Class SwissprotProcessor

  • All Implemented Interfaces:
    SeqIOListener, SequenceBuilder, ParseErrorSource

    public class SwissprotProcessor
    extends SequenceBuilderFilter
    implements ParseErrorSource
    Deprecated.
    Use org.biojavax.bio.seq.io framework instead
    Simple filter which handles attribute lines from an Swissprot entry. Skeleton implementation, please add more functionality.

    FIXME: Note that this is currently rather incomplete, and doesn't handle any of the header information sensibly except for ID and AC.

    Since:
    1.1
    Author:
    Thomas Down, Matthew Pocock, Greg Cox
    • Field Detail

      • PROPERTY_SWISSPROT_ACCESSIONS

        public static final java.lang.String PROPERTY_SWISSPROT_ACCESSIONS
        Deprecated.
        See Also:
        Constant Field Values
      • PROPERTY_SWISSPROT_COMMENT

        public static final java.lang.String PROPERTY_SWISSPROT_COMMENT
        Deprecated.
        See Also:
        Constant Field Values
      • PROPERTY_SWISSPROT_FEATUREATTRIBUTE

        public static final java.lang.String PROPERTY_SWISSPROT_FEATUREATTRIBUTE
        Deprecated.
        See Also:
        Constant Field Values
    • Constructor Detail

      • SwissprotProcessor

        public SwissprotProcessor​(SequenceBuilder delegate,
                                  java.lang.String theSource)
        Deprecated.
        Constructor that sets the source of the feature to theSource.
        Parameters:
        delegate - The sequecence builder to be used in constructing the sequence
        theSource - The source of the features. e.g. "SWISS-PROT", "TrEMBL"
      • SwissprotProcessor

        public SwissprotProcessor​(SequenceBuilder delegate)
        Deprecated.