net.imglib2.type.label

Class BasePairBitType

java.lang.Object

net.imglib2.type.AbstractBitType<T>

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.

Author:

Stephan Preibisch, Stephan Saalfeld

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BasePairBitType.Base

Field Summary

Fields inherited from class net.imglib2.type.AbstractBitType

dataAccess, i, img, nBits

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
byte	baseToValue()
int	compareTo(BasePairBitType c)
void	complement()
BasePairBitType	copy() Creates a new Type variable that has the value of this Type
NativeImg<BasePairBitType,? extends LongAccess>	createSuitableNativeImg(NativeImgFactory<BasePairBitType> storageFactory, long[] dim) The NativeType creates the NativeImg used for storing image data; based on the given storage strategy and its size.
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()
void	set(BasePairBitType.Base base)
void	set(BasePairBitType c) Sets the value of another Type.
String	toString()
boolean	valueEquals(BasePairBitType t)

Methods inherited from class net.imglib2.type.AbstractBit64Type

getBits, setBits

Methods inherited from class net.imglib2.type.AbstractBitType

decIndex, decIndex, getEntitiesPerPixel, getIndex, incIndex, incIndex, updateContainer, updateIndex

Methods inherited from class java.lang.Object

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

Constructor Detail

BasePairBitType

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

BasePairBitType

public BasePairBitType(BasePairBitType.Base value)

BasePairBitType

public BasePairBitType()

Method Detail

createSuitableNativeImg

public NativeImg<BasePairBitType,? extends LongAccess> createSuitableNativeImg(NativeImgFactory<BasePairBitType> storageFactory,
                                                                               long[] dim)

Description copied from interface: NativeType

The NativeType creates the NativeImg used for storing image data; based on the given storage strategy and its size. It basically only decides here which BasicType it uses (float, int, byte, bit, ...) and how many entities per pixel it needs (e.g. 2 floats per pixel for a complex number). This enables the separation of containers and the basic types.

Specified by:

createSuitableNativeImg in interface NativeType<BasePairBitType>

Parameters:

storageFactory - which storage strategy is used

dim - the dimensions

Returns:

the instantiated NativeImg where only the Type knows the BasicType it contains.

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

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>