org.bdgenomics.formats.avro

Class Fragment

java.lang.Object

org.apache.avro.specific.SpecificRecordBase

org.bdgenomics.formats.avro.Fragment

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 Fragment
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Fragment.Builder RecordBuilder for Fragment instances.

Field Summary

Fields

Modifier and Type	Field and Description
List<Alignment>	alignments Deprecated.
Integer	insertSize Deprecated.
String	name Deprecated.
String	readGroupId Deprecated.
static org.apache.avro.Schema	SCHEMA$

Constructor Summary

Constructors

Constructor and Description
Fragment() Default constructor.
Fragment(String name, String readGroupId, Integer insertSize, List<Alignment> alignments) All-args constructor.

Method Summary

Modifier and Type	Method and Description
static org.apache.avro.message.BinaryMessageDecoder<Fragment>	createDecoder(org.apache.avro.message.SchemaStore resolver) Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.
static Fragment	fromByteBuffer(ByteBuffer b) Deserializes a Fragment from a ByteBuffer.
Object	get(int field$)
List<Alignment>	getAlignments() Gets the value of the 'alignments' field.
static org.apache.avro.Schema	getClassSchema()
static org.apache.avro.message.BinaryMessageDecoder<Fragment>	getDecoder() Return the BinaryMessageDecoder instance used by this class.
Integer	getInsertSize() Gets the value of the 'insertSize' field.
String	getName() Gets the value of the 'name' field.
String	getReadGroupId() Gets the value of the 'readGroupId' field.
org.apache.avro.Schema	getSchema()
static Fragment.Builder	newBuilder() Creates a new Fragment RecordBuilder.
static Fragment.Builder	newBuilder(Fragment.Builder other) Creates a new Fragment RecordBuilder by copying an existing Builder.
static Fragment.Builder	newBuilder(Fragment other) Creates a new Fragment RecordBuilder by copying an existing Fragment instance.
void	put(int field$, Object value$)
void	readExternal(ObjectInput in)
void	setAlignments(List<Alignment> value) Sets the value of the 'alignments' field.
void	setInsertSize(Integer value) Sets the value of the 'insertSize' field.
void	setName(String value) Sets the value of the 'name' field.
void	setReadGroupId(String value) Sets the value of the 'readGroupId' field.
ByteBuffer	toByteBuffer() Serializes this Fragment to a ByteBuffer.
void	writeExternal(ObjectOutput out)

Methods inherited from class org.apache.avro.specific.SpecificRecordBase

compareTo, equals, get, getConverion, getConversion, getConversion, hashCode, put, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

SCHEMA$

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

name

@Deprecated
public String name

Deprecated.

Name of this fragment.

readGroupId

@Deprecated
public String readGroupId

Deprecated.

Read group identifier for this fragment. Join with ReadGroup.id for read group metadata.

insertSize

@Deprecated
public Integer insertSize

Deprecated.

Insert size for this fragment, derived from alignment, if the reads have been aligned.

alignments

@Deprecated
public List<Alignment> alignments

Deprecated.

Reads from this fragment.

Constructor Detail

Fragment

public Fragment()

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().

Fragment

public Fragment(String name,
                String readGroupId,
                Integer insertSize,
                List<Alignment> alignments)

All-args constructor.

Parameters:

name - Name of this fragment.

readGroupId - Read group identifier for this fragment. Join with ReadGroup.id for read group metadata.

insertSize - Insert size for this fragment, derived from alignment, if the reads have been aligned.

alignments - Reads from this fragment.

Method Detail

getClassSchema

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

getDecoder

public static org.apache.avro.message.BinaryMessageDecoder<Fragment> getDecoder()

Return the BinaryMessageDecoder instance used by this class.

createDecoder

public static org.apache.avro.message.BinaryMessageDecoder<Fragment> 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

toByteBuffer

public ByteBuffer toByteBuffer()
                        throws IOException

Serializes this Fragment to a ByteBuffer.

Throws:

IOException

fromByteBuffer

public static Fragment fromByteBuffer(ByteBuffer b)
                               throws IOException

Deserializes a Fragment from a ByteBuffer.

Throws:

IOException

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 fragment.

setName

public void setName(String value)

Sets the value of the 'name' field. Name of this fragment.

Parameters:

value - the value to set.

getReadGroupId

public String getReadGroupId()

Gets the value of the 'readGroupId' field.

Returns:

Read group identifier for this fragment. Join with ReadGroup.id for read group metadata.

setReadGroupId

public void setReadGroupId(String value)

Sets the value of the 'readGroupId' field. Read group identifier for this fragment. Join with ReadGroup.id for read group metadata.

Parameters:

value - the value to set.

getInsertSize

public Integer getInsertSize()

Gets the value of the 'insertSize' field.

Returns:

Insert size for this fragment, derived from alignment, if the reads have been aligned.

setInsertSize

public void setInsertSize(Integer value)

Sets the value of the 'insertSize' field. Insert size for this fragment, derived from alignment, if the reads have been aligned.

Parameters:

value - the value to set.

getAlignments

public List<Alignment> getAlignments()

Gets the value of the 'alignments' field.

Returns:

Reads from this fragment.

setAlignments

public void setAlignments(List<Alignment> value)

Sets the value of the 'alignments' field. Reads from this fragment.

Parameters:

value - the value to set.

newBuilder

public static Fragment.Builder newBuilder()

Creates a new Fragment RecordBuilder.

Returns:

A new Fragment RecordBuilder

newBuilder

public static Fragment.Builder newBuilder(Fragment.Builder other)

Creates a new Fragment RecordBuilder by copying an existing Builder.

Parameters:

other - The existing builder to copy.

Returns:

A new Fragment RecordBuilder

newBuilder

public static Fragment.Builder newBuilder(Fragment other)

Creates a new Fragment RecordBuilder by copying an existing Fragment instance.

Parameters:

other - The existing instance to copy.

Returns:

A new Fragment RecordBuilder

writeExternal

public void writeExternal(ObjectOutput out)
                   throws IOException

Specified by:

writeExternal in interface Externalizable

Overrides:

writeExternal in class org.apache.avro.specific.SpecificRecordBase

Throws:

IOException

readExternal

public void readExternal(ObjectInput in)
                  throws IOException

Specified by:

readExternal in interface Externalizable

Overrides:

readExternal in class org.apache.avro.specific.SpecificRecordBase

Throws:

IOException