java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaSequencePe

All Implemented Interfaces:: Serializable, Cloneable, 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 final Coder

coder
Constructor Summary

Constructors

Constructor

Description

DnaSequencePe(String seqStr)

DnaSequencePe(String seqStr1, 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()

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(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 from a string

void

setGap(int gap)

String

toString()

void

write(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 Details
- coder
  
  public static final Coder coder
Constructor Details
- DnaSequencePe
  
  public DnaSequencePe(String seqStr)
- DnaSequencePe
  
  public DnaSequencePe(String seqStr1, String seqStr2, int gap)
Method Details
- 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 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(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Specified by:
  
  read in class BinarySequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException
- readDataStream
  
  protected void readDataStream(DataInputStream dataInStream) throws IOException
  
  Read data in binary format
  
  Specified by:
  
  readDataStream in class BinarySequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException
- reverseWc
  
  public BinarySequence reverseWc()
  
  Description copied from class: BinarySequence
  
  Reverse Watson-Cricks complement
  
  Specified by:
  
  reverseWc in class BinarySequence
- set
  
  public void set(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 String toString()
  
  Overrides:
  
  toString in class Object
- write
  
  public void write(DataOutputStream dataOutStream) throws IOException
  
  Write data in binary format
  
  Specified by:
  
  write in class BinarySequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  IOException

Class DnaSequencePe

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.binseq.BinarySequence

Methods inherited from class java.lang.Object

Field Details

coder

Constructor Details

DnaSequencePe

DnaSequencePe

Method Details

compareTo

getCode

getCoder

getGap

getSeq1

getSeq2

getSequence

hashCode

intLen

length

read

readDataStream

reverseWc

set

setGap

toString

write