Package org.snpeff.binseq
Class DnaNSequence
java.lang.Object
org.snpeff.binseq.BinarySequence
org.snpeff.binseq.DnaSequence
org.snpeff.binseq.DnaNSequence
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<BinarySequence>
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
- Author:
- pcingola
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic DnaNSequence
empty()
Empty sequence singletonprotected DnaNSequence
factory()
Create sequenceschar
getBase
(int index) Return the base at position 'index'getBases
(int index, int len) Get a few bases from this sequenceread
(DataInputStream dataInStream) Read data in binary formatprotected void
readDataStream
(DataInputStream dataInStream) Read data in binary formatReverse Watson-Cricks complementvoid
Set sequencevoid
setBase
(int index, char base) Replace a base in the sequencetoString()
void
write
(DataOutputStream dataOutStream) Write data in binary formatMethods 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
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Constructor Details
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DnaNSequence
public DnaNSequence(int length, long[] codes) -
DnaNSequence
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Method Details
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empty
Empty sequence singleton -
factory
Create sequences- Overrides:
factory
in classDnaSequence
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getBase
public char getBase(int index) Description copied from class:BinarySequence
Return the base at position 'index'- Overrides:
getBase
in classDnaSequence
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getBases
Get a few bases from this sequence- Overrides:
getBases
in classDnaSequence
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read
Read data in binary format- Overrides:
read
in classDnaSequence
- Throws:
IOException
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readDataStream
Read data in binary format- Overrides:
readDataStream
in classDnaSequence
- Throws:
IOException
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reverseWc
Description copied from class:BinarySequence
Reverse Watson-Cricks complement- Overrides:
reverseWc
in classDnaSequence
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set
Description copied from class:DnaSequence
Set sequence- Overrides:
set
in classDnaSequence
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setBase
public void setBase(int index, char base) Replace a base in the sequence- Overrides:
setBase
in classDnaSequence
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toString
- Overrides:
toString
in classDnaSequence
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write
Write data in binary format- Overrides:
write
in classDnaSequence
- Throws:
IOException
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