Package org.bdgenomics.formats.avro

Class Sequence

  • 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 Sequence
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
    Contiguous sequence from an alphabet, e.g. a DNA contig, an RNA transcript, or a protein translation.
    See Also:
    Serialized Form

    • Field Detail

      • SCHEMA$

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

    • Constructor Detail

      • Sequence

        public Sequence()
        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().

      • Sequence

        public Sequence​(String name,
                String description,
                Alphabet alphabet,
                String sequence,
                Long length,
                String sampleId,
                Map<String,​String> attributes)
        All-args constructor.
        Parameters:
        name - Name of this sequence.
        description - Description for this sequence.
        alphabet - Alphabet for this sequence, defaults to Alphabet.DNA.
        sequence - Sequence.
        length - Length of this sequence.
        sampleId - Sample identifier for this sequence. Join with Sample.id for sample metadata.
        attributes - Map of attributes.

    • Method Detail

      • getClassSchema

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

      • getEncoder

        public static org.apache.avro.message.BinaryMessageEncoder<Sequence> 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<Sequence> 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<Sequence> 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 Sequence 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 Sequence fromByteBuffer​(ByteBuffer b)
                               throws IOException
        Deserializes a Sequence from a ByteBuffer.
        Parameters:
        b - a byte buffer holding serialized data for an instance of this class
        Returns:
        a Sequence 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

      • getName

        public String getName()
        Gets the value of the 'name' field.
        Returns:
        Name of this sequence.

      • setName

        public void setName​(String value)
        Sets the value of the 'name' field. Name of this sequence.
        Parameters:
        value - the value to set.

      • getDescription

        public String getDescription()
        Gets the value of the 'description' field.
        Returns:
        Description for this sequence.

      • setDescription

        public void setDescription​(String value)
        Sets the value of the 'description' field. Description for this sequence.
        Parameters:
        value - the value to set.

      • getAlphabet

        public Alphabet getAlphabet()
        Gets the value of the 'alphabet' field.
        Returns:
        Alphabet for this sequence, defaults to Alphabet.DNA.

      • setAlphabet

        public void setAlphabet​(Alphabet value)
        Sets the value of the 'alphabet' field. Alphabet for this sequence, defaults to Alphabet.DNA.
        Parameters:
        value - the value to set.

      • getSequence

        public String getSequence()
        Gets the value of the 'sequence' field.
        Returns:
        Sequence.

      • setSequence

        public void setSequence​(String value)
        Sets the value of the 'sequence' field. Sequence.
        Parameters:
        value - the value to set.

      • getLength

        public Long getLength()
        Gets the value of the 'length' field.
        Returns:
        Length of this sequence.

      • setLength

        public void setLength​(Long value)
        Sets the value of the 'length' field. Length of this sequence.
        Parameters:
        value - the value to set.

      • getSampleId

        public String getSampleId()
        Gets the value of the 'sampleId' field.
        Returns:
        Sample identifier for this sequence. Join with Sample.id for sample metadata.

      • setSampleId

        public void setSampleId​(String value)
        Sets the value of the 'sampleId' field. Sample identifier for this sequence. Join with Sample.id for sample metadata.
        Parameters:
        value - the value to set.

      • getAttributes

        public Map<String,​String> getAttributes()
        Gets the value of the 'attributes' field.
        Returns:
        Map of attributes.

      • setAttributes

        public void setAttributes​(Map<String,​String> value)
        Sets the value of the 'attributes' field. Map of attributes.
        Parameters:
        value - the value to set.

      • newBuilder

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

      • newBuilder

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

      • newBuilder

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