public class Nucleobase
extends java.lang.Object
Constructor and Description |
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Nucleobase(char genotype,
long uniqueID,
int targetCoverage)
Initialise a new Nucleobase object.
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Modifier and Type | Method and Description |
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void |
addCoveringRead(Read read)
Add a read to the list of reads which cover this nucleobase.
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char |
getComplementGenotype()
GEt the complement of the nucleobase's genotype.
|
int |
getCoverage()
Get the coverage for this nucleobase i.e.
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java.util.ArrayList<Read> |
getCoveringReads()
Get the list of covering reads - the reads which include this nucleobase.
|
char |
getGenotype()
Get the nucleobase's genotype.
|
int |
getTargetCoverage()
Get the target coverage for this nucleobase (the number of reads that we want to
include this nucleobase).
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long |
getUniqueID()
Get the nucleobase's unique integer ID.
|
boolean |
hasTargetCoverage()
Checks whether a nucleobase's coverage matches its target coverage.
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void |
setGenotype(char genotype)
Set the nucleobase's genotype.
|
void |
setTargetCoverage(int targetCoverage)
Set the target coverage for this nucleobase (the number of reads we want to include
this nucleobase).
|
java.lang.String |
toString() |
public Nucleobase(char genotype, long uniqueID, int targetCoverage)
genotype
- - the nucleobase's genotype.uniqueID
- - the nucleobase's unique integer ID.targetCoverage
- - the nucleobase's target coverage.public char getGenotype()
public char getComplementGenotype()
public void setGenotype(char genotype)
public void addCoveringRead(Read read)
read
- - the read which covers this nucleobase.public int getCoverage()
public java.util.ArrayList<Read> getCoveringReads()
public long getUniqueID()
public int getTargetCoverage()
public void setTargetCoverage(int targetCoverage)
targetCoverage
- - the nucleobase's target coverage.public boolean hasTargetCoverage()
public java.lang.String toString()
toString
in class java.lang.Object