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

java.lang.Object
  extended by 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
GFFErrorHandler.SkipRecordErrorHandler()
           
 
Method Summary
 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

GFFErrorHandler.SkipRecordErrorHandler

public GFFErrorHandler.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.