Package net.sf.basedb.util.gtf

Class GtfValidationAction

java.lang.Object

net.sf.basedb.util.fileset.SingleFileValidationAction

net.sf.basedb.util.gtf.GtfValidationAction

All Implemented Interfaces:

Action, ValidationAction

public class GtfValidationAction
extends SingleFileValidationAction

Action for validation of GTF files in a file set. The GTF file must be connected with an 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) $

Field Summary

Fields

Modifier and Type	Field	Description
private DbControl	dc
private ArrayDesign	design
private int	linesToParse

Constructor Summary

Constructors

Constructor	Description
GtfValidationAction(DbControl dc, ArrayDesign design, int linesToParse)	Create a new action.

Method Summary

Modifier and Type	Method	Description
void	resetMetadata()	Reset all metadata that this class normally can set.
void	validateAndExtractMetadata()	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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

dc

private final DbControl dc

design

private final ArrayDesign design

linesToParse

private final int linesToParse

Constructor Details

GtfValidationAction

public GtfValidationAction(DbControl dc,
ArrayDesign design,
int linesToParse)

Create a new action.

Parameters:

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_VALUE to ensure that the entire file is parsed. The lowest value is 10

Method Details

validateAndExtractMetadata

public void validateAndExtractMetadata()
                                throws InvalidDataException,
InvalidRelationException

Description copied from interface: ValidationAction

Validate and extract metadata from the file(s) that has been added to this validator. If the ValidationAction.acceptFile(FileSetMember) method returns Accept.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 type InvalidRelationException 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 file

InvalidRelationException - If the validator detects that the file is valid but another file that it depends on is not, metadata extract will still happen

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.