Package org.snpeff.binseq

Class DnaSequencePe

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaSequencePe

All Implemented Interfaces:

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

public class DnaSequencePe
extends BinarySequence

Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.

Author:

pcingola

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static Coder	coder

Constructor Summary

Constructors

Constructor	Description
DnaSequencePe(java.lang.String seqStr)
DnaSequencePe(java.lang.String seqStr1, java.lang.String seqStr2, int gap)

Method Summary

Modifier and Type	Method	Description
int	compareTo(BinarySequence o)
int	getCode(int index)	Return the code at position 'index'
Coder	getCoder()	Get sequence encoder & decoder
int	getGap()
DnaSequence	getSeq1()
DnaSequence	getSeq2()
java.lang.String	getSequence()	Get the sequence as a String
int	hashCode()
int	intLen(int len)	Calculate the length of a sequence
int	length()	Get sequence length
DnaSequencePe	read(java.io.DataInputStream dataInStream)	Read data in binary format
protected void	readDataStream(java.io.DataInputStream dataInStream)	Read data in binary format
BinarySequence	reverseWc()	Reverse Watson-Cricks complement
void	set(java.lang.String seqStr)	Set sequence from a string
void	setGap(int gap)
java.lang.String	toString()
void	write(java.io.DataOutputStream dataOutStream)	Write data in binary format

Methods inherited from class org.snpeff.binseq.BinarySequence

clone, getBase, overlap, setQuality

Methods inherited from class java.lang.Object

equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

coder

public static final Coder coder

Constructor Detail

DnaSequencePe

public DnaSequencePe(java.lang.String seqStr)

DnaSequencePe

public DnaSequencePe(java.lang.String seqStr1,
                     java.lang.String seqStr2,
                     int gap)

Method Detail

compareTo

public int compareTo(BinarySequence o)

getCode

public int getCode(int index)

Description copied from class: BinarySequence

Return the code at position 'index'

Specified by:

getCode in class BinarySequence

getCoder

public Coder getCoder()

Description copied from class: BinarySequence

Get sequence encoder & decoder

Specified by:

getCoder in class BinarySequence

getGap

public int getGap()

getSeq1

public DnaSequence getSeq1()

getSeq2

public DnaSequence getSeq2()

getSequence

public java.lang.String getSequence()

Description copied from class: BinarySequence

Get the sequence as a String

Specified by:

getSequence in class BinarySequence

hashCode

public int hashCode()

Specified by:

hashCode in class BinarySequence

intLen

public int intLen(int len)

Calculate the length of a sequence

Parameters:

len -

Returns:

length

public int length()

Description copied from class: BinarySequence

Get sequence length

Specified by:

length in class BinarySequence

read

public DnaSequencePe read(java.io.DataInputStream dataInStream)
                   throws java.io.IOException

Read data in binary format

Specified by:

read in class BinarySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException

readDataStream

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

Read data in binary format

Specified by:

readDataStream in class BinarySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException

reverseWc

public BinarySequence reverseWc()

Description copied from class: BinarySequence

Reverse Watson-Cricks complement

Specified by:

reverseWc in class BinarySequence

set

public void set(java.lang.String seqStr)

Description copied from class: BinarySequence

Set sequence from a string

Specified by:

set in class BinarySequence

setGap

public void setGap(int gap)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

write

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

Write data in binary format

Specified by:

write in class BinarySequence

Parameters:

dataOutStream -

Throws:

java.io.IOException