Class 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 Detail

      • linesToParse

        private final int linesToParse
    • Constructor Detail

      • 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 Detail

      • 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.