Package org.snpeff.binseq

Class DnaNSequence

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaSequence

org.snpeff.binseq.DnaNSequence

All Implemented Interfaces:

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

public class DnaNSequence
extends DnaSequence

Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DnaNSequence(int length, long[] codes)
DnaNSequence(java.lang.String seqStr)

Method Summary

Modifier and Type	Method	Description
static DnaNSequence	empty()	Empty sequence singleton
protected DnaNSequence	factory()	Create sequences
char	getBase(int index)	Return the base at position 'index'
java.lang.String	getBases(int index, int len)	Get a few bases from this sequence
BinarySequence	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
void	setBase(int index, char base)	Replace a base in the sequence
java.lang.String	toString()
void	write(java.io.DataOutputStream dataOutStream)	Write data in binary format

Methods inherited from class org.snpeff.binseq.DnaSequence

clone, compareTo, getCode, getCoder, getCodes, getSequence, hashCode, isEmpty, length, overlap, set, 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 Detail

DnaNSequence

public DnaNSequence(int length,
                    long[] codes)

DnaNSequence

public DnaNSequence(java.lang.String seqStr)

Method Detail

empty

public static DnaNSequence empty()

Empty sequence singleton

factory

protected DnaNSequence factory()

Create sequences

Overrides:

factory in class DnaSequence

getBase

public char getBase(int index)

Description copied from class: BinarySequence

Return the base at position 'index'

Overrides:

getBase in class DnaSequence

getBases

public java.lang.String getBases(int index,
                                 int len)

Get a few bases from this sequence

Overrides:

getBases in class DnaSequence

read

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

Read data in binary format

Overrides:

read in class DnaSequence

Throws:

java.io.IOException

readDataStream

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

Read data in binary format

Overrides:

readDataStream in class DnaSequence

Throws:

java.io.IOException

reverseWc

public BinarySequence reverseWc()

Description copied from class: BinarySequence

Reverse Watson-Cricks complement

Overrides:

reverseWc in class DnaSequence

set

public void set(java.lang.String seqStr)

Description copied from class: DnaSequence

Set sequence

Overrides:

set in class DnaSequence

setBase

public void setBase(int index,
                    char base)

Replace a base in the sequence

Overrides:

setBase in class DnaSequence

toString

public java.lang.String toString()

Overrides:

toString in class DnaSequence

write

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

Write data in binary format

Overrides:

write in class DnaSequence

Throws:

java.io.IOException