org.biojava.bio.program.gff
Class GFFErrorHandler.SkipRecordErrorHandler
java.lang.Object
org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
- All Implemented Interfaces:
- GFFErrorHandler
- Enclosing class:
- GFFErrorHandler
- public static class GFFErrorHandler.SkipRecordErrorHandler
- 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.SkipRecordErrorHandler
public GFFErrorHandler.SkipRecordErrorHandler()
invalidStart
public int invalidStart(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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.