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
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. |
ABORT_PARSING
public static final GFFErrorHandler ABORT_PARSING
SKIP_RECORD
public static final GFFErrorHandler SKIP_RECORD
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.