BasePairBitType (ImgLib2 Javadocs 0-SNAPSHOT API)

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

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)

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

Method Summary

All Methods Instance Methods Concrete Methods
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`
`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.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
getEntitiesPerPixel, index, updateContainer

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.imglib2.type.NativeType
decIndex, decIndex, getIndex, incIndex, incIndex, updateIndex

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

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

Methods inherited from interface net.imglib2.type.NativeType

Constructor Detail

BasePairBitType

BasePairBitType

BasePairBitType

Method Detail

duplicateTypeOnSameNativeImg

getNativeTypeFactory

set

get

compareTo

complement

baseToValue

set

createVariable

copy

toString

valueEquals