AllenCompartment (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.annotation.AllenCompartment

All Implemented Interfaces:

BrainAnnotation
```
public class AllenCompartment
extends 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, Cameron Arshadi

Field Summary
- Fields inherited from interface sc.fiji.snt.annotation.BrainAnnotation
  ANY_HEMISPHERE, LEFT_HEMISPHERE, RIGHT_HEMISPHERE

Constructor Summary

Constructors
Modifier	Constructor and Description
	`AllenCompartment(int id)` Instantiates a new ARA annotation from its identifier.
`protected`	`AllenCompartment(org.json.JSONObject jsonObj, UUID uuid)`
	`AllenCompartment(UUID uuid)` Instantiates a new ARA annotation from an UUID (as used by MouseLight's database).

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`acronym()`
`String[]`	`aliases()`
`protected int`	`depth()`
`boolean`	`equals(Object obj)`
`AllenCompartment`	`getAncestor(int level)` Gets the nth ancestor of this compartment.
`List<AllenCompartment>`	`getAncestors()` Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.
`List<AllenCompartment>`	`getChildren()` Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
`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.
`protected int`	`getParentStructureId()`
`protected String`	`getStructureIdPath()`
`List<AllenCompartment>`	`getTreePath()` Gets the tree path of this compartment.
`UUID`	`getUUID()`
`protected int`	`graphOrder()`
`int`	`hashCode()`
`int`	`id()`
`boolean`	`isChildOf(BrainAnnotation childCompartment)` Assesses if this annotation is a child of a specified compartment.
`boolean`	`isMeshAvailable()` Checks whether a mesh is known to be available for this compartment.
`boolean`	`isParentOf(BrainAnnotation childCompartment)` Assesses if this annotation is the parent of the specified compartment.
`static void`	`main(String[] args)`
`String`	`name()`
`String`	`toString()`

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

Methods inherited from interface sc.fiji.snt.annotation.BrainAnnotation
getHemisphereFlag

- Constructor Detail
  - AllenCompartment
```
public AllenCompartment(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
  - AllenCompartment
```
protected AllenCompartment(org.json.JSONObject jsonObj,
                           UUID uuid)
```
- Method Detail
  - depth
```
protected int depth()
```
  - graphOrder
```
protected int graphOrder()
```
  - getStructureIdPath
```
protected String getStructureIdPath()
```
  - getParentStructureId
```
protected int getParentStructureId()
```
  - isChildOf
```
public boolean isChildOf(BrainAnnotation childCompartment)
```
    Assesses if this annotation is a child of a specified compartment.
    
    Specified by:
    
    isChildOf in interface BrainAnnotation
    
    Parameters:
    
    childCompartment - the compartment to be tested
    
    Returns:
    
    true, if successful, i.e., parentCompartment is not this compartment and getTreePath() contains parentCompartment
  - getTreePath
```
public 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. In practice, this is equivalent to appending this compartment to the the list returned by getAncestors().
    
    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.
    
    Specified by:
    
    getOntologyDepth in interface BrainAnnotation
    
    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.
    
    Specified by:
    
    getParent in interface BrainAnnotation
    
    Returns:
    
    the parent of this compartment, of null if this compartment is root.
  - getAncestors
```
public List<AllenCompartment> getAncestors()
```
    Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.
    
    Returns:
    
    the "flattened" list of ancestors
    
    See Also:
    
    getTreePath()
  - getAncestor
```
public AllenCompartment getAncestor(int level)
```
    Gets the nth ancestor of this compartment.
    
    Specified by:
    
    getAncestor in interface BrainAnnotation
    
    Parameters:
    
    level - the ancestor level as negative 1-based index. E.g., -1 retrieves the last ancestor (parent), -2 retrieves the second to last, etc, all the way down to -getOntologyDepth(), which retrieves the root ontology ("Whole Brain")
    
    Returns:
    
    the nth ancestor
  - getChildren
```
public List<AllenCompartment> getChildren()
```
    Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
    
    Returns:
    
    the "flattened" ontologies list
  - getChildren
```
public 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 String name()
```
    Specified by:
    
    name in interface BrainAnnotation
    
    Returns:
    
    the compartment's name
  - acronym
```
public String acronym()
```
    Specified by:
    
    acronym in interface BrainAnnotation
    
    Returns:
    
    the compartment's acronym
  - aliases
```
public 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.
    
    Specified by:
    
    isMeshAvailable in interface BrainAnnotation
    
    Returns:
    
    true, if a mesh is available.
  - getMesh
```
public OBJMesh getMesh()
```
    Specified by:
    
    getMesh in interface BrainAnnotation
    
    Returns:
    
    the mesh associated with this compartment
  - isParentOf
```
public boolean isParentOf(BrainAnnotation childCompartment)
```
    Assesses if this annotation is the parent of the specified compartment.
    
    Specified by:
    
    isParentOf in interface BrainAnnotation
    
    Parameters:
    
    childCompartment - the compartment to be tested
    
    Returns:
    
    true, if successful, i.e., childCompartment is not this compartment and is present in getChildren()
  - getUUID
```
public UUID getUUID()
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object
  - main
```
public static void main(String[] args)
```

Class AllenCompartment

Field Summary

Fields inherited from interface sc.fiji.snt.annotation.BrainAnnotation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface sc.fiji.snt.annotation.BrainAnnotation

Constructor Detail

AllenCompartment

AllenCompartment

AllenCompartment

Method Detail

depth

graphOrder

getStructureIdPath

getParentStructureId

isChildOf

getTreePath

getOntologyDepth

getParent

getAncestors

getAncestor

getChildren

getChildren

id

name

acronym

aliases

isMeshAvailable

getMesh

isParentOf

getUUID

toString

hashCode

equals

main