Class BasePairBitType

java.lang.Object

net.imglib2.type.AbstractBitType<BasePairBitType>

net.imglib2.type.AbstractBit64Type<BasePairBitType>

net.imglib2.type.label.BasePairBitType

All Implemented Interfaces:

Comparable<BasePairBitType>, BasePairType<BasePairBitType>, NativeType<BasePairBitType>, ValueEquals<BasePairBitType>, Type<BasePairBitType>

public class BasePairBitType
extends AbstractBit64Type<BasePairBitType>
implements BasePairType<BasePairBitType>

Representation of base pairs using 3 bits per entry, supported characters: gap, N, A, T, G, C, U Bases are handled using the BasePairBitType.Base enumeration.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	BasePairBitType.Base

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	NBITS
private static final NativeTypeFactory<BasePairBitType, LongAccess>	typeFactory

Fields inherited from class AbstractBitType

dataAccess, i, img, nBits

Constructor Summary

Constructors

Constructor	Description
BasePairBitType()
BasePairBitType(NativeImg<?, ? extends LongAccess> bitStorage)
BasePairBitType(BasePairBitType.Base value)

Method Summary

Modifier and Type	Method	Description
byte	baseToValue()
int	compareTo(BasePairBitType c)
void	complement()
BasePairBitType	copy()	Creates a new Type variable that has the value of this Type
BasePairBitType	createVariable()	Creates a new Type variable which can only store one value.
BasePairBitType	duplicateTypeOnSameNativeImg()	Creates a new NativeType which stores in the same physical array.
BasePairBitType.Base	get()
NativeTypeFactory<BasePairBitType, LongAccess>	getNativeTypeFactory()
void	set(BasePairBitType c)	Sets the value of another Type.
void	set(BasePairBitType.Base base)
String	toString()
boolean	valueEquals(BasePairBitType t)

Methods inherited from class AbstractBit64Type

getBits, setBits

Methods inherited from class AbstractBitType

getEntitiesPerPixel, index, updateContainer

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface NativeType

decIndex, decIndex, getIndex, incIndex, incIndex, updateIndex

Field Details

NBITS

private static final int NBITS

See Also:

• Constant Field Values

typeFactory

private static final NativeTypeFactory<BasePairBitType, LongAccess> typeFactory

Constructor Details

BasePairBitType

public BasePairBitType(NativeImg<?, ? extends LongAccess> bitStorage)

BasePairBitType

public BasePairBitType(BasePairBitType.Base value)

BasePairBitType

public BasePairBitType()

Method Details

duplicateTypeOnSameNativeImg

public BasePairBitType duplicateTypeOnSameNativeImg()

Description copied from interface: NativeType

Creates a new NativeType which stores in the same physical array. This is only used internally.

Specified by:

duplicateTypeOnSameNativeImg in interface NativeType<BasePairBitType>

Returns:

a new NativeType instance working on the same NativeImg

getNativeTypeFactory

public NativeTypeFactory<BasePairBitType, LongAccess> getNativeTypeFactory()

Specified by:

getNativeTypeFactory in interface NativeType<BasePairBitType>

Specified by:

getNativeTypeFactory in class AbstractBitType<BasePairBitType>

set

public void set(BasePairBitType.Base base)

Specified by:

set in interface BasePairType<BasePairBitType>

get

public BasePairBitType.Base get()

Specified by:

get in interface BasePairType<BasePairBitType>

compareTo

public int compareTo(BasePairBitType c)

Specified by:

compareTo in interface Comparable<BasePairBitType>

complement

public void complement()

Specified by:

complement in interface BasePairType<BasePairBitType>

baseToValue

public byte baseToValue()

Specified by:

baseToValue in interface BasePairType<BasePairBitType>

set

public void set(BasePairBitType c)

Description copied from interface: Type

Sets the value of another Type.

Specified by:

set in interface Type<BasePairBitType>

Parameters:

c - the new value

createVariable

public BasePairBitType createVariable()

Description copied from interface: Type

Creates a new Type variable which can only store one value.

Specified by:

createVariable in interface Type<BasePairBitType>

Returns:

a new Type variable

copy

public BasePairBitType copy()

Description copied from interface: Type

Creates a new Type variable that has the value of this Type

Specified by:

copy in interface Type<BasePairBitType>

Returns:

a new Type variable

toString

public String toString()

Overrides:

toString in class Object

valueEquals

public boolean valueEquals(BasePairBitType t)

Specified by:

valueEquals in interface ValueEquals<BasePairBitType>