Package org.snpeff.binseq
Class BinarySequence
java.lang.Object
org.snpeff.binseq.BinarySequence
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<BinarySequence>
- Direct Known Subclasses:
DnaAndQualitySequence
,DnaSequence
,DnaSequencePe
public abstract class BinarySequence
extends Object
implements Comparable<BinarySequence>, Serializable, Cloneable
Base class for a binary 'read'. I.e. a binary representation of a sequencer's read
A read is a short DNA fragment (short now means anywhere from 36 bases to 10K).
- Author:
- pcingola
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionclone()
char
getBase
(int index) Return the base at position 'index'abstract int
getCode
(int index) Return the code at position 'index'abstract Coder
getCoder()
Get sequence encoder invalid input: '&' decoderabstract String
Get the sequence as a Stringabstract int
hashCode()
abstract int
length()
Get sequence lengthoverlap
(BinarySequence sequence, int start) Creates a new sequence by overlapping 'this' and 'sequence' E.g.abstract BinarySequence
read
(DataInputStream dataInStream) Read a sequence from a data streamprotected abstract void
readDataStream
(DataInputStream dataInStream) abstract BinarySequence
Reverse Watson-Cricks complementabstract void
Set sequence from a stringvoid
setQuality
(int index, int quality) Set the quality at position 'index'abstract void
write
(DataOutputStream dataOutStream) Write to a binary streamMethods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Comparable
compareTo
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Constructor Details
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BinarySequence
public BinarySequence()
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Method Details
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getBase
public char getBase(int index) Return the base at position 'index' -
clone
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getCode
public abstract int getCode(int index) Return the code at position 'index' -
getCoder
Get sequence encoder invalid input: '&' decoder -
getSequence
Get the sequence as a String -
hashCode
public abstract int hashCode() -
length
public abstract int length()Get sequence length -
overlap
Creates a new sequence by overlapping 'this' and 'sequence' E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO | other.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOOyyyyyyyyyyyyyyyyy| this.sequence : | OOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO | |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOOxxxxxxxxxxxxxxxxxxxx| Another case is when a sequence is fully included in the other sequence. In this case the result is just a copy of the longest sequence (with the quality updated) E.g. this.sequence : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| other.sequence : | OOOOOOOOOOOOOOO | | |start=20 | result : |xxxxxxxxxxxxxxxxxxxxOOOOOOOOOOOOOOOOOOOOOOOO| this.sequence : | OOOOOOOOOOO | other.sequence : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO| |start=-20 | result : |yyyyyyyyyyyyyyyyyyyyyyyyOOOOOOOOOOOOOOOOOOOOOOOO| -
read
Read a sequence from a data stream- Throws:
IOException
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readDataStream
- Throws:
IOException
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reverseWc
Reverse Watson-Cricks complement -
set
Set sequence from a string- Parameters:
seqStr
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setQuality
public void setQuality(int index, int quality) Set the quality at position 'index' -
write
Write to a binary stream- Throws:
IOException
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