFF entry was not a valid value.

Specified by:

invalidScore in interface GFFErrorHandler

Parameters:

token - The score token found.

Returns:

A parsed value, if this is possible

Throws:

IgnoreRecordException - If this record should be silently skipped.

invalidFrame

public int invalidFrame(String token)
                 throws IgnoreRecordException

Description copied from interface: GFFErrorHandler

The `frame' field of the GFF entry was not a valid value.

Specified by:

invalidFrame in interface GFFErrorHandler

Parameters:

token - The frame token found.

Returns:

A parsed value, if this is possible

Throws:

IgnoreRecordException - If this record should be silently skipped.

invalidStrand

public StrandedFeature.Strand invalidStrand(String token)
                                     throws IgnoreRecordException

Description copied from interface: GFFErrorHandler

The `strand' field of the GFF entry was not a valid value.

Specified by:

invalidStrand in interface GFFErrorHandler

Parameters:

token - The strand token found.

Returns:

A parsed value, if this is possible

Throws:

IgnoreRecordException - If this record should be silently skipped.