Package org.snpeff.binseq

Class DnaSequence

java.lang.Object

org.snpeff.binseq.BinarySequence

org.snpeff.binseq.DnaSequence

All Implemented Interfaces:

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

Direct Known Subclasses:

DnaNSequence, DnaSequenceId

public class DnaSequence
extends BinarySequence

Binary packed DNA sequence Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'words' (integers) - Most significant bits are the first bases in the sequence (makes comparison easier)

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
DnaSequence	clone()
int	compareTo(BinarySequence o)
static DnaSequence	empty()	Empty sequence singleton
protected DnaSequence	factory()	Create a new sequence
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
int	getCode(int index)	Return the base at position 'index'
Coder	getCoder()	Get sequence encoder & decoder
long[]	getCodes()
java.lang.String	getSequence()	Get the sequence as a String
int	hashCode()
boolean	isEmpty()	Is this sequence empty?
int	length()	Sequence lenth
BinarySequence	overlap(BinarySequence sequence, int start)	Creates a new sequence by overlapping 'this' and 'sequence' E.g.
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	set(java.lang.String seqStr, boolean ignoreErrors)
void	setBase(int index, char base)	Replace a base in the sequence
void	setCodes(long[] codes)
java.lang.String	toString()
void	write(java.io.DataOutputStream dataOutStream)	Write data in binary format

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

DnaSequence

public DnaSequence(int length,
                   long[] codes)

DnaSequence

public DnaSequence(java.lang.String seqStr)

DnaSequence

public DnaSequence(java.lang.String seqStr,
                   boolean ignoreErrors)

Method Detail

empty

public static DnaSequence empty()

Empty sequence singleton

clone

public DnaSequence clone()

Overrides:

clone in class BinarySequence

compareTo

public int compareTo(BinarySequence o)

factory

protected DnaSequence factory()

Create a new sequence

getBase

public char getBase(int index)

Description copied from class: BinarySequence

Return the base at position 'index'

Overrides:

getBase in class BinarySequence

getBases

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

Get a few bases from this sequence

getCode

public int getCode(int index)

Return the base 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

getCodes

public long[] getCodes()

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

isEmpty

public boolean isEmpty()

Is this sequence empty?

Returns:

length

public int length()

Sequence lenth

Specified by:

length in class BinarySequence

Returns:

overlap

public BinarySequence overlap(BinarySequence sequence,
                              int start)

Creates a new sequence by overlapping 'this' and 'sequence' E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO | other.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| this.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO | |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| Another case is when a sequence is fully included in the other sequence. In this case the result is just a copy of the longest sequence (with the quality updated) E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOzzzzzzzzz| other.sequence : | OOOOOOOOOOOOOOO | | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOzzzzzzzzz| this.sequence : | OOOOOOOOOOO | other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOzzzzzzzzzzzzz| |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOzzzzzzzzzzzzz|

Overrides:

overlap in class BinarySequence

Parameters:

start -

Returns:

A new sequence

read

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

Read data in binary format

Specified by:

read in class BinarySequence

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

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)

Set sequence

Specified by:

set in class BinarySequence

set

public void set(java.lang.String seqStr,
                boolean ignoreErrors)

setBase

public void setBase(int index,
                    char base)

Replace a base in the sequence

setCodes

public void setCodes(long[] codes)

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

Throws:

java.io.IOException