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