Package org.snpeff.binseq
Class DnaSequencePe
- java.lang.Object
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- org.snpeff.binseq.BinarySequence
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- org.snpeff.binseq.DnaSequencePe
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,java.lang.Comparable<BinarySequence>
public class DnaSequencePe extends BinarySequence
Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.- Author:
- pcingola
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description DnaSequencePe(java.lang.String seqStr)
DnaSequencePe(java.lang.String seqStr1, java.lang.String seqStr2, int gap)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
compareTo(BinarySequence o)
int
getCode(int index)
Return the code at position 'index'Coder
getCoder()
Get sequence encoder & decoderint
getGap()
DnaSequence
getSeq1()
DnaSequence
getSeq2()
java.lang.String
getSequence()
Get the sequence as a Stringint
hashCode()
int
intLen(int len)
Calculate the length of a sequenceint
length()
Get sequence lengthDnaSequencePe
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 sequence from a stringvoid
setGap(int gap)
java.lang.String
toString()
void
write(java.io.DataOutputStream dataOutStream)
Write data in binary format-
Methods inherited from class org.snpeff.binseq.BinarySequence
clone, getBase, overlap, setQuality
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Field Detail
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coder
public static final Coder coder
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Method Detail
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compareTo
public int compareTo(BinarySequence o)
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getCode
public int getCode(int index)
Description copied from class:BinarySequence
Return the code at position 'index'- Specified by:
getCode
in classBinarySequence
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getCoder
public Coder getCoder()
Description copied from class:BinarySequence
Get sequence encoder & decoder- Specified by:
getCoder
in classBinarySequence
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getGap
public int getGap()
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getSeq1
public DnaSequence getSeq1()
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getSeq2
public DnaSequence getSeq2()
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getSequence
public java.lang.String getSequence()
Description copied from class:BinarySequence
Get the sequence as a String- Specified by:
getSequence
in classBinarySequence
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hashCode
public int hashCode()
- Specified by:
hashCode
in classBinarySequence
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intLen
public int intLen(int len)
Calculate the length of a sequence- Parameters:
len
-- Returns:
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length
public int length()
Description copied from class:BinarySequence
Get sequence length- Specified by:
length
in classBinarySequence
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read
public DnaSequencePe read(java.io.DataInputStream dataInStream) throws java.io.IOException
Read data in binary format- Specified by:
read
in classBinarySequence
- 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- Specified by:
readDataStream
in classBinarySequence
- Parameters:
dataOutStream
-- Throws:
java.io.IOException
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reverseWc
public BinarySequence reverseWc()
Description copied from class:BinarySequence
Reverse Watson-Cricks complement- Specified by:
reverseWc
in classBinarySequence
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set
public void set(java.lang.String seqStr)
Description copied from class:BinarySequence
Set sequence from a string- Specified by:
set
in classBinarySequence
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setGap
public void setGap(int gap)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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write
public void write(java.io.DataOutputStream dataOutStream) throws java.io.IOException
Write data in binary format- Specified by:
write
in classBinarySequence
- Parameters:
dataOutStream
-- Throws:
java.io.IOException
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