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
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static DnaNSequence
empty()
Empty sequence singletonprotected DnaNSequence
factory()
Create sequenceschar
getBase(int index)
Return the base at position 'index'java.lang.String
getBases(int index, int len)
Get a few bases from this sequenceBinarySequence
read(java.io.DataInputStream dataInStream)
Read data in binary formatprotected void
readDataStream(java.io.DataInputStream dataInStream)
Read data in binary formatBinarySequence
reverseWc()
Reverse Watson-Cricks complementvoid
set(java.lang.String seqStr)
Set sequencevoid
setBase(int index, char base)
Replace a base in the sequencejava.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
-
-
-
-
Method Detail
-
empty
public static DnaNSequence empty()
Empty sequence singleton
-
factory
protected DnaNSequence factory()
Create sequences- Overrides:
factory
in classDnaSequence
-
getBase
public char getBase(int index)
Description copied from class:BinarySequence
Return the base at position 'index'- Overrides:
getBase
in classDnaSequence
-
getBases
public java.lang.String getBases(int index, int len)
Get a few bases from this sequence- Overrides:
getBases
in classDnaSequence
-
read
public BinarySequence read(java.io.DataInputStream dataInStream) throws java.io.IOException
Read data in binary format- Overrides:
read
in classDnaSequence
- Throws:
java.io.IOException
-
readDataStream
protected void readDataStream(java.io.DataInputStream dataInStream) throws java.io.IOException
Read data in binary format- Overrides:
readDataStream
in classDnaSequence
- Throws:
java.io.IOException
-
reverseWc
public BinarySequence reverseWc()
Description copied from class:BinarySequence
Reverse Watson-Cricks complement- Overrides:
reverseWc
in classDnaSequence
-
set
public void set(java.lang.String seqStr)
Description copied from class:DnaSequence
Set sequence- Overrides:
set
in classDnaSequence
-
setBase
public void setBase(int index, char base)
Replace a base in the sequence- Overrides:
setBase
in classDnaSequence
-
toString
public java.lang.String toString()
- Overrides:
toString
in classDnaSequence
-
write
public void write(java.io.DataOutputStream dataOutStream) throws java.io.IOException
Write data in binary format- Overrides:
write
in classDnaSequence
- Throws:
java.io.IOException
-
-