public class GtfValidationAction extends SingleFileValidationAction
The validation uses the
GtfInputStream. The number of lines
to parse is configurable. If the entire file is parsed, it will
ArrayDesign.getNumFileFeatures() value to the number
of unique transcript_id values found in the file.
- Last modified
- $Date: 2015-04-21 08:26:57 +0200 (ti, 21 apr 2015) $
Modifier and Type Method Description
()Reset all metadata that this class normally can set.
()Validate and extract metadata from the file(s) that has been added to this validator.
Methods inherited from class net.sf.basedb.util.fileset.SingleFileValidationAction
GtfValidationActionCreate a new action.
dc- An open DbControl
design- The array design the GTF file is connected with
linesToParse- The maximum number of lines to parse from the GTF file. Use
Integer.MAX_VALUEto ensure that the entire file is parsed. The lowest value is 10
validateAndExtractMetadataDescription copied from interface:
ValidationActionValidate and extract metadata from the file(s) that has been added to this validator. If the
Accept.VALIDATE_IMMEDIATELYthis method is called and the validator should work on the last accepted file.
This method is also called after all files has been processed if at least one file returned
This method is recommended to throw an
InvalidDataExceptionor a subclass if the file is not a valid file.
PermissionDeniedException:s are ignored by the core and will not change the validation status. An exception of type
InvalidRelationExceptioncan be thrown if the file itself is valid, but a related file that it depends on is not. The core will still mark the file as invalid and store the error message, but extracted metadata will not be reset.
resetMetadatapublic void resetMetadata()Description copied from interface:
ValidationActionReset all metadata that this class normally can set. This method is called if the validation of a file failed or if a file is removed from the file set. Any previous metadata that may signal that a valid file is present should be reset.