Package org.snpeff.binseq
Class DnaSequenceId
java.lang.Object
org.snpeff.binseq.BinarySequence
org.snpeff.binseq.DnaSequence
org.snpeff.binseq.DnaSequenceId
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<BinarySequence>
Binary packed DNA sequence with an ID (long)
- Author:
- pcingola
- See Also:
-
Constructor Summary
ConstructorsConstructorDescriptionDnaSequenceId
(long id, int length, long[] codes) DnaSequenceId
(long id, String seqStr) DnaSequenceId
(String seqStr) -
Method Summary
Modifier and TypeMethodDescriptionstatic DnaSequenceId
empty()
Empty sequence singletonprotected DnaSequence
factory()
Create sequenceslong
getId()
read
(DataInputStream dataInStream) Read data in binary formatprotected void
readDataStream
(DataInputStream dataInStream) Read data in binary formattoString()
void
write
(DataOutputStream dataOutStream) Write data in binary formatMethods inherited from class org.snpeff.binseq.DnaSequence
clone, compareTo, getBase, getBases, getCode, getCoder, getCodes, getSequence, hashCode, isEmpty, length, overlap, reverseWc, set, set, setBase, setCodes
Methods inherited from class org.snpeff.binseq.BinarySequence
setQuality
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Constructor Details
-
DnaSequenceId
public DnaSequenceId(long id, int length, long[] codes) -
DnaSequenceId
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DnaSequenceId
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Method Details
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empty
Empty sequence singleton- Returns:
-
factory
Create sequences- Overrides:
factory
in classDnaSequence
- Returns:
-
getId
public long getId() -
read
Read data in binary format- Overrides:
read
in classDnaSequence
- Parameters:
dataOutStream
-- Throws:
IOException
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readDataStream
Read data in binary format- Overrides:
readDataStream
in classDnaSequence
- Parameters:
dataOutStream
-- Throws:
IOException
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toString
- Overrides:
toString
in classDnaSequence
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write
Write data in binary format- Overrides:
write
in classDnaSequence
- Parameters:
dataOutStream
-- Throws:
IOException
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