org.snpeff.binseq.DnaNSequence

All Implemented Interfaces:: Serializable, Cloneable, 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(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'

String

getBases(int index, int len)

Get a few bases from this sequence

BinarySequence

read(DataInputStream dataInStream)

Read data in binary format

protected void

readDataStream(DataInputStream dataInStream)

Read data in binary format

BinarySequence

reverseWc()

Reverse Watson-Cricks complement

void

set(String seqStr)

Set sequence

void

setBase(int index, char base)

Replace a base in the sequence

String

toString()

void

write(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 Details
- DnaNSequence
  
  public DnaNSequence(int length, long[] codes)
- DnaNSequence
  
  public DnaNSequence(String seqStr)
Method Details
- 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 String getBases(int index, int len)
  
  Get a few bases from this sequence
  
  Overrides:
  
  getBases in class DnaSequence
- read
  
  public BinarySequence read(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Overrides:
  
  read in class DnaSequence
  
  Throws:
  
  IOException
- readDataStream
  
  protected void readDataStream(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Overrides:
  
  readDataStream in class DnaSequence
  
  Throws:
  
  IOException
- reverseWc
  
  public BinarySequence reverseWc()
  
  Description copied from class: BinarySequence
  
  Reverse Watson-Cricks complement
  
  Overrides:
  
  reverseWc in class DnaSequence
- set
  
  public void set(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 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
  
  Throws:
  
  IOException

Class DnaNSequence

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.binseq.DnaSequence

Methods inherited from class org.snpeff.binseq.BinarySequence

Methods inherited from class java.lang.Object

Constructor Details

DnaNSequence

DnaNSequence

Method Details

empty

factory

getBase

getBases

read

readDataStream

reverseWc

set

setBase

toString

write