DnaSequenceId (SnpEff 5.2 API)

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaSequence

org.snpeff.binseq.DnaSequenceId

All Implemented Interfaces:: Serializable, Cloneable, Comparable<BinarySequence>

public class DnaSequenceId extends DnaSequence

Binary packed DNA sequence with an ID (long)

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor

Description

DnaSequenceId(long id, int length, long[] codes)

DnaSequenceId(long id, String seqStr)

DnaSequenceId(String seqStr)
Method Summary

Modifier and Type

Method

Description

static DnaSequenceId

empty()

Empty sequence singleton

protected DnaSequence

factory()

Create sequences

long

getId()

BinarySequence

read(DataInputStream dataInStream)

Read data in binary format

protected void

readDataStream(DataInputStream dataInStream)

Read data in binary format

String

toString()

void

write(DataOutputStream dataOutStream)

Write data in binary format

Methods inherited from class org.snpeff.binseq.DnaSequence
clone, compareTo, getBase, getBases, getCode, getCoder, getCodes, getSequence, hashCode, isEmpty, length, overlap, reverseWc, set, set, setBase, setCodes

Methods inherited from class org.snpeff.binseq.BinarySequence
setQuality

Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details
- DnaSequenceId
  
  public DnaSequenceId(long id, int length, long[] codes)
- DnaSequenceId
  
  public DnaSequenceId(long id, String seqStr)
- DnaSequenceId
  
  public DnaSequenceId(String seqStr)
Method Details
- empty
  
  public static DnaSequenceId empty()
  
  Empty sequence singleton
  
  Returns:
- factory
  
  protected DnaSequence factory()
  
  Create sequences
  
  Overrides:
  
  factory in class DnaSequence
  
  Returns:
- getId
  
  public long getId()
- read
  
  public BinarySequence read(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Overrides:
  
  read in class DnaSequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException
- readDataStream
  
  protected void readDataStream(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Overrides:
  
  readDataStream in class DnaSequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class DnaSequence
- write
  
  public void write(DataOutputStream dataOutStream) throws IOException
  
  Write data in binary format
  
  Overrides:
  
  write in class DnaSequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException