Package org.biojava3.core.sequence.storage

Class BitSequenceReader.BitArrayWorker<C extends Compound>

java.lang.Object

org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>

Type Parameters:

C - The Compound to use

Direct Known Subclasses:

FourBitSequenceReader.FourBitArrayWorker, TwoBitSequenceReader.TwoBitArrayWorker

Enclosing class:

BitSequenceReader<C extends Compound>

public abstract static class BitSequenceReader.BitArrayWorker<C extends Compound>
extends Object

The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code. This class behaves just like a Sequence without the interface

Author:

ayates

Field Summary

Fields

Modifier and Type	Field	Description
static final int	BYTES_PER_INT

Constructor Summary

Constructors

Constructor	Description
BitArrayWorker(String sequence, CompoundSet<C> compoundSet)
BitArrayWorker(CompoundSet<C> compoundSet, int length)
BitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
BitArrayWorker(Sequence<C> sequence)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
C	getCompoundAt(int position)	Returns the compound at the specified biological index
CompoundSet<C>	getCompoundSet()	Returns the compound set backing this store
int	getLength()
int	hashCode()
void	populate(String sequence)	Loops through the chars in a String and passes them onto setCompoundAt(char, int)
void	populate(Sequence<C> sequence)	Loops through the Compounds in a Sequence and passes them onto setCompoundAt(Compound, int)
int	seqArraySize(int length)
void	setCompoundAt(char base, int position)	Converts from char to Compound and sets it at the given biological index
void	setCompoundAt(C compound, int position)	Sets the compound at the specified biological index

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Field Details

BYTES_PER_INT

public static final int BYTES_PER_INT

See Also:

• Constant Field Values

Constructor Details

BitArrayWorker

public BitArrayWorker(Sequence<C> sequence)

BitArrayWorker

public BitArrayWorker(String sequence,
 CompoundSet<C> compoundSet)

BitArrayWorker

public BitArrayWorker(CompoundSet<C> compoundSet,
 int length)

BitArrayWorker

public BitArrayWorker(CompoundSet<C> compoundSet,
 int[] sequence)

Method Details

seqArraySize

public int seqArraySize(int length)

populate

public void populate(Sequence<C> sequence)

Loops through the Compounds in a Sequence and passes them onto setCompoundAt(Compound, int)

populate

public void populate(String sequence)

Loops through the chars in a String and passes them onto setCompoundAt(char, int)

setCompoundAt

public void setCompoundAt(char base,
 int position)

Converts from char to Compound and sets it at the given biological index

setCompoundAt

public void setCompoundAt(C compound,
 int position)

Sets the compound at the specified biological index

getCompoundAt

public C getCompoundAt(int position)

Returns the compound at the specified biological index

getCompoundSet

public CompoundSet<C> getCompoundSet()

Returns the compound set backing this store

getLength

public int getLength()

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object