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

Description

static enum

BasePairBitType.Base
Field Summary

Fields inherited from class net.imglib2.type.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

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 c)

Sets the value of another Type.

void

set(BasePairBitType.Base base)

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 Details
- BasePairBitType
  
  public BasePairBitType(NativeImg<?,? extends LongAccess> bitStorage)
- BasePairBitType
  
  public BasePairBitType(BasePairBitType.Base value)
- BasePairBitType
  
  public BasePairBitType()
Method Details
- 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>

Class BasePairBitType

Nested Class Summary

Field Summary

Fields inherited from class net.imglib2.type.AbstractBitType

Constructor Summary

Method Summary

Methods inherited from class net.imglib2.type.AbstractBit64Type

Methods inherited from class net.imglib2.type.AbstractBitType

Methods inherited from class java.lang.Object

Constructor Details

BasePairBitType

BasePairBitType

BasePairBitType

Method Details

createSuitableNativeImg

duplicateTypeOnSameNativeImg

set

get

compareTo

complement

baseToValue

set

createVariable

copy

toString

valueEquals