Uses of Class
sc.fiji.snt.annotation.AllenCompartment

Packages that use AllenCompartment

Package	Description
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.

Uses of AllenCompartment in sc.fiji.snt.analysis

Methods in sc.fiji.snt.analysis with parameters of type AllenCompartment

Modifier and Type	Method and Description
void	MultiTreeColorMapper.mapRootDistanceToCentroid(AllenCompartment compartment, net.imglib2.display.ColorTable colorTable)

Uses of AllenCompartment in sc.fiji.snt.annotation

Methods in sc.fiji.snt.annotation that return AllenCompartment

Modifier and Type	Method and Description
static AllenCompartment	AllenUtils.getCompartment(int id) Constructs a compartment from its CCF id
static AllenCompartment	AllenUtils.getCompartment(java.lang.String nameOrAcronym) Constructs a compartment from its CCF name or acronym
AllenCompartment	AllenCompartment.getParent() Gets the parent of this compartment

Methods in sc.fiji.snt.annotation that return types with arguments of type AllenCompartment

Modifier and Type	Method and Description
java.util.List<AllenCompartment>	AllenCompartment.getAncestors(int level) Gets the ancestor ontologies of this compartment as a flat (non-hierarchical) list.
java.util.List<AllenCompartment>	AllenCompartment.getChildren() Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
java.util.List<AllenCompartment>	AllenCompartment.getChildren(int level) Gets the child ontologies of this compartment as a flat (non-hierarchical) list.
static java.util.Collection<AllenCompartment>	AllenUtils.getOntologies() Gets the Allen CCF as a flat (non-hierarchical) collection of ontologies.
java.util.List<AllenCompartment>	AllenCompartment.getTreePath() Gets the tree path of this compartment.

Methods in sc.fiji.snt.annotation with parameters of type AllenCompartment

Modifier and Type	Method and Description
boolean	AllenCompartment.containedBy(AllenCompartment parentCompartment) Assesses if this annotation is a child of a specified compartment.
boolean	AllenCompartment.contains(AllenCompartment childCompartment) Assesses if this annotation is parent of a specified compartment.

Uses of AllenCompartment in sc.fiji.snt.io

Methods in sc.fiji.snt.io with parameters of type AllenCompartment

Modifier and Type	Method and Description
static java.util.List<java.lang.String>	MouseLightQuerier.getIDs(AllenCompartment compartment) Gets the IDs of the cells publicly available in the MouseLight database having the soma associated with the specified compartment.