org.biojava.bio.program.gff
Class GFFErrorHandler.AbortErrorHandler
java.lang.Object
|
+--org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
- Enclosing class:
- GFFErrorHandler
- public static class GFFErrorHandler.AbortErrorHandler
- extends java.lang.Object
- implements GFFErrorHandler
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. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
GFFErrorHandler.AbortErrorHandler
public GFFErrorHandler.AbortErrorHandler()
invalidStart
public int invalidStart(java.lang.String token)
throws ParserException
- Description copied from interface: GFFErrorHandler
- The `start' field of the GFF entry was not a valid value.
- Specified by:
- invalidStart in interface GFFErrorHandler
- Tags copied from interface: GFFErrorHandler
- 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
- Description copied from interface: GFFErrorHandler
- The `end' field of the GFF entry was not a valid value.
- Specified by:
- invalidEnd in interface GFFErrorHandler
- Tags copied from interface: GFFErrorHandler
- 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
- Description copied from interface: GFFErrorHandler
- The `score' field of the GFF entry was not a valid value.
- Specified by:
- invalidScore in interface GFFErrorHandler
- Tags copied from interface: GFFErrorHandler
- 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
- Description copied from interface: GFFErrorHandler
- The `frame' field of the GFF entry was not a valid value.
- Specified by:
- invalidFrame in interface GFFErrorHandler
- Tags copied from interface: GFFErrorHandler
- 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
- Description copied from interface: GFFErrorHandler
- The `strand' field of the GFF entry was not a valid value.
- Specified by:
- invalidStrand in interface GFFErrorHandler
- Tags copied from interface: GFFErrorHandler
- Parameters:
token
- The strand token found.- Throws:
- ParserException - If parsing should be aborted
- IgnoreRecordException - If this record should be silently skipped.