Package net.imglib2.type.label

Class BasePairCharType

java.lang.Object

net.imglib2.type.AbstractNativeType<BasePairCharType>

net.imglib2.type.label.BasePairCharType

All Implemented Interfaces:

java.lang.Comparable<BasePairCharType>, BasePairType<BasePairCharType>, NativeType<BasePairCharType>, ValueEquals<BasePairCharType>, Type<BasePairCharType>

public class BasePairCharType
extends AbstractNativeType<BasePairCharType>
implements BasePairType<BasePairCharType>

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

Field Summary

Fields

Modifier and Type	Field	Description
protected CharAccess	dataAccess
protected NativeImg<?,? extends CharAccess>	img
private static NativeTypeFactory<BasePairCharType,CharAccess>	typeFactory

Fields inherited from class net.imglib2.type.AbstractNativeType

i

Constructor Summary

Constructors

Constructor	Description
BasePairCharType()
BasePairCharType(char value)
BasePairCharType(NativeImg<?,? extends CharAccess> charStorage)
BasePairCharType(BasePairBitType.Base value)

Method Summary

Modifier and Type	Method	Description
byte	baseToValue()
int	compareTo(BasePairCharType c)
void	complement()
BasePairCharType	copy()	Creates a new Type variable that has the value of this Type
BasePairCharType	createVariable()	Creates a new Type variable which can only store one value.
BasePairCharType	duplicateTypeOnSameNativeImg()	Creates a new NativeType which stores in the same physical array.
BasePairBitType.Base	get()
char	getChar()
Fraction	getEntitiesPerPixel()	Get the number of entities in the storage array required to store one pixel value.
NativeTypeFactory<BasePairCharType,CharAccess>	getNativeTypeFactory()
void	set(BasePairBitType.Base base)
void	set(BasePairCharType c)	Sets the value of another Type.
void	setChar(char f)
java.lang.String	toString()
void	updateContainer(java.lang.Object c)	This method is used by an accessor (e.g., a Cursor) to request an update of the current data array.
boolean	valueEquals(BasePairCharType t)

Methods inherited from class net.imglib2.type.AbstractNativeType

index

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

Field Detail

img

protected final NativeImg<?,? extends CharAccess> img

dataAccess

protected CharAccess dataAccess

typeFactory

private static final NativeTypeFactory<BasePairCharType,CharAccess> typeFactory

Constructor Detail

BasePairCharType

public BasePairCharType(NativeImg<?,? extends CharAccess> charStorage)

BasePairCharType

public BasePairCharType(BasePairBitType.Base value)

BasePairCharType

public BasePairCharType(char value)

BasePairCharType

public BasePairCharType()

Method Detail

getEntitiesPerPixel

public Fraction getEntitiesPerPixel()

Description copied from interface: NativeType

Get the number of entities in the storage array required to store one pixel value. A pixel value may be spread over several or less than one entity. For example, a complex number may require 2 entries of a float[] array to store one pixel. Or a 12-bit type might need 12/64th entries of a long[] array.

Specified by:

getEntitiesPerPixel in interface NativeType<BasePairCharType>

Returns:

the number of storage type entities required to store one pixel value.

updateContainer

public void updateContainer(java.lang.Object c)

Description copied from interface: NativeType

This method is used by an accessor (e.g., a Cursor) to request an update of the current data array.

As an example consider a CellCursor moving on a CellImg. The cursor maintains a NativeType which provides access to the image data. When the cursor moves from one cell to the next, the underlying data array of the NativeType must be switched to the data array of the new cell.

To achieve this, the CellCursor calls updateContainer() with itself as the argument. updateContainer() in turn will call NativeImg.update(Object) on it's container, passing along the reference to the cursor. In this example, the container would be a CellImg. While the NativeType does not know about the type of the cursor, the container does. CellImg knows that it is passed a CellCursor instance, which can be used to figure out the current cell and the underlying data array, which is then returned to the NativeType.

The idea behind this concept is maybe not obvious. The NativeType knows which basic type is used (float, int, byte, ...). However, it does not know how the data is stored (ArrayImg, CellImg, ...). This prevents the need for multiple implementations of NativeType .

Specified by:

updateContainer in interface NativeType<BasePairCharType>

Parameters:

c - reference to an accessor which can be passed on to the container (which will know what to do with it).

duplicateTypeOnSameNativeImg

public BasePairCharType 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<BasePairCharType>

Returns:

a new NativeType instance working on the same NativeImg

getNativeTypeFactory

public NativeTypeFactory<BasePairCharType,CharAccess> getNativeTypeFactory()

Specified by:

getNativeTypeFactory in interface NativeType<BasePairCharType>

getChar

public char getChar()

setChar

public void setChar(char f)

set

public void set(BasePairBitType.Base base)

Specified by:

set in interface BasePairType<BasePairCharType>

get

public BasePairBitType.Base get()

Specified by:

get in interface BasePairType<BasePairCharType>

set

public void set(BasePairCharType c)

Description copied from interface: Type

Sets the value of another Type.

Specified by:

set in interface Type<BasePairCharType>

Parameters:

c - the new value

compareTo

public int compareTo(BasePairCharType c)

Specified by:

compareTo in interface java.lang.Comparable<BasePairCharType>

complement

public void complement()

Specified by:

complement in interface BasePairType<BasePairCharType>

baseToValue

public byte baseToValue()

Specified by:

baseToValue in interface BasePairType<BasePairCharType>

createVariable

public BasePairCharType createVariable()

Description copied from interface: Type

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

Specified by:

createVariable in interface Type<BasePairCharType>

Returns:

a new Type variable

copy

public BasePairCharType copy()

Description copied from interface: Type

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

Specified by:

copy in interface Type<BasePairCharType>

Returns:

a new Type variable

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

valueEquals

public boolean valueEquals(BasePairCharType t)

Specified by:

valueEquals in interface ValueEquals<BasePairCharType>