Package org.snpeff.binseq

Class DnaAndQualitySequenceWithId

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaAndQualitySequence

org.snpeff.binseq.DnaAndQualitySequenceWithId

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<BinarySequence>

public class DnaAndQualitySequenceWithId
extends DnaAndQualitySequence

DnaAndQualitySequence with an ID

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DnaAndQualitySequenceWithId(java.lang.String seqStr)
DnaAndQualitySequenceWithId(java.lang.String seqStr, java.lang.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(java.io.DataInputStream dataInStream)	Read data in binary format
void	write(java.io.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 Detail

DnaAndQualitySequenceWithId

public DnaAndQualitySequenceWithId(java.lang.String seqStr)

DnaAndQualitySequenceWithId

public DnaAndQualitySequenceWithId(java.lang.String seqStr,
                                   java.lang.String qualityStr,
                                   org.biojava.nbio.genome.io.fastq.FastqVariant type)

Method Detail

empty

public static DnaAndQualitySequenceWithId empty()

getId

public long getId()

readDataStream

protected void readDataStream(java.io.DataInputStream dataInStream)
                       throws java.io.IOException

Read data in binary format

Overrides:

readDataStream in class DnaAndQualitySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException

write

public void write(java.io.DataOutputStream dataOutStream)
           throws java.io.IOException

Write data in binary format

Overrides:

write in class DnaAndQualitySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException