Package org.bdgenomics.formats.avro

Class OntologyTerm

  • All Implemented Interfaces:
    Externalizable, Serializable, Comparable<org.apache.avro.specific.SpecificRecord>, org.apache.avro.generic.GenericContainer, org.apache.avro.generic.GenericRecord, org.apache.avro.generic.IndexedRecord, org.apache.avro.specific.SpecificRecord
    public class OntologyTerm
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
    Ontology term cross reference in GFF3 style DBTAG:ID format.
    See Also:
    Serialized Form

    • Field Detail

      • SCHEMA$

        public static final org.apache.avro.Schema SCHEMA$

    • Constructor Detail

      • OntologyTerm

        public OntologyTerm()
        Default constructor. Note that this does not initialize fields to their default values from the schema. If that is desired then one should use newBuilder().

      • OntologyTerm

        public OntologyTerm​(String db,
                    String accession)
        All-args constructor.
        Parameters:
        db - Ontology abbreviation in GFF3 style DBTAG:ID format, e.g. GO in GO:0046703.
        accession - Ontology term accession number or identifer in GFF3 style DBTAG:ID format, e.g. 0046703 in GO:0046703.

    • Method Detail

      • getClassSchema

        public static org.apache.avro.Schema getClassSchema()

      • getEncoder

        public static org.apache.avro.message.BinaryMessageEncoder<OntologyTerm> getEncoder()
        Return the BinaryMessageEncoder instance used by this class.
        Returns:
        the message encoder used by this class

      • getDecoder

        public static org.apache.avro.message.BinaryMessageDecoder<OntologyTerm> getDecoder()
        Return the BinaryMessageDecoder instance used by this class.
        Returns:
        the message decoder used by this class

      • createDecoder

        public static org.apache.avro.message.BinaryMessageDecoder<OntologyTerm> createDecoder​(org.apache.avro.message.SchemaStore resolver)
        Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.
        Parameters:
        resolver - a SchemaStore used to find schemas by fingerprint
        Returns:
        a BinaryMessageDecoder instance for this class backed by the given SchemaStore

      • toByteBuffer

        public ByteBuffer toByteBuffer()
                        throws IOException
        Serializes this OntologyTerm to a ByteBuffer.
        Returns:
        a buffer holding the serialized data for this instance
        Throws:
        IOException - if this instance could not be serialized

      • fromByteBuffer

        public static OntologyTerm fromByteBuffer​(ByteBuffer b)
                                   throws IOException
        Deserializes a OntologyTerm from a ByteBuffer.
        Parameters:
        b - a byte buffer holding serialized data for an instance of this class
        Returns:
        a OntologyTerm instance decoded from the given buffer
        Throws:
        IOException - if the given bytes could not be deserialized into an instance of this class

      • getSpecificData

        public org.apache.avro.specific.SpecificData getSpecificData()
        Overrides:
        getSpecificData in class org.apache.avro.specific.SpecificRecordBase

      • getSchema

        public org.apache.avro.Schema getSchema()
        Specified by:
        getSchema in interface org.apache.avro.generic.GenericContainer
        Specified by:
        getSchema in class org.apache.avro.specific.SpecificRecordBase

      • get

        public Object get​(int field$)
        Specified by:
        get in interface org.apache.avro.generic.IndexedRecord
        Specified by:
        get in class org.apache.avro.specific.SpecificRecordBase

      • put

        public void put​(int field$,
                Object value$)
        Specified by:
        put in interface org.apache.avro.generic.IndexedRecord
        Specified by:
        put in class org.apache.avro.specific.SpecificRecordBase

      • getDb

        public String getDb()
        Gets the value of the 'db' field.
        Returns:
        Ontology abbreviation in GFF3 style DBTAG:ID format, e.g. GO in GO:0046703.

      • setDb

        public void setDb​(String value)
        Sets the value of the 'db' field. Ontology abbreviation in GFF3 style DBTAG:ID format, e.g. GO in GO:0046703.
        Parameters:
        value - the value to set.

      • getAccession

        public String getAccession()
        Gets the value of the 'accession' field.
        Returns:
        Ontology term accession number or identifer in GFF3 style DBTAG:ID format, e.g. 0046703 in GO:0046703.

      • setAccession

        public void setAccession​(String value)
        Sets the value of the 'accession' field. Ontology term accession number or identifer in GFF3 style DBTAG:ID format, e.g. 0046703 in GO:0046703.
        Parameters:
        value - the value to set.

      • newBuilder

        public static OntologyTerm.Builder newBuilder()
        Creates a new OntologyTerm RecordBuilder.
        Returns:
        A new OntologyTerm RecordBuilder

      • newBuilder

        public static OntologyTerm.Builder newBuilder​(OntologyTerm.Builder other)
        Creates a new OntologyTerm RecordBuilder by copying an existing Builder.
        Parameters:
        other - The existing builder to copy.
        Returns:
        A new OntologyTerm RecordBuilder

      • newBuilder

        public static OntologyTerm.Builder newBuilder​(OntologyTerm other)
        Creates a new OntologyTerm RecordBuilder by copying an existing OntologyTerm instance.
        Parameters:
        other - The existing instance to copy.
        Returns:
        A new OntologyTerm RecordBuilder

      • hasCustomCoders

        protected boolean hasCustomCoders()
        Overrides:
        hasCustomCoders in class org.apache.avro.specific.SpecificRecordBase

      • customEncode

        public void customEncode​(org.apache.avro.io.Encoder out)
                  throws IOException
        Overrides:
        customEncode in class org.apache.avro.specific.SpecificRecordBase
        Throws:
        IOException

      • customDecode

        public void customDecode​(org.apache.avro.io.ResolvingDecoder in)
                  throws IOException
        Overrides:
        customDecode in class org.apache.avro.specific.SpecificRecordBase
        Throws:
        IOException