sc.fiji.snt.annotation

Class AllenCompartment

java.lang.Object

sc.fiji.snt.annotation.AllenCompartment

All Implemented Interfaces:

BrainAnnotation

public class AllenCompartment
extends java.lang.Object
implements BrainAnnotation

Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate Framework] annotation. A Compartment is defined by either a UUID (as per MouseLight's database) or its unique integer identifier. To improve performance, a compartment's metadata (reference to its mesh, its aliases, etc.) are not loaded at initialization, but retrieved only when such getters are called.

Author:

Tiago Ferreira

Constructor Summary

Constructors

Constructor and Description
AllenCompartment(int id) Instantiates a new ARA annotation from its identifier.
AllenCompartment(java.util.UUID uuid) Instantiates a new ARA annotation from an UUID (as used by MouseLight's database).

Method Summary

Modifier and Type	Method and Description
java.lang.String	acronym()
java.lang.String[]	aliases()
boolean	containedBy(AllenCompartment parentCompartment) Assesses if this annotation is a child of a specified compartment.
boolean	contains(AllenCompartment childCompartment) Assesses if this annotation is parent of a specified compartment.
boolean	equals(java.lang.Object o)
java.util.List<AllenCompartment>	getAncestors(int level) Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.
java.util.List<AllenCompartment>	getChildren() Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
java.util.List<AllenCompartment>	getChildren(int level) Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
OBJMesh	getMesh()
int	getOntologyDepth() Gets the ontology depth of this compartment.
AllenCompartment	getParent() Gets the parent of this compartment
java.util.List<AllenCompartment>	getTreePath() Gets the tree path of this compartment.
int	id()
boolean	isMeshAvailable() Checks whether a mesh is known to be available for this compartment.
java.lang.String	name()
java.lang.String	toString()

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AllenCompartment

public AllenCompartment(java.util.UUID uuid)

Instantiates a new ARA annotation from an UUID (as used by MouseLight's database).

Parameters:

uuid - the ML UUID identifying the annotation

AllenCompartment

public AllenCompartment(int id)

Instantiates a new ARA annotation from its identifier.

Parameters:

id - the integer identifying the annotation

Method Detail

contains

public boolean contains(AllenCompartment childCompartment)

Assesses if this annotation is parent of a specified compartment.

Parameters:

childCompartment - the compartment to be tested

Returns:

true, if successful, i.e., childCompartment's getTreePath() contains this compartment

containedBy

public boolean containedBy(AllenCompartment parentCompartment)

Assesses if this annotation is a child of a specified compartment.

Parameters:

parentCompartment - the compartment to be tested

Returns:

true, if successful, i.e., getTreePath() contains parentCompartment

getTreePath

public java.util.List<AllenCompartment> getTreePath()

Gets the tree path of this compartment. The TreePath is the list of parent compartments that uniquely identify this compartment in the ontologies hierarchical tree. The elements of the list are ordered with the root ('Whole Brain") as the first element of the list.

Returns:

the tree path that uniquely identifies this compartment as a node in the CCF ontologies tree

getOntologyDepth

public int getOntologyDepth()

Gets the ontology depth of this compartment.

Returns:

the ontological depth of this compartment, i.e., its ontological distance relative to the root (e.g., a compartment of hierarchical level 9, has a depth of 8).

getParent

public AllenCompartment getParent()

Gets the parent of this compartment

Returns:

the parent of this compartment, of null if this compartment is root.

getAncestors

public java.util.List<AllenCompartment> getAncestors(int level)

Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.

Parameters:

level - maximum depth that should be considered.

Returns:

the "flattened" ontologies list

getChildren

public java.util.List<AllenCompartment> getChildren()

Gets the child ontologies of this compartment as a flat (non-hierarchical) list.

Returns:

the "flattened" ontologies list

getChildren

public java.util.List<AllenCompartment> getChildren(int level)

Gets the child ontologies of this compartment as a flat (non-hierarchical) list.

Parameters:

level - maximum depth that should be considered.

Returns:

the "flattened" ontologies list

id

public int id()

Specified by:

id in interface BrainAnnotation

Returns:

the compartment's unique id

name

public java.lang.String name()

Specified by:

name in interface BrainAnnotation

Returns:

the compartment's name

acronym

public java.lang.String acronym()

Specified by:

acronym in interface BrainAnnotation

Returns:

the compartment's acronym

aliases

public java.lang.String[] aliases()

Specified by:

aliases in interface BrainAnnotation

Returns:

the compartment's alias(es)

isMeshAvailable

public boolean isMeshAvailable()

Checks whether a mesh is known to be available for this compartment.

Returns:

true, if a mesh is available.

getMesh

public OBJMesh getMesh()

Specified by:

getMesh in interface BrainAnnotation

Returns:

the mesh associated with this compartment

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object