Package 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
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
static class
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Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionint
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.invalidStrand
(String token) The `strand' field of the GFF entry was not a valid value.
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Field Details
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ABORT_PARSING
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SKIP_RECORD
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Method Details
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invalidStart
The `start' field of the GFF entry was not a valid value.- Parameters:
token
- The start token found.- Returns:
- A parsed value, if this is possible
- Throws:
ParserException
- If parsing should be abortedIgnoreRecordException
- If this record should be silently skipped.
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invalidEnd
The `end' field of the GFF entry was not a valid value.- Parameters:
token
- The end token found.- Returns:
- A parsed value, if this is possible
- Throws:
ParserException
- If parsing should be abortedIgnoreRecordException
- If this record should be silently skipped.
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invalidScore
The `score' field of the GFF entry was not a valid value.- Parameters:
token
- The score token found.- Returns:
- A parsed value, if this is possible
- Throws:
ParserException
- If parsing should be abortedIgnoreRecordException
- If this record should be silently skipped.
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invalidFrame
The `frame' field of the GFF entry was not a valid value.- Parameters:
token
- The frame token found.- Returns:
- A parsed value, if this is possible
- Throws:
ParserException
- If parsing should be abortedIgnoreRecordException
- If this record should be silently skipped.
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invalidStrand
The `strand' field of the GFF entry was not a valid value.- Parameters:
token
- The strand token found.- Returns:
- A parsed value, if this is possible
- Throws:
ParserException
- If parsing should be abortedIgnoreRecordException
- If this record should be silently skipped.
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