Class GtfValidationAction
- All Implemented Interfaces:
Action
,ValidationAction
ArrayDesign
.
The validation uses the GtfInputStream
. The number of lines
to parse is configurable. If the entire file is parsed, it will
set the ArrayDesign.getNumFileFeatures()
value to the number
of unique transcript_id values found in the file.
- Since:
- 3.0
- Author:
- Nicklas
- Last modified
- $Date: 2015-04-21 08:26:57 +0200 (ti, 21 apr 2015) $
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Field Summary
Modifier and TypeFieldDescriptionprivate final DbControl
private final ArrayDesign
private final int
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Constructor Summary
ConstructorDescriptionGtfValidationAction
(DbControl dc, ArrayDesign design, int linesToParse) Create a new action. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Reset all metadata that this class normally can set.void
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
acceptFile, getAcceptedFile
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Field Details
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dc
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design
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linesToParse
private final int linesToParse
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Constructor Details
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GtfValidationAction
Create a new action.- Parameters:
dc
- An open DbControldesign
- The array design the GTF file is connected withlinesToParse
- The maximum number of lines to parse from the GTF file. UseInteger.MAX_VALUE
to ensure that the entire file is parsed. The lowest value is 10
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Method Details
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validateAndExtractMetadata
Description copied from interface:ValidationAction
Validate and extract metadata from the file(s) that has been added to this validator. If theValidationAction.acceptFile(FileSetMember)
method returnsAccept.VALIDATE_IMMEDIATELY
this 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
Accept.VALIDATE_LATER
.This method is recommended to throw an
InvalidDataException
or 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 typeInvalidRelationException
can 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.- Throws:
InvalidDataException
- If the validator detects an invalid fileInvalidRelationException
- If the validator detects that the file is valid but another file that it depends on is not, metadata extract will still happen
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resetMetadata
public void resetMetadata()Description copied from interface:ValidationAction
Reset 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.
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