Package org.snpeff.binseq
Class DnaSequencePe
java.lang.Object
org.snpeff.binseq.BinarySequence
org.snpeff.binseq.DnaSequencePe
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<BinarySequence>
Pair end DNA sequence (binary packed)
It consists of 2 DNA sequences separated by a gap.
- Author:
- pcingola
- See Also:
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionDnaSequencePe
(String seqStr) DnaSequencePe
(String seqStr1, String seqStr2, int gap) -
Method Summary
Modifier and TypeMethodDescriptionint
int
getCode
(int index) Return the code at position 'index'getCoder()
Get sequence encoder invalid input: '&' decoderint
getGap()
getSeq1()
getSeq2()
Get the sequence as a Stringint
hashCode()
int
intLen
(int len) Calculate the length of a sequenceint
length()
Get sequence lengthread
(DataInputStream dataInStream) Read data in binary formatprotected void
readDataStream
(DataInputStream dataInStream) Read data in binary formatReverse Watson-Cricks complementvoid
Set sequence from a stringvoid
setGap
(int gap) toString()
void
write
(DataOutputStream dataOutStream) Write data in binary formatMethods inherited from class org.snpeff.binseq.BinarySequence
clone, getBase, overlap, setQuality
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Field Details
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coder
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Constructor Details
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DnaSequencePe
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DnaSequencePe
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Method Details
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compareTo
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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
Description copied from class:BinarySequence
Get sequence encoder invalid input: '&' decoder- Specified by:
getCoder
in classBinarySequence
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getGap
public int getGap() -
getSeq1
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getSeq2
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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
Read data in binary format- Specified by:
read
in classBinarySequence
- Parameters:
dataOutStream
-- Throws:
IOException
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readDataStream
Read data in binary format- Specified by:
readDataStream
in classBinarySequence
- Parameters:
dataOutStream
-- Throws:
IOException
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reverseWc
Description copied from class:BinarySequence
Reverse Watson-Cricks complement- Specified by:
reverseWc
in classBinarySequence
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set
Description copied from class:BinarySequence
Set sequence from a string- Specified by:
set
in classBinarySequence
- Parameters:
seqStr
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setGap
public void setGap(int gap) -
toString
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write
Write data in binary format- Specified by:
write
in classBinarySequence
- Parameters:
dataOutStream
-- Throws:
IOException
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