DnaAndQualitySequenceWithId (SnpEff 5.1 API)

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaAndQualitySequence

org.snpeff.binseq.DnaAndQualitySequenceWithId

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

public class DnaAndQualitySequenceWithId extends DnaAndQualitySequence

DnaAndQualitySequence with an ID

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor

Description

DnaAndQualitySequenceWithId(String seqStr)

DnaAndQualitySequenceWithId(String seqStr, String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant type)
Method Summary

Modifier and Type

Method

Description

static DnaAndQualitySequenceWithId

empty()

long

getId()

protected void

readDataStream(DataInputStream dataInStream)

Read data in binary format

void

write(DataOutputStream dataOutStream)

Write data in binary format

Methods inherited from class org.snpeff.binseq.DnaAndQualitySequence
compareTo, getBase, getCode, getCoder, getCodes, getQuality, getQuality, getSequence, hashCode, indexOf, lastIndexOf, length, overlap, read, reverseWc, set, set, toString

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

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

Constructor Details
- DnaAndQualitySequenceWithId
  
  public DnaAndQualitySequenceWithId(String seqStr)
- DnaAndQualitySequenceWithId
  
  public DnaAndQualitySequenceWithId(String seqStr, String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant type)
Method Details
- empty
  
  public static DnaAndQualitySequenceWithId empty()
- getId
  
  public long getId()
- readDataStream
  
  protected void readDataStream(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Overrides:
  
  readDataStream in class DnaAndQualitySequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException
- write
  
  public void write(DataOutputStream dataOutStream) throws IOException
  
  Write data in binary format
  
  Overrides:
  
  write in class DnaAndQualitySequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException