Package sc.fiji.snt.annotation

Interface BrainAnnotation

All Known Implementing Classes:
AllenCompartment, DrosophilaCompartment, InsectBrainCompartment
public interface BrainAnnotation
Classes extending this interface implement a neuropil label/annotation aka "compartment".
Author:
Tiago Ferreira

  • Field Details

    • LEFT_HEMISPHERE

      static final char LEFT_HEMISPHERE
      Character constant representing the left hemisphere
      See Also:

    • RIGHT_HEMISPHERE

      static final char RIGHT_HEMISPHERE
      Character constant representing the right hemisphere
      See Also:

    • ANY_HEMISPHERE

      static final char ANY_HEMISPHERE
      Character constant representing any hemisphere (null character)
      See Also:

  • Method Details

    • id

      int id()
      Returns the compartment's unique id.

    • name

      String name()
      Returns the compartment's name.

    • acronym

      String acronym()
      Returns the compartment's acronym.

    • aliases

      String[] aliases()
      Returns the compartment's alias(es).

    • getMesh

      OBJMesh getMesh()
      Returns the mesh associated with this compartment.

    • isChildOf

      boolean isChildOf(BrainAnnotation annotation)
      Returns whether this compartment is a sub-compartment of annotation.

    • isParentOf

      boolean isParentOf(BrainAnnotation parentCompartment)
      Returns whether this compartment is a parent of parentCompartment.

    • getOntologyDepth

      int getOntologyDepth()
      Returns the ontology depth of this compartment.

    • isMeshAvailable

      boolean isMeshAvailable()
      Returns whether a mesh is available for this compartment.

    • getAncestor

      BrainAnnotation getAncestor(int level)
      Returns the ancestor of this compartment at the specified level.
      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
      Returns:
      the ancestor at the given level

    • getParent

      BrainAnnotation getParent()
      Returns the parent of this compartment.

    • color

      org.scijava.util.ColorRGB color()
      Returns the display color of this compartment (if known).

    • getHemisphereFlag

      static char getHemisphereFlag(String hemisphere)

    • comparator

      static Comparator<BrainAnnotation> comparator()

    • simplifiedString

      static String simplifiedString(BrainAnnotation annotation)