MutableGenome

All children of this parent

If true, then a Feature within the Genome may have multiple parents. If false, no Feature in the Genome may have multiple parents. Recommended to be false as multiple parentage can lead to unintuitive results.

This number increases with the number of topological modifications (adding, removing, and sorting) applied to the Genome. Useful for preventing concurrent modification.

Makes subType a subtype of superType.

Makes child have a part-of relationship with parent.

Makes all synonym rough synonyms of existing.

Makes all synonym synonyms of existing.

PLANNED

All children of this parent of type type (including its synonyms), or all children if type is null.

True iff a feature with id property id exists in this genome.

True iff a feature with name property name exists in this genome.

True iff type is in the type schema.

Creates a deep copy of this Genome. If this is MutableGenome, the copy will be mutable. It will be immutable otherwise.

Defines a type with the specified properties.

All descendants of this parent of type type (including its synonyms) in depth-first order, or all descendants if type is null. Iterating over the descendants while modifying the topology of the tree will produce a ConcurrentModificationException (non-topological modifications are permissible). Multiple parentage will result in duplicate values

Creates an immutable deep copy of this genome

Inserts a feature with the specified properties as the child of this feature. If this MutableParent is not a MutableGenome, the inserted type must have a part-of relationship with this feature's type. This means that either the part-of relationship was explicitly defined by the user or exists in the Sequence Ontology.

Alias for insert for features without discontinuous regions. Behaves analogously.

True any type associated with the name subType is transitively a subtype of any type associated with the name superType

True iff all elements of other are rough synonyms of name. Always false if name is not in the schema.

True iff all elements of other are exact synonyms of name. Always false if name is not in the schema.

Iterates over children

Creates mutable deep copy of this genome

True iff child has a part-of relationship to parent, either from the Sequence Ontology or due to manual definition of PLANNED: Implementation of TypeSchema the type (MutableGenome.defineType or MutableGenome.addPartOf).

All rough and exact synonyms of type

Sorts the children by comparator.

All exact synonyms of type.

DOT format representation of the type schema where nodes represent a type and edges represent a part-Of relationship. Can be visualized with DOT visualization tools, such as Graphviz.